# Disulfide bond formation and cysteine exclusion in gram-positive bacteria.

Robert Daniels, Peter Mellroth, Andreas Bernsel, Fabrice Neiers, Staffan Normark, Gunnar von Heijne, Birgitta Henriques-Normark

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Robert Daniels, Peter Mellroth, Andreas Bernsel, Fabrice Neiers, Staffan Normark, et al.. Disulfide bond formation and cysteine exclusion in gram-positive bacteria.. Journal of Biological Chemistry, 2010, 285 (5), pp.3300-9. 10.1074/jbc.M109.081398. hal-00679428

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# Disulfide Bond Formation and Cysteine Exclusion in Gram-positive Bacteria*§♦

Received for publication, November 3, 2009, and in revised form, November 23, 2009 Published, JBC Papers in Press, November 24, 2009, DOI 10.1074/jbc.M109.081398

Robert Daniels<sup>±§1</sup>, Peter Mellroth<sup>±§1</sup>, Andreas Bernsel<sup>¶1</sup>, Fabrice Neiers<sup>±§</sup>, Staffan Normark<sup>±§</sup>, Gunnar von Heijne<sup>¶2</sup>, and Birgitta Henriques-Normark<sup>±§3</sup>

From the <sup>†</sup>Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, the <sup>§</sup>Swedish Institute for Infectious Disease Control, 171 82 Solna, and the <sup>¶</sup>Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden

Most secretion pathways in bacteria and eukaryotic cells are challenged by the requirement for their substrate proteins to mature after they traverse a membrane barrier and enter a reactive oxidizing environment. For Gram-positive bacteria, the mechanisms that protect their exported proteins from misoxidation during their post-translocation maturation are poorly understood. To address this, we separated numerous bacterial species according to their tolerance for oxygen and divided their proteomes based on the predicted subcellular localization of their proteins. We then applied a previously established computational approach that utilizes cysteine incorporation patterns in proteins as an indicator of enzymatic systems that may exist in each species. The Sec-dependent exported proteins from aerobic Gram-positive Actinobacteria were found to encode cysteines in an even-biased pattern indicative of a functional disulfide bond formation system. In contrast, aerobic Gram-positive Firmicutes favor the exclusion of cysteines from both their cytoplasmic proteins and their substantially longer exported proteins. Supporting these findings, we show that Firmicutes, but not Actinobacteria, tolerate growth in reductant. We further demonstrate that the actinobacterium *Corynebacterium glutamicum* possesses disulfide-bonded proteins and two dimeric Dsb-like enzymes that can efficiently catalyze the formation of disulfide bonds. Our results suggest that cysteine exclusion is an important adaptive strategy against the challenges presented by oxidative environments.

Proper protein targeting and maturation are fundamental to the homeostasis of all organisms. Whereas many of the features that direct the membrane topology and localization of a protein

are known, the strategies employed by cells to promote the proper maturation of their proteins under different environmental conditions are not entirely understood.

Protein secretion is a dynamic and complex process due to the membrane separation of synthesis and folding (1–3). The majority of secreted proteins are translocated across a membrane into an oxidizing environment, where their folding and maturation occur. Bacteria have evolved several secretory pathways for translocating their proteins across the plasma membrane that can be categorized as either Sec-dependent or Sec-independent (4, 5). The Sec-dependent pathway, which is essential in all organisms, is the major route of protein secretion.

In bacteria, the majority of proteins that are targeted for Sec-dependent secretion contain a canonical N-terminal signal peptide that is either directly recognized by SecA or delivered to SecA with the aid of the secretion-dedicated chaperone SecB (6). SecA then drives the translocation of the protein through the SecYEG channel. Alternatively, most plasma membrane proteins and a small number of secretory proteins are recognized as ribosome-bound nascent chains by the signal recognition particle, which directs them to SecYEG, where they are co-translationally inserted into or translocated across the plasma membrane. Upon emergence from the translocon, nascent secretory proteins mature after removal of their signal peptide by either the type I signal peptidase or, in the case of lipoproteins, the type II signal peptidase (7).

Although the obstacles associated with protein folding are fundamentally similar across all organisms, the machinery involved in this process and the environment where it occurs can differ dramatically (8–10). In Gram-negative bacteria, secreted proteins mature in the oxidative periplasm with the aid of molecular chaperones and disulfide bond-forming machinery (11–13). Gram-positive bacteria lack this protected compartment due to the absence of an outer membrane. Thus, their secreted proteins have to mature in the unregulated environment of the thick, negatively charged cell wall composed of multilayered networks of peptidoglycan and teichoic acids (supplemental Fig. S1).

Cysteine residues perform a variety of essential functions in proteins, from metal binding and enzyme catalysis to structural stability through the formation of disulfide bonds (14). However, the reactive thiol side chain that is amenable to these roles can also negatively impact the function of a protein by the formation of incorrect disulfide bonds or other deleterious modifications

<footnote>* This work was supported by a postdoctoral fellowship from the Wenner-Gren Foundation (to R. D.) and the Swedish Research Council, the Torsten and Ragnar Söderbergs Foundation, the Swedish Royal Academy of Sciences, and the Swedish Foundation for Strategic Research.</footnote>

<footnote>§ *Author's Choice*—Final version full access.</footnote>

<footnote>♦ This article was selected as a Paper of the Week.</footnote>

<footnote>¶ The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1–S13 and Table 1.</footnote>

<footnote n="1">¹ These authors contributed equally to this work.</footnote>

<footnote n="2">² To whom correspondence may be addressed: Center for Biomembrane Research, Dept. of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius vag 16, SE-106 91 Stockholm, Sweden. Fax: 46-8-153-679; E-mail: gunnar@dbb.su.se.</footnote>

<footnote n="3">³ To whom correspondence may be addressed: Dept. of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 16 Nobels vag, SE-171 77 Stockholm, Sweden. Fax: 46-8-302-566; E-mail: birgitta.henriques@smi.se.</footnote>
# Cysteine Exclusion and Oxidation in Gram-positive Bacteria

fications. The high reactivity of cysteine thiols and their susceptibility to attack by reactive oxygen species likely create an oxidative selection pressure on cysteine-containing proteins that relates directly to their environment and localization (15). Consequently, bacteria have evolved systems that keep their cytoplasm in a reducing state and maintain the proper oxidation state of the cysteines in their extracellular proteins (16–19).

The periplasm-localized disulfide oxidoreductases of the Dsb family have been best characterized in *Escherichia coli*. *E. coli* DsbA is a soluble monomeric enzyme with a thioredoxin-like fold and a Cys-X-X-Cys active site that aids in the maturation of secreted proteins by catalyzing their disulfide bond formation immediately after their translocation into the periplasm (supplemental Fig. S1) (20, 21). DsbA is maintained in its oxidized state by the membrane-bound protein DsbB (22, 23). DsbC and DsbG, homodimers that function as disulfide isomerases or reductases, and DsbE, a thioredoxin-like protein involved in cytochrome c maturation, are all kept in their reducing state by the membrane-bound protein DsbD (19, 24–26). Together, the Dsb proteins in Gram-negative bacteria aid in the maturation of exported proteins and protect them from improper oxidation.

Several studies have searched for homologs of the known disulfide bond-forming machinery to predict whether certain bacteria are capable of oxidizing their secreted proteins (16, 27, 28). Mallick *et al*. (29) were the first to demonstrate that hyperthermophilic Archaea, which possess disulfide bonds in their cytoplasmic proteins, have a bias for encoding proteins with an even number of cysteine residues. Recently, Beckwith and coworkers (27) applied a similar reasoning to examine whether the predicted exported proteins from a large number of bacterial species have an even-number cysteine bias. These results were then correlated to whether DsbA and DsbB homologs were present in the corresponding genomes.

We used a combined computational and experimental approach to investigate the different strategies Gram-positive bacteria have evolved to compensate for changes in the oxidative environment that accompanies the localization of their proteins and their tolerance for oxygen. In agreement with recent work, our predictions indicate that Gram-positive Actinobacteria likely form disulfide bonds in their exported proteins (as do Gram-negative Proteobacteria) and that aerobic Gram-positive Firmicutes tend to generally exclude cysteines from their exported proteins (27). Additionally, we also found that aerobic Firmicutes have substantially longer exported proteins and favor the exclusion of cysteines from their cytoplasmic proteins. Supporting these predictions, we show that Firmicutes, but not Actinobacteria, can tolerate high levels of reductant, indicating that Firmicutes do not rely on disulfide-bonded proteins for growth. We observed several disulfide-bonded proteins in Actinobacteria, but not in Firmicutes, and show that two different dimeric Dsb-like proteins from the actinobacterial species *Corynebacterium glutamicum* are capable of productive disulfide bond formation. These results provide further insight into how organisms combat oxidative challenges and how their proteins have coevolved in the absence or presence of various enzymatic redox systems to overcome these obstacles.

## EXPERIMENTAL PROCEDURES

**Acquisition, Classification, and Homology Reduction of Bacterial Genomes**—Proteomes from the 340 analyzed bacterial species were downloaded from the European Bioinformatics Institute (EMBL-EBI Database). When several sequenced strains from a given species were available, one proteome from an ATCC strain was chosen to represent that species. The species were manually classified into their respective phyla (Proteobacteria, Firmicutes, and Actinobacteria) and for their ability to grow in the presence of oxygen (strict aerobes and facultative anaerobes versus strict anaerobes). Supplemental Table 1 shows the species distribution in each category. The individual bacterial proteomes were restricted to those proteins that were at least 80 amino acid residues in length. To prevent bias due to redundant protein families in the individual species, each bacterial proteome sequence set was internally homology-reduced using CD-HIT with a sequence identity threshold of 40% (30). These two initial screening steps retained 945,399 amino acid sequences for analysis and discarded 121,981 proteins based on homology reduction and 64,920 sequences as peptides.

**Protein Topology Prediction and Cysteine Analysis**—Protein sequences were classified according to predictions for the presence of transmembrane (TM)<fnref n="4" /> regions using SCAMPI and signal peptidase (SPase) type I and II signal peptides using SignalP 3.0 and LipoP 1.0, respectively (supplemental Fig. S2) (31–33). The proteome sets for each of the four classifications were compiled and analyzed for their cysteine content: (i) lipoproteins, containing a SPase II signal peptide and no TM regions (21,826 or 2.3% of the sequences); (ii) secreted proteins, containing a SPase I signal peptide, no SPase II signal peptide, and no TM regions (77,419 or 8.2% of the sequences); (iii) TM proteins, containing at least one TM region, no SPase II signal peptide, but possibly a SPase I signal peptide (213,419 or 22.6% of the sequences); and (iv) cytoplasmic proteins, containing no signal peptide or TM regions (631,735 or 66.8% of the sequences). Sequences predicted to contain a SPase I signal peptide by only one of the neural network and hidden Markov model predictors and those with both a SPase II signal peptide and a TM region were discarded (1,000 or 0.1% of the sequences). In all sequence sets, the predicted signal peptides were removed and analyzed independently for cysteine occurrence. For lipoproteins, the N-terminal cysteine was excluded from the calculations.

**Experimentally Investigated Bacterial Strains**—*Arthrobacter luteus* (ATCC 21606), *Bacillus cereus* (ATCC 14579), *Bacillus subtilis* (ATCC 6051), *Corynebacterium glutamicum* (ATCC 13032), *E. coli* (UPEC (UTI89)) (34), *Enterococcus faecalis* (ATCC 29212), *Haemophilus influenzae* (SMI 120 strain 1 type B), *Micrococcus luteus* (ATCC 11880), *Pseudomonas aeruginosa* (ATCC 33357), *Rhodococcus equi* (ATCC 6939), *Salmonella typhimurium* (ATCC 14028), *Staphylococcus aureus* (ATCC 25923), and *Streptococcus pyogenes* (ATCC 11434) were used in this study.

<figure><img src="image_3.png" /></figure>

<footnote n="4">⁴The abbreviations used are: TM, transmembrane; SPase, signal peptidase; DTT, dithiothreitol; BisTris, 2-[bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)propane-1,3-diol.</footnote>
## Cysteine Exclusion and Oxidation in Gram-positive Bacteria

**Two-dimensional SDS-PAGE**—Bacterial cultures were grown in brain-heart infusion medium to mid-log phase and sedimented by centrifugation at 15,000 × g for 10 min. Pellets were resuspended in 20 mM Tris-Cl, pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 20 mM N-ethylmaleimide, and 200 µg/ml mutanolysin (Sigma) and rotated for 30 min at 4 °C. Lysates were then adjusted to 1% SDS and 8 mM urea and passed through a French press. Insoluble cell debris was removed by centrifugation at 15,000 × g for 10 min. Samples were resolved in the first dimension via nonreducing SDS-PAGE. For the second dimension, the lanes were excised with a razor, placed in sample buffer containing 100 mM dithiothreitol (DTT), heated for 5 min at 95 °C, overlaid onto a 1.0-mm 2D-Well NuPAGE 10% BisTris gel, separated by electrophoresis, and resolved by Coomassie Blue staining (35).

**Bacterial DTT Susceptibility Assay**—Bacterial strains were grown at 37 °C to mid-log phase in brain-heart infusion medium supplemented with 10% glucose bouillon (10% horse serum, 1% meat extract, 1% peptone, 1% dextrose, and 0.5% NaCl, pH 7.5). Cultures were diluted to OD<sub>600 nm</sub> = 0.050 in unconditioned growth medium and transferred to wells of a Honeycomb 2 plate (Isotron) containing DTT. The growth kinetics were monitored by changes in the OD<sub>600 nm</sub> at 37 °C using a Bioscreen C plate reader (Labsystems). For *H. influenzae*, the growth medium was supplemented with 0.2 mM NAD.

**DNA Constructs**—The coding sequences for CG0026, CG0354, and CG2799 from *C. glutamicum* (ATCC 13032) and DsbA (C4447) from *E. coli* (UTI89) were PCR-amplified from chromosomal DNA with 5'-primers that excluded the N-terminal signal peptide and replaced it with a His<sub>6</sub> tag. The PCR products were subcloned into the pET21d expression vector (Novagen), and each construct was verified by DNA sequencing.

**Recombinant Protein Expression, Purification, and Size Exclusion Chromatography**—Bacterial cultures were grown to A<sub>600 nm</sub> = 0.6; induced with 1 mM isopropyl β-D-thiogalactopyranoside for 3 h; sedimented; and resuspended in 20 mM Tris, pH 7.5, 500 mM NaCl, and 20 mM imidazole with 200 µg/ml lysozyme and 200 µg/ml DNase I. Following rotation for 30 min at 4 °C, the lysates were sonicated and clarified by centrifugation at 15,000 × g for 10 min. Proteins were then isolated using nickel-Sepharose 6 Fast Flow (GE Healthcare); washed; eluted with 500 mM imidazole in 20 mM Tris, pH 7.5, and 500 mM NaCl; and dialyzed against 20 mM Tris, pH 7.5.

Protein concentrations were determined by the absorbance at 280 nm using their respective extinction coefficients and molecular masses. Size exclusion chromatography was performed on an ÄKTA FPLC system (GE Healthcare) equipped with a Superdex 75 column. The molecular mass standards were run according to the manufacturer's instructions; all protein samples were dialyzed into and separated with phosphate-buffered saline, pH 7.4; and the absorbance was monitored at 260 and 280 nm.

**Determination of Oxidase and Reductase Activities**—Oxidase activity was assayed by analyzing the cleavage of cCMP by reduced RNase A refolded in the presence of each enzyme (36). RNase A (Sigma) was reduced by overnight incubation at 27 °C in 100 mM Tris acetate, pH 8.0, containing 6 mM guanidine HCl

and 140 mM DTT. DTT and guanidine were removed by size exclusion chromatography with Sepharose G-10 beads. RNase A reduction was verified by the mobility shift created by the large 525-Da free thiol-modifying agent maleimide-polyethylene oxide-biotin and with 5,5'-dithiobis(2-nitrobenzoic acid) (supplemental Fig. S11A). Each enzyme was assayed in a 1-ml solution containing 100 mM Tris acetate, pH 8.0, 2 mM EDTA, 0.2 mM GSSG, 1 mM GSH, and 10 µM reduced RNase A. Following a 2-min incubation, cCMP was added at a final concentration of 4.5 mM, and the absorbance at 296 nm was recorded. Reductase activity was determined at 27 °C by measuring the turbidity of insulin at OD<sub>600 nm</sub> that occurs upon precipitation of the reduced B chain (37). Insulin (Sigma) was resuspended at 5 mg/ml in 100 mM potassium acetate, pH 7.5, by dropping the pH to 3.0 with HCl and titrating back to pH 7.5 with KOH prior to adjusting to 2 mM EDTA and 10 µM DTT. The enzymes were assayed in a 200-µl solution containing 100 mM potassium acetate, pH 7.5, 2 mM EDTA, 320 µM DTT, and 200 µg of insulin.

## RESULTS

**Aerobic Gram-positive Actinobacteria Are Predicted to Stabilize Exported Proteins with Disulfide Bonds, Whereas Aerobic Firmicutes Exclude Cysteines**—To gain an understanding of how Gram-positive bacteria have evolved to protect and stabilize their proteins in the different oxidative environments, we compared the cysteine incorporation patterns in different types of proteins from Gram-positive bacteria (Firmicutes and Actinobacteria) with those from Gram-negative bacteria (Proteobacteria). Initially, we downloaded the available proteomes from the 340 bacterial species of the major phyla of Gram-positive and Gram-negative bacteria (EMBL-EBI Database). The strict anaerobic species were then classified as “anaerobes,” and all bacteria capable of aerobic respiration, including strict aerobes and facultative anaerobes, were grouped together as “aerobes” (supplemental Fig. S1 and Table 1).

Computational analysis was performed on the proteomes to separate them into the following subproteomes: lipoproteins, secreted proteins, TM proteins, and cytoplasmic proteins (Fig. 1A and supplemental Fig. S2). Because only cysteines with free thiols in mature secreted proteins are susceptible to oxidation, the signal peptides were removed and examined separately, and the lipoprotein lipid-linked N-terminal cysteines were excluded prior to analysis (supplemental Fig. S3) (38).

Bacteria with the capacity for disulfide bond formation have previously been shown to favor the incorporation of cysteines in pairs (i.e. an even-biased manner) in their substrate proteins (27, 29, 39). Thus, this characteristic can be used as a strong indication of disulfide bond formation. We first analyzed the average cysteine distribution in all of the predicted secreted proteins, lipoproteins, TM proteins, and signal peptides from aerobic and anaerobic Gram-positive and Gram-negative bacteria.

All but anaerobic Gram-positive bacteria favored an even number of cysteines in their secreted proteins and lipoproteins, and no obvious trends were observed in the signal peptides and TM protein loops (supplemental Fig. S3). However, when the exported protein (lipoprotein and secreted protein) subproteomes were analyzed separately, a large number of those from
Cysteine Exclusion and Oxidation in Gram-positive Bacteria

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /><figcaption>FIGURE 1. Exported proteins from aerobic Firmicutes largely exclude cysteines, whereas those from Actinobacteria favor paired cysteines. A, the schematics depict the protein characteristics used to classify the subproteomes. The SPase type I and II signal peptides (SP) and TM regions were used to identify and sort each proteome into its respective topology or subproteome. B, the exported proteins (secreted proteins and lipoproteins) from Actinobacteria show a profile suggestive of disulfide bond formation, whereas those from Firmicutes preferentially exclude cysteines. The subpro- teomes containing the exported proteins from Gram-positive bacteria were separated into two major cysteine incorporation patterns. All aerobic Gram-positive Actinobacteria possess an "even-numbered cysteine bias" (left panel) in their exported proteins, and the large majority of Gram-positive Firmicutes show a cysteine exclusion trend (right panel). Each line represents the cysteine distribution in the exported proteins from one bacterial proteome.</figcaption></figure>

aerobic Gram-positive bacteria (~60%) were found to average less than one cysteine/protein and to lack the even-numbered cysteine bias (supplemental Fig. S4). From these observations, we were able to classify the vast majority of all of the exported protein subproteomes by one of two patterns.

The first is an “even cysteine-biased” pattern defined by an up-and-down trend in the percentage of exported proteins that correspond to an even (up) and odd (down) number of cysteines (0 Cys > 1 Cys and 2 Cys > 1 Cys), and the second is a “cysteine exclusion trend” (0 Cys > 1 Cys > 2 Cys) (Table 1). Only 5% of the exported protein subproteomes did not follow either pat- tern and were labeled as “remaining,” and those with fewer than 25 proteins were excluded from further analysis (supplemental Fig. S5 and Table 1). Following this separation, we could con- firm a conclusion in a recent study that an obvious distinction

exists between the two major phyla of Gram-positive bacteria (27).

All exported protein subproteomes from aerobic Actinobac-
teria fell into the even cysteine-biased pattern, whereas those
from aerobic Firmicutes followed mainly the cysteine exclusion
trend (Fig. 1B, Table 1, and supplemental Fig. S6). The exported
proteins from aerobic Firmicutes have a mean of ~0.5 Cys, and
an astonishing 70% of them are devoid of cysteine residues,
compared with only 33% in anaerobic Firmicutes (supplemen-
tal Fig. S7). In contrast, the exported proteins from aerobic
Actinobacteria have a mean of ~2.2 Cys, only 25% of them lack
cysteine residues, and about 60% contain even numbers of cys-
teines, which is significantly higher than for aerobic Gram-neg-
ative Proteobacteria (supplemental Figs. S3A, S6, and S7). Thus,
the maturation of the exported proteins from aerobic Acti-
# Cysteine Exclusion and Oxidation in Gram-positive Bacteria

<caption>**TABLE 1**
Distribution of bacterial exported and cytoplasmic subproteomes to the indicated cysteine incorporation trends</caption>

The number of subproteomes that were classifiable into one of the two cysteine incorporation trends is displayed with respect to the total number of subproteomes that were analyzed from each class of bacteria. For the specific species distribution and those that were not classifiable by these trends, see the supplemental data.

<table><thead><tr><th rowspan="2"></th><th rowspan="2">Phyla</th><th colspan="2">Exported proteins</th><th colspan="2">Cytoplasmic proteins</th></tr><tr><th>Even bias</th><th>Exclusion</th><th>Semi-normal</th><th>Exclusion</th></tr></thead><tbody><tr><td colspan="6"><strong>Gram-positive bacteria</strong></td></tr><tr><td rowspan="2">Aerobic</td><td>Actinobacteria</td><td>31/31</td><td></td><td>27/31</td><td>4/31</td></tr><tr><td>Firmicutes</td><td>10/64</td><td>51/64</td><td>17/64</td><td>43/64</td></tr><tr><td rowspan="2">Anaerobic</td><td>Actinobacteria</td><td>1/3</td><td>2/3</td><td>2/3</td><td>1/3</td></tr><tr><td>Firmicutes</td><td>2/20</td><td>11/20</td><td>16/20</td><td>2/20</td></tr><tr><td colspan="6"><strong>Gram-negative Proteobacteria</strong></td></tr><tr><td rowspan="8">Aerobic</td><td>Alpha</td><td>49/52</td><td></td><td>50/52</td><td>2/52</td></tr><tr><td>Beta</td><td>34/34</td><td></td><td>33/34</td><td>1/34</td></tr><tr><td>Delta</td><td>3/5</td><td>2/5</td><td>4/5</td><td></td></tr><tr><td>Epsilon</td><td>12/12</td><td></td><td>8/12</td><td></td></tr><tr><td>Gamma</td><td>80/86</td><td></td><td>83/86</td><td>1/12</td></tr><tr><td>Alpha</td><td>5/13</td><td>4/13</td><td>12/13</td><td>1/86</td></tr><tr><td>Beta</td><td>2/2</td><td></td><td>2/2</td><td></td></tr><tr><td>Delta</td><td>2/11</td><td>9/11</td><td>11/11</td><td>1/13</td></tr><tr><td rowspan="6">Anaerobic</td><td>Epsilon</td><td>1/1</td><td></td><td>1/1</td><td></td></tr><tr><td>Gamma</td><td>5/6</td><td></td><td>5/6</td><td></td></tr></tbody></table>

nobacteria likely involves disulfide bond formation, and aerobic Firmicutes tend to exclude cysteines from their exported proteins (27).

*Exported Proteins from Firmicutes Are Significantly Longer*— To understand how the exported proteins from Firmicutes have evolved in the absence of disulfide bond stabilization, we examined their length in comparison with that of their cytoplasmic proteins. In Firmicutes, Actinobacteria, and Gram-negative bacteria, the average length of their mature exported proteins is longer than that of their respective cytosolic proteins, which are ~325 amino acids in length (Fig. 2A). However, the mature exported proteins from aerobic Firmicutes have an average length that is ~70 amino acids longer than that of their cytoplasmic proteins. This difference is substantially greater than the 7- and 16-amino acid increases seen in aerobic Actinobacteria and Gram-negative Proteobacteria, respectively. Although different cell wall attachment motifs in the Firmicute exported proteins may contribute to the increase in length, it is also possible that these proteins require more extensive non-covalent structural interactions to stabilize their proteins in the absence of disulfide bonds.

*Aerobic Firmicutes Exclude Cysteines from Their Cytoplasmic Proteins*—Analysis of the cytoplasmic subproteomes revealed that aerobic Gram-positive bacteria encode cysteines with a low frequency, resulting in a unique distribution profile that peaks at 0 Cys compared with 2 Cys in Gram-negative Proteobacteria and Gram-positive anaerobes (Fig. 2B and supplemental Fig. S8). Upon investigating the population variations of the cytoplasmic subproteomes from Gram-positive bacteria, we were able to assign them to either a cysteine exclusion trend (0 Cys > 1 Cys > 2 Cys) or a “semi-normal cysteine trend” (1 Cys > 0 Cys). Using these parameters, the majority of aerobic Firmicutes (67%) were found to have a cysteine exclusion trend in their cytoplasmic proteins, whereas Actinobacteria and anaerobic Firmicutes had a strong inclination toward a semi-normal cysteine trend (Fig. 2C and Table 1). Thus, aerobic Firmicutes appear to possess a general tendency to exclude cysteines from their proteins in comparison with other bacteria.

*Actinobacteria Possess Disulfide-bonded Proteins*—To examine whether aerobic Actinobacteria possess disulfide-bonded

proteins, whole cell lysates from *C. glutamicum* were separated and resolved by two-dimensional nonreducing/reducing SDS-PAGE (35). In accordance with the predictive data, both inter-molecular (Fig. 3, below the diagonal) and large intramolecular (above the diagonal) disulfide-bonded proteins were present in *C. glutamicum* and in the control lysate from *E. coli*. As expected, no obvious disulfide-bonded proteins were detected in the lysate from the Firmicute *S. aureus*. Because some exported Firmicute proteins do not bind to the cell envelope following secretion, concentrated conditioned LB media from *S. aureus* and other Firmicutes were examined, but only a few proteins were observed, and none of them showed mobility shifts attributed to disulfide bond formation (data not shown).

*Firmicutes Are Resistant to Highly Reducing Conditions*— Many proteins contain intramolecular disulfide bonds that do not cause a mobility shift when comparing their nonreduced and reduced states following separation by SDS-PAGE. Therefore, as a second test of our predictions, we investigated the ability of various bacteria to tolerate growth in rich media containing the disulfide bond-reducing agent DTT. We hypothesized that Firmicutes, whose exported proteins are predicted to lack disulfide bonds, would tolerate higher levels of DTT in comparison with the disulfide bond-forming Actinobacteria. Strikingly, 20 mM DTT had little effect on the liquid growth of various aerobic Firmicute species, and more impressively, they were all capable of growth in 100 mM DTT (Fig. 4 and supplemental Fig. S9). In contrast, the growth of numerous species from Actinobacteria and Gram-negative Proteobacteria was sensitive to DTT in a concentration-dependent manner, with 20 mM DTT almost entirely inhibiting growth.

*Actinobacteria Encode Two Dimeric Oxidoreductases Capable of Productive Disulfide Bond Formation*—In Gram-negative Proteobacteria, the enzymes that facilitate disulfide bond formation are oxidoreductases or DsbA homologs that reside in the periplasm and are recharged by a membrane-bound DsbB homolog (12). Several studies have identified the presence of DsbA and DsbB homologs across bacteria and used them as an indication of disulfide bond formation (16, 27, 28). To examine whether *C. glutamicum* possesses Dsb homologs capable of catalyzing disulfide bond formation, we identified three putative
Cysteine Exclusion and Oxidation in Gram-positive Bacteria

<figure><img src="image_6.png" /><figcaption>B</figcaption></figure>

<figure><img src="image_7.png" /><figcaption>C</figcaption></figure>

<figure><img src="image_8.png" /></figure>

FIGURE 2. Cysteine exclusion from the exported proteins, but not from the cytoplasmic proteins, of aerobic Firmicutes correlates with a substantial increase in protein length. A, the average lengths of the predicted cytoplasmic and exported proteins from the indicated class of bacteria are displayed. The exported proteins from aerobic and anaerobic Firmicutes have an average length that is 22 and 32% longer than their respective cytoplasmic proteins, whereas those from aerobic and anaerobic Actinobacteria have average lengths that are only 2 and 5% longer, respectively. B, aerobic Gram-positive bacteria have a unique distribution in their cytoplasmic proteins with respect to cysteine content. Each *line* represents the percentage of cytoplasmic proteins from the different classes of bacteria that possess the indicated number of cysteine residues. C, the majority of aerobic Gram-positive Firmicutes show a cysteine incorporation pattern in their cytoplasmic proteins that follows the cysteine exclusion trend (**left panel**) versus the semi-normal cysteine distribution (**right panel**) favored by Actinobacteria and anaerobic Firmicutes.

tive secreted soluble Dsb-like proteins with Cys-X-X-Cys motifs (CG26, CG354, and CG2799) and analyzed their reductase and oxidase activities (Fig. 5).

In contrast to the DsbA homologs in Gram-negative bacteria, all three putative oxidoreductases from *C. glutamicum* exist as homodimers and not monomers (Fig. 5C). To test for reductase activity, equal molar amounts of each enzyme were examined for their ability to reduce insulin *in vitro* (37). CG26 reduced the highest amount of insulin, followed by DsbA from *E. coli* and CG2799, which showed weak activity. All of these enzymes functioned in a concentration-dependent manner, with the exception of CG354, which was inactive (Fig. 5D and supplemental Fig. S10).

Oxidation activity was determined by the ability of the enzymes to properly oxidize reduced RNase A (36). Both CG26 and CG2799, but not CG354, could productively oxidize reduced RNase A in a concentration-dependent manner (Fig.

5E and supplemental Fig. S11). Homology searches revealed that CG26 is a conserved secreted enzyme with its closest homologs in a diverse number of Actinobacteria (supplemental Fig. S12). In contrast, CG2799 has only two homologs, indicating that it likely performs a specific function for Corynebacteria (supplemental Fig. S13). Together, these data indicate that Actinobacteria also possess a functional DsbA-like homolog (A-DsbA) that potentially acts as a homodimer to oxidize their exported proteins during maturation.

DISCUSSION

Although several mechanisms are known for how Gram-
negative bacteria and their proteins have adapted to the chal-
lenges posed by oxidative environments, very little is known
about how Gram-positive bacteria have evolved to overcome
these problems. To address this issue, we predicted the subcel-
lular location of ~1,000,000 bacterial proteins by computa-

<figure><img src="image_9.png" /></figure>
Cysteine Exclusion and Oxidation in Gram-positive Bacteria

<figure><img src="image_10.png" /><figcaption>FIGURE 3. **Actinobacteria possess disulfide-bonded proteins.** Actinobacteria (*C. glutamicum*) and Gram-negative Proteobacteria (*E. coli*) express proteins with both inter- and intramolecular disulfide bonds. Whole cell lysates from the indicated bacteria were separated by two-dimensional nonreducing/reducing SDS-PAGE and visualized by Coomassie Blue staining. Intramolecular disulfide-bonded proteins lie above the *diagonal*, and intermolecular disulfide-bonded proteins lie below the *diagonal*.</figcaption></figure>

<figure><img src="image_11.png" /><figcaption>FIGURE 4. **Firmicutes have a unique tolerance for high levels of reductant.** The reductant DTT severely impaired the growth of aerobic Gram-negative Proteobacteria and Actinobacteria, whereas aerobic Firmicutes were capable of growth even at high DTT concentrations (for additional species, see supplemental Fig. S9). Representative growth curves from three independent experiments are displayed as changes in OD<sub>600 nm</sub>. The indicated bacterial strains were grown in brain-heart infusion medium in the presence of 0, 1, 5, 10, and 20 mM DTT (*E. coli* and *C. glutamicum*) or 0, 10, 20, 80, and 100 mM DTT (*S. aureus*).</figcaption></figure>

tional analysis and examined their respective cysteine incorpo-
ration patterns to identify potential strategies these bacteria
have evolved in response to oxidative pressure on their pro-
teins. We further determined the sensitivity of a range of bac-
terial species to the reductant DTT, looked for disulfide-
bonded proteins by two-dimensional nonreducing/reducing
SDS-PAGE, and identified two dimeric actinobacterial Dsb
homologs capable of productive oxidation. Together, our pre-
dictive and experimental results, combined with those from
previous studies (16, 27, 28), strongly suggest that aerobic
Gram-positive Actinobacteria possess the capacity for regu-
lated disulfide bond formation, whereas Firmicutes do not.
Instead, aerobic Firmicutes largely exclude cysteine residues
from both their exported and cytoplasmic proteins.

The complexity of the folding process is largely dependent on
the environment and the amino acid composition of a protein.
Oxidative environments present a challenge for proteins that
contain cysteines due to their susceptibility to attack by reactive
oxygen species (15, 40, 41). To alleviate this problem, Gram-
negative bacteria are known to maintain their cytoplasm in a
reducing state by the thioredoxin and glutaredoxin systems (42,

43). In their periplasm, they localize a soluble enzyme (DsbA) that functions together with the plasma membrane-bound DsbB to catalyze disulfide bond formation in their exported proteins, which increases their stability and protects them from deleterious oxidation (16, 17).

Two different strategies were found for how Gram-positive
bacteria address the environmental pressure that accompanies
the localization of their proteins. As noted previously by Dutton
et al. (27), each maturation strategy correlates with a distinct
cysteine incorporation pattern that depends on whether the
proteomes originate from the Firmicute or Actinobacteria
phyla. Firmicutes appear to use a simple and unique method to
cope with the oxidative pressure on their exported proteins that
we term “cysteine exclusion.”

Cysteine exclusion could have evolved by a selective growth
advantage; however, its implementation as a protective strategy
is evident based on the following findings. (i) Cysteine incorpo-
ration patterns are different between aerobic and anaerobic Fir-
micutes; (ii) compared with Actinobacteria and Gram-negative
bacteria, Firmicutes have a high tolerance for reductant in the
growth medium; and (iii) conserved cysteines that form disul-
Supplemental Material can be found at:
http://www.jbc.org/content/suppl/2009/11/24/M109.081398.DC1.html
http://www.jbc.org/content/suppl/2010/01/21/285.5.3300.DC1.html

Cysteine Exclusion and Oxidation in Gram-positive Bacteria

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

FIGURE 5. **The Actinobacterium C. glutamicum** possesses two secreted dimeric oxidoreductases. A, schematic representations and characteristics of the three putative oxidoreductases from C. glutamicum and DsbA from E. coli. The recombinant proteins were expressed with an N-terminal His tag replacing the signal peptide. The amino acid numbering refers to the unprocessed wild-type proteins, and the active-site Cys-X-X-Cys motifs are displayed. B, Coomassie Blue-stained gel of the recombinant proteins that were purified following expression in E. coli. C, size exclusion profiles of the purified proteins separated on a Superdex 75 column and monitored by the absorbance at 280 nm. The relative size of each standard is indicated with an arrow. mAbs, milli-absorbance. D, the actinobacterial enzyme CG26 from C. glutamicum efficiently reduces insulin *in vitro*, whereas CG2799 shows slight activity. Each enzyme was analyzed for the capacity to reduce insulin at 27 °C by monitoring precipitation of the reduced B chain observed by changes in OD<sub>600</sub>. E, CG26 and CG2799 can correctly oxidize reduced RNase A *in vitro*. The ability of each enzyme to properly oxidize reduced RNase A (*rRNase*) in a glutathione redox buffer was assayed at 27 °C by monitoring the change in the absorbance at 296 nm that results from cleavage of cCMP by RNase A. The activities of native RNase A and reduced RNase A were included as controls.

fide bonds in class A β-lactamases and alkaline phosphatases from Gram-negative bacteria are not present in many of the aerobic Firmicute homologs (27, 44–47). Thus, the exported proteins in aerobic Firmicutes that contain cysteines, such as lipoproteins and the sortase enzymes involved in pilus biogenesis, do so as a functional requirement; otherwise, they would have been excluded.

Next, we characterized two disulfide bond-forming proteins in *C. glutamicum* and found that one (CG26) is conserved within the phylum of Actinobacteria. Like the oxidoreductase in the Actinobacterium *Mycobacterium tuberculosis*, which was identified by DsbE homology (48), these enzymes are not entirely homologous to the classical DsbA from Gram-negative bacteria. The differences in sequence (~15% identity) and oligomeric state from the *E. coli* DsbA suggest that, as a group, these enzymes should be classified as actinobacterial or A-DsbA. Together, these findings indicate that, although homology searches are useful to identify potential disulfide

bond-forming enzymes (16, 27, 28), experimental validation is essential to confirm that these proteins function as predicted (41).

The fact that A-DsbA enzymes exist as a dimer and not a monomer like the *E. coli* DsbA has several functional implications. The dimerization of A-DsbA potentially creates specificity for its membrane-bound partner, and it also places two Cys-X-X-Cys active sites in close proximity, which mimics the eukaryotic protein-disulfide isomerases that reside in the endoplasmic reticulum (49). The major difference is that protein-disulfide isomerases are monomeric proteins with two Cys-X-X-Cys active sites. It has recently been proposed that homologs of the vitamin K epoxide reductase enzyme recharge actinobacterial DsbA at the plasma membrane (27, 50). The vitamin K epoxide reductase enzyme that has been proposed to recycle A-DsbA also has potential analogy to eukaryotic oxidation, as homologs exist in the endoplasmic reticulum (27, 50). Thus, disulfide bond formation in Actinobacteria may be more evo-

<figure><img src="image_17.png" /></figure>
# Cysteine Exclusion and Oxidation in Gram-positive Bacteria

lutionarily related to eukaryotes than to Gram-negative bacteria, suggesting that eukaryotic vitamin K epoxide reductase homologs may be responsible for recharging protein-disulfide isomerase.

One intriguing concept that arose from this study is that Firmicutes also favor cysteine exclusion in their cytoplasmic proteins. This suggests that aerobic Firmicutes may have a high level of oxidative pressure on their cytoplasmic proteins as well. A possible explanation for this is that the outer membrane, which is absent in Firmicutes, provides an additional permeability barrier that aids in the regulation of the cytoplasmic redox conditions.

These findings indicate that aerobic Actinobacteria likely possess a regulated compartment that contains the machinery for disulfide bond formation (27, 48). Supporting this, cryo-electron tomography studies have shown that the mycolic acids covalently linked to the peptidoglycan of Actinobacteria create an outer membrane-like structure that is absent in Firmicutes (51, 52). Thus, the presence of an outer membrane appears to be a strong driving force for evolving a system that facilitates disulfide bond formation by creating a regulated folding environment that co-localizes the enzymes and substrates.

Firmicutes such as *B. subtilis*, *S. aureus*, *E. faecalis*, and *Listeria monocytogenes* have previously been reported to encode homologs of DsbA from Gram-negative bacteria (16, 27, 28). Of these, *B. subtilis* is the only Firmicute that also encodes DsbB and for which substrates have been identified, but neither of these two substrates are involved in essential processes (53–57). In the case of *S. aureus*, where no disulfide-bonded substrates have been identified, the lipoprotein homolog of DsbA is thought to function independently by utilizing extracellular oxidants for its recycling in the absence of DsbB (28, 58, 59). Our analysis, combined with the existence of only two validated substrates that possess enzyme-catalyzed disulfide bonds, accentuates that Firmicutes generally exclude cysteines from their exported proteins. Thus, the few Firmicutes that contain DsbA and DsbB homologs likely utilize them for disulfide bond formation in proteins with nonessential niche functions.

From an evolutionary perspective, cysteine exclusion likely provides a selective advantage in extreme redox environments, potentially explaining why Firmicutes are over-represented among the bacteria that colonize and infect oxygen-exposed tissues such as the epidermis and the respiratory tract (60). This is supported by our finding that Firmicutes tolerate strong reductants and by the fact that Firmicute pathogens such as *Streptococcus pneumoniae* actively produce high levels of the powerful oxidant hydrogen peroxide (61). Moreover, the simple strategy of cysteine exclusion may provide Firmicutes with some protection against the oxidation-based immune defenses employed at the host-pathogen interface by neutrophils and macrophages. On the negative side, the inability of Firmicutes to cope with cysteine residues could create a barrier for lateral gene transfer, reducing the variability of their exported proteins, which constitute the majority of bacterial virulence factors. However, recent studies have demonstrated that Firmicutes can also maintain the structural stability of their exported proteins by utilizing alternative covalent bonds, which likely contributes to their ability to exclude cysteines (62). Although it

is clear that Firmicutes in general do not possess the capacity for disulfide bond formation, further investigation into whether they protect their few exported proteins with single cysteines by a reductase system that is functionally analogous to the one recently described in *E. coli* is warranted (19).

*Acknowledgments*—We thank members of the Normark laboratory for helpful comments and critical reading of the manuscript.

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<figure><img src="image_18.png" /></figure>
Gram-negative bacteria

Aerobes
(Aerobes and Facultative Anaerobes)

<figure><img src="image_19.png" /></figure>

Anaerobes
(Strict Anaerobes)

<figure><img src="image_20.png" /></figure>

Gram-positive bacteria

<figure><img src="image_21.png" /></figure>

<figure><img src="image_22.png" /></figure>

**Figure S1.** Illustrations of the oxidizing and reducing conditions that the cytoplasmic and Sec-dependent exported proteins encounter in Gram-positive and Gram-negative aerobic bacteria (aerobes and facultative anaerobes) and anaerobic bacteria (strict anaerobes). The cytosolic (2) and the two Sec-dependent translocation pathways are depicted: co-translational targeting by SRP (1A) and SecB-dependent post-translational targeting (1B), which has yet to be identified in Gram-positive bacteria.
Method for the prediction of protein topology

<figure><img src="image_23.png" /><figcaption>**Figure S2.** Method outline for the prediction of protein topology. (1) Bacterial proteomes were obtained from EBI (http://www.ebc.ac.uk/).</figcaption></figure>

(2) Proteins were identified by ORFs that encode proteins 80 amino acids or longer. (3) Protein sets were homology reduced within each genome using a cut-off of 40% identity. (4), LipoP 1.0 was used to predict all potential lipoproteins based on the presence of a SPase II cleavable signal peptide (SP) (Juncker *et al.* 2003). (5 and 6) The lipoprotein signal peptides and N-terminal cysteine residues were removed and all identified lipoproteins underwent a secondary screen to exclude those that contained potential transmembrane (TM) regions using SCAMPI (Bernsel *et al.* 2008). (7) Proteins lacking a lipoprotein signal sequence were analyzed for the presence of a SPase I cleavable signal peptide using SignalP 3.0 (Bendtsen *et al.* 2004). Positive predictions by both the Neural Network and Hidden Markov Model were required to determine the presence of a SPase I signal peptide. Proteins predicted by only one model were discarded. (8 and 9) Signal peptides were removed and the proteins were characterized as secreted proteins or TM proteins based on the absence or presence of potential TM regions identified by SCAMPI. (10) Proteins lacking both a SPase I and SPase II cleavable signal peptide were characterized as cytoplasmic proteins or TM proteins based on the absence or presence of potential TM regions identified by SCAMPI.
A

<figure><img src="image_24.png" /></figure>

B

<figure><img src="image_25.png" /></figure>

C

<figure><img src="image_26.png" /><figcaption>Figure S3. Average cysteine distribution profiles in the lipoproteins, secreted proteins, their signal peptides and the transmembrane protein loops from aerobic and anaerobic Gram-negative Proteobacteria and Gram-positive bacteria.</figcaption></figure>

(A) Gram-negative Proteobacteria and aerobic Gram-positive bacteria encode cysteine residues in an even biased pattern in their secreted proteins and lipoproteins. Graphs displaying the percentage of the bacterial secreted proteins (left panel) and lipoproteins (right panel) that contain the indicated number of cysteine residues. The N-terminal cysteines on the mature lipoproteins were excluded from the calculations. (B) The cysteine frequency in the SPase I (secreted proteins) and SPase II (lipoprotein) signal peptides are shown. (C) The percentage of transmembrane (TM) proteins containing the indicated number of cysteine residues in their outer loops (left panel) and inner loops (right panel) are shown. The inner and outer loops of each TM protein were assigned using SCAMPI.
<figure><img src="image_27.png" /><figcaption>B</figcaption></figure>

<figure><img src="image_28.png" /></figure>

**Figure S4.** Gram-positive aerobes encode cysteines at a low frequency in their exported proteins and show two different incorporation trends. (A) A distinct subset of aerobic Gram-positive bacteria possess very low cysteine incorporation frequencies (average < 1 Cys per protein) in their secreted proteins and lipoproteins (exported proteins). Proteomes from the aerobic and anaerobic Gram-positive and Gram-negative bacteria were analyzed based on the average number of cysteines in their exported proteins. (B) Individual bacterial proteomes were analyzed for their frequency of encoding an odd versus even number of cysteines within their exported proteins (proteins with 0 Cys were excluded). One cluster of aerobic Gram-positive bacteria is distributed with the aerobic Gram-negative proteobacteria in the lower half of the quadrant (grey) where the majority of their exported proteins contain an even number of cysteines. The other cluster of aerobic Gram-positive bacteria is found in the upper quadrant with a low number of exported proteins encoding cysteine residues in a non-even biased manner.
A

<figure><img src="image_29.png" /></figure>

B

<figure><img src="image_30.png" /></figure>

C

<figure><img src="image_31.png" /></figure>

<figure><img src="image_32.png" /></figure>

**Figure S5.** Gram-negative and Gram-positive bacteria have evolved either to exclude cysteine residues from their secreted proteins and lipoproteins or encode them in pairs. (A) The large majority of bacterial proteomes can be separated based on their exported proteins showing a preference for encoding cysteine residues in an even-numbered bias (left panel), or in an exclusionary trend (right panel). The even-numbered bias is defined as the percentage of proteins containing 0 Cys > 1 Cys and 2 Cys > 1 Cys and the exclusionary trend is defined as 0 Cys > 1 Cys > 2 Cys. The cysteines within the SPase I and II signal peptides were analyzed separately (Figure S3), and the N-terminal cysteines on the mature lipoproteins were excluded from the calculations. (B) The few bacterial exported protein subproteomes that did not fit either of the even bias or exclusionary trend are displayed as 'remaining subproteomes', and (C) those encoding less than 25 exported proteins were excluded due to statistically irrelevant data.
A

<figure><img src="image_33.png" /></figure>

B

<figure><img src="image_34.png" /></figure>

<figure><img src="image_35.png" /></figure>

**Figure S6.** The exported protein cysteine incorporation profiles in Gram-positive bacteria have an even bias in Actinobacteria and an exclusionary bias in Firmicutes. (A) All aerobic Actinobacteria favor even numbers of cysteines in their exported proteins. Each dot represents the number of exported cysteine-containing proteins with an even (grey quadrant) versus odd number of cysteines within a given bacterial proteome. (B) Actinobacteria average more than 1 Cys in their exported proteins while 92% of aerobic Firmicutes average less than 1 Cys.
A

Exported proteins

<figure><img src="image_36.png" /></figure>

B

Cytoplasmic proteins

<figure><img src="image_37.png" /></figure>

<figure><img src="image_38.png" /></figure>

**Figure S7.** Firmicutes favor cysteine exclusion, whereas Actinobacteria have a strong even-number cysteine bias in their exported proteins. (A) The percentages of exported, and (B) cytoplasmic proteins from aerobic and anaerobic Firmicutes and aerobic Actinobacteria that contain the indicated number of cysteine residues are displayed. Anaerobic Actinobacteria were excluded due to the small number (3) of proteomes.
<figure><img src="image_39.png" /><figcaption>**Figure S8.** Cytoplasmic proteins from aerobic Gram-positive Firmicutes encode cysteines at a low frequency. Compared to Actinobacteria and Gram-negative bacteria, the cytoplasmic proteins from aerobic Gram-positive Firmicutes contain on average the fewest numbers of cysteine residues.</figcaption></figure>
A

Gram-negative Proteobacteria

<figure><img src="image_40.png" /></figure>

B

Gram-positive Actinobacteria

<figure><img src="image_41.png" /></figure>

C

Gram-positive Firmicutes

<figure><img src="image_42.png" /></figure>

**Figure S9. Firmicutes do not possess disulfide-bonded proteins essential for growth like Actinobacteria and Gram-negative Proteobacteria.** (A) Additional strains of Gram-negative aerobic Proteobacteria, (B) Gram-positive aerobic Actinobacteria, and (C) aerobic Firmicutes demonstrating how reductant (DTT) severely impairs the growth of Proteobacteria and Actinobacteria, but not Firmicutes. Representative growth curves of 3 independent experiments are displayed as changes in the OD at 600 nm. The indicated bacterial strains were grown at 37°C in BHI in the presence of 0, 1, 5, 10 and 20 mM DTT (A and B) or 0, 10, 20, 80 and 100 mM DTT (C).
A

<figure><img src="image_43.png" /></figure>

B

<figure><img src="image_44.png" /></figure>

C

<figure><img src="image_45.png" /></figure>

D

<figure><img src="image_46.png" /><figcaption>Figure S10. The putative oxidoreductases, CG26 and CG2799, from *C. glutamicum* have reductase activity.</figcaption></figure>

(A) The *in vitro* reductase activity of the three purified CG26, (B), CG354, and (C) CG2799 are shown with the control

(D) DsbA from *E. coli*. The reductase activity was monitored by measuring the turbidity of insulin that occurs upon precipitation of the reduced B chain. The indicated concentration of each enzyme was assayed at 27°C in a 200 µl solution containing 100 mM KOAc pH = 7.5, 2 mM EDTA, 320 µM DTT and 200 µg of insulin and the OD at 600 nm was followed for 30 min.
A

<figure><img src="image_47.png" /></figure>

B

<figure><img src="image_48.png" /></figure>

C

<figure><img src="image_49.png" /></figure>

D

<figure><img src="image_50.png" /></figure>

E

<figure><img src="image_51.png" /></figure>

**Figure S11.** CG26 and CG2799 from *C. glutamicum* correctly oxidize reduced Rnase A in vitro. (A) Native RnaseA and reduced RnaseA were incubated with the free thiol-modifying agent Maleimide-PEO₂-Biotin (PMAL) for 1 hr at 4°C prior to (lanes 2 and 5) and after reduction with DTT for 1 hr at 27°C (lanes 3 and 6). Samples were resolved by SDS-PAGE followed by coomassie staining. The free thiol percentage was also calculated for samples 1 and 4 using 5,5'-Dithiobis(2nitrobenzoic acid) (DTNB). (B) The in vitro oxidase activity of the purified CG26, (C), CG354 and (D), CG2799 are shown in comparison to (E) DsbA from *E. coli*. The oxidase activity was monitored by measuring the cleavage of cCMP by properly oxidized RnaseA. The indicated concentration of each enzyme was assayed at 27°C in a solution containing 100 mM Tris-Acetate pH = 8.0, 2 mM EDTA, 0.2 mM GSSG pH = 8.0, 1 mM GSH pH = 8.0 and 10 µM of reduced RnaseA in a final volume of 1 ml. The reaction was equilibrated for 2 min, adjusted to 4.5 mM cCMP and the Absorbance (Abs) at 296 nm was followed for 30 min.
<figure><img src="image_52.png" /></figure>

<figure><img src="image_53.png" /></figure>

<figure><img src="image_54.png" /></figure>

<figure><img src="image_55.png" /></figure>

<figure><img src="image_56.png" /><figcaption>**Figure S12.** Sequence alignments of homologs to CG26 from *Corynebacterium glutamicum*. ClustalW alignments of the sequences using a homology cutoff of e⁻¹⁹ are shown with conserved, strongly similar and weakly similar residues colored in red, green and blue, respectively. The signal sequences are highlighted in grey, and the CXXC and the putative *cis*Pro are boxed. CG, *Corynebacterium glutamicum*; CE, *Corynebacterium efficiens*; BL, *Brevibacterium linens*; pRELI, *Rhodococcus erythropolis*; DIP, *Corynebacterium diphtheriae*; SACE, *Saccharopolyspora erythraea*; MVAN, *Mycobacterium vanbaalenii*; MAB, *Mycobacterium abscessus*; SCO, *Streptomyces coelicolor*; SGR, *Streptomyces griseus*; and Rxyl, *Rubrobacter xylanophilus*. The asterisk denotes the only strain, Rcas, or *Roseiflexus castenholzii* that is not an Actinobacteria and comes from the phylum Chloroflexi.</figcaption></figure>
<figure><img src="image_57.png" /><figcaption>**Figure S13. Sequence alignments of homologs to CG2799 from Corynebacterium glutamicum.**</figcaption></figure>

ClustalW alignments of the sequences using a homology cutoff of $e^{-11}$ are shown with conserved, strongly similar and weakly similar residues colored in red, green and blue, respectively. The signal sequences are highlighted in grey, and the CXXC motif and the putative cisPro are boxed. CG, *Corynebacterium glutamicum*; DIP, *Corynebacterium diphtheriae*; and NFA, *Nocardia Farcinica*. All homologs are from the Actinobacteria phylum.
Supplemental Table1A Daniels *et al.* 2009

<table><caption>Mature bacterial exported proteins (secreted proteins and lipoproteins)</caption><thead><tr><th rowspan="2"></th><th rowspan="2">Species</th><th rowspan="2">Trend</th><th colspan="4">Number of secreted proteins</th><th colspan="4">Number of lipoproteins</th></tr><tr><th>0 Cys</th><th>1 Cys</th><th>2 Cys</th><th>3 Cys</th><th>0 Cys</th><th>1 Cys</th><th>2 Cys</th><th>3 Cys</th></tr></thead><tbody><tr><td rowspan="12">Gram-negative Bacteria<br>Alpha proteobacteria</td><td>Acidiphilium cryptum (strain JF-5)</td><td>Even-bias</td><td>105</td><td>32</td><td>65</td><td>16</td><td>21</td><td>2</td><td>14</td><td>1</td></tr><tr><td>Agrobacterium tumefaciens (strain C58 / ATCC 33970)</td><td>Even-bias</td><td>166</td><td>50</td><td>157</td><td>17</td><td>23</td><td>2</td><td>15</td><td>1</td></tr><tr><td>Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571)</td><td>Even-bias</td><td>130</td><td>26</td><td>104</td><td>17</td><td>12</td><td>1</td><td>8</td><td>0</td></tr><tr><td>Bartonella bacilliformis (strain ATCC 35685 / KC583)</td><td>Even-bias</td><td>31</td><td>4</td><td>16</td><td>2</td><td>6</td><td>0</td><td>7</td><td>1</td></tr><tr><td>Bartonella henselae (strain Houston 1 / ATCC 49882)</td><td>Even-bias</td><td>31</td><td>7</td><td>27</td><td>4</td><td>9</td><td>2</td><td>8</td><td>2</td></tr><tr><td>Bartonella quintana (strain Toulouse)</td><td>Even-bias</td><td>25</td><td>12</td><td>20</td><td>1</td><td>9</td><td>3</td><td>7</td><td>3</td></tr><tr><td>Bartonella tribocorum CIP 105476</td><td>Even-bias</td><td>36</td><td>10</td><td>30</td><td>5</td><td>9</td><td>5</td><td>9</td><td>2</td></tr><tr><td>Bradyrhizobium japonicum (strain USDA 110)</td><td>Even-bias</td><td>220</td><td>70</td><td>227</td><td>39</td><td>18</td><td>7</td><td>10</td><td>1</td></tr><tr><td>Brucella abortus (strain 2308)</td><td>Even-bias</td><td>92</td><td>18</td><td>83</td><td>8</td><td>15</td><td>3</td><td>13</td><td>0</td></tr><tr><td>Brucella canis ATCC 23365</td><td>Even-bias</td><td>100</td><td>19</td><td>85</td><td>13</td><td>17</td><td>3</td><td>15</td><td>0</td></tr><tr><td>Brucella melitensis (biovar 1, strain NCTC 10094 / ATCC 23456 / 16M)</td><td>Even-bias</td><td>71</td><td>13</td><td>59</td><td>7</td><td>9</td><td>2</td><td>10</td><td>0</td></tr><tr><td>Brucella suis ATCC 23445</td><td>Even-bias</td><td>96</td><td>21</td><td>82</td><td>13</td><td>15</td><td>4</td><td>14</td><td>0</td></tr><tr><td>Caulobacter crescentus (strain CB15 / ATCC 19089)</td><td>Even-bias</td><td>139</td><td>30</td><td>118</td><td>14</td><td>36</td><td>4</td><td>15</td><td>0</td></tr><tr><td>Dinoroseobacter shibae DFL 12</td><td>Even-bias</td><td>137</td><td>23</td><td>123</td><td>8</td><td>26</td><td>3</td><td>19</td><td>0</td></tr><tr><td>Ehrlichia canis (strain Jake)</td><td>Even-bias</td><td>6</td><td>4</td><td>13</td><td>5</td><td>2</td><td>0</td><td>1</td><td>0</td></tr><tr><td>Ehrlichia chaffeensis (strain Arkansas)</td><td>Even-bias</td><td>7</td><td>4</td><td>7</td><td>6</td><td>2</td><td>1</td><td>2</td><td>0</td></tr><tr><td>Ehrlichia ruminantium (strain Gardel)</td><td>Even-bias</td><td>5</td><td>5</td><td>17</td><td>3</td><td>2</td><td>1</td><td>1</td><td>0</td></tr><tr><td>Erythrobacter litoralis (strain HTCC2594)</td><td>Even-bias</td><td>101</td><td>16</td><td>86</td><td>3</td><td>38</td><td>5</td><td>32</td><td>0</td></tr><tr><td>Gluconacetobacter diazotrophicus PAI 5</td><td>Even-bias</td><td>96</td><td>37</td><td>76</td><td>14</td><td>23</td><td>6</td><td>7</td><td>0</td></tr><tr><td>Gluconobacter oxydans (strain 621H)</td><td>Even-bias</td><td>80</td><td>30</td><td>78</td><td>11</td><td>28</td><td>4</td><td>14</td><td>0</td></tr><tr><td>Granulobacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1)</td><td>Even-bias</td><td>53</td><td>14</td><td>44</td><td>10</td><td>16</td><td>1</td><td>10</td><td>0</td></tr><tr><td>Hyphomonas neptunium (strain ATCC 15444)</td><td>Even-bias</td><td>117</td><td>19</td><td>101</td><td>9</td><td>74</td><td>7</td><td>68</td><td>0</td></tr><tr><td>Jannaschia sp. (strain CCS1)</td><td>Even-bias</td><td>137</td><td>18</td><td>145</td><td>12</td><td>26</td><td>3</td><td>18</td><td>0</td></tr><tr><td>Magnetospirillum magneticum (strain AMB-1 / ATCC 700264)</td><td>Even-bias</td><td>104</td><td>26</td><td>76</td><td>11</td><td>28</td><td>7</td><td>20</td><td>0</td></tr><tr><td>Maricaulis maris (strain MCS10)</td><td>Even-bias</td><td>142</td><td>19</td><td>126</td><td>10</td><td>52</td><td>4</td><td>41</td><td>0</td></tr><tr><td>Mesorhizobium sp. (strain BNC1)</td><td>Even-bias</td><td>152</td><td>31</td><td>138</td><td>17</td><td>20</td><td>4</td><td>17</td><td>0</td></tr><tr><td>Methyllobacterium extorquens PA1</td><td>Even-bias</td><td>208</td><td>45</td><td>128</td><td>16</td><td>19</td><td>4</td><td>12</td><td>0</td></tr><tr><td>Neorickettsia sennetsu (strain Miyayama)</td><td>Even-bias</td><td>9</td><td>4</td><td>9</td><td>3</td><td>1</td><td>0</td><td>0</td><td>0</td></tr><tr><td>Nitrobacter hamburgensis (strain X14 / DSM 10229)</td><td>Even-bias</td><td>134</td><td>37</td><td>124</td><td>18</td><td>17</td><td>2</td><td>13</td><td>0</td></tr><tr><td>Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391)</td><td>Even-bias</td><td>91</td><td>27</td><td>89</td><td>19</td><td>13</td><td>4</td><td>11</td><td>0</td></tr><tr><td>Novosphingobium aromaticivorans (strain DSM 12444)</td><td>Even-bias</td><td>142</td><td>21</td><td>122</td><td>15</td><td>30</td><td>6</td><td>28</td><td>0</td></tr><tr><td>Orientia tsutsugamushi (strain Boryong)</td><td>Remaining</td><td>4</td><td>6</td><td>5</td><td>7</td><td>1</td><td>0</td><td>0</td><td>0</td></tr><tr><td>Paracoccus denitrificans (strain Pd 1222)</td><td>Even-bias</td><td>184</td><td>38</td><td>136</td><td>18</td><td>25</td><td>4</td><td>24</td><td>0</td></tr><tr><td>Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)</td><td>Even-bias</td><td>120</td><td>18</td><td>78</td><td>9</td><td>27</td><td>2</td><td>15</td><td>0</td></tr><tr><td>Pelagibacter ubique (strain HTCC1062)</td><td>Even-bias</td><td>16</td><td>4</td><td>30</td><td>2</td><td>11</td><td>0</td><td>5</td><td>0</td></tr><tr><td>Rhizobium etli (strain CFN 42 / ATCC 51251)</td><td>Even-bias</td><td>156</td><td>55</td><td>159</td><td>17</td><td>26</td><td>1</td><td>21</td><td>0</td></tr><tr><td>Rhizobium leguminosarum bv. viciae (strain 3841)</td><td>Even-bias</td><td>194</td><td>72</td><td>196</td><td>24</td><td>26</td><td>3</td><td>23</td><td>0</td></tr><tr><td>Rhizobium loti (strain MAFF303099)</td><td>Even-bias</td><td>150</td><td>38</td><td>185</td><td>20</td><td>25</td><td>2</td><td>17</td><td>0</td></tr><tr><td>Rhizobium meliloti (strain 1021)</td><td>Even-bias</td><td>181</td><td>44</td><td>187</td><td>17</td><td>19</td><td>4</td><td>14</td><td>0</td></tr><tr><td>Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)</td><td>Even-bias</td><td>115</td><td>24</td><td>116</td><td>15</td><td>22</td><td>6</td><td>21</td><td>0</td></tr><tr><td>Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)</td><td>Even-bias</td><td>167</td><td>44</td><td>134</td><td>21</td><td>25</td><td>2</td><td>14</td><td>0</td></tr><tr><td>Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255)</td><td>Even-bias</td><td>127</td><td>25</td><td>58</td><td>14</td><td>32</td><td>2</td><td>11</td><td>0</td></tr><tr><td>Roseobacter denitrificans (strain OCh 114 / ATCC 33942)</td><td>Even-bias</td><td>131</td><td>30</td><td>121</td><td>15</td><td>21</td><td>5</td><td>13</td><td>0</td></tr><tr><td>Silicibacter pomeroyi (strain ATCC 700808 / DSS-3 / DSM 15171)</td><td>Even-bias</td><td>103</td><td>27</td><td>120</td><td>14</td><td>24</td><td>5</td><td>14</td><td>0</td></tr><tr><td>Silicibacter sp. (strain TM1040)</td><td>Even-bias</td><td>112</td><td>17</td><td>103</td><td>12</td><td>23</td><td>2</td><td>18</td><td>1</td></tr><tr><td>Sinorhizobium medicae (strain WSM419)</td><td>Even-bias</td><td>182</td><td>48</td><td>190</td><td>28</td><td>24</td><td>5</td><td>21</td><td>1</td></tr><tr><td>Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)</td><td>Even-bias</td><td>197</td><td>35</td><td>163</td><td>19</td><td>39</td><td>2</td><td>16</td><td>1</td></tr><tr><td>Sphingopyxis alaskensis</td><td>Even-bias</td><td>130</td><td>27</td><td>105</td><td>13</td><td>40</td><td>2</td><td>34</td><td>0</td></tr><tr><td>Wolbachia pipientis wMel</td><td>Remaining</td><td>7</td><td>8</td><td>5</td><td>5</td><td>0</td><td>1</td><td>1</td><td>1</td></tr><tr><td>Wolbachia sp. (subsp. Brugia malayi, strain TRS)</td><td>Remaining</td><td>4</td><td>5</td><td>6</td><td>2</td><td>1</td><td>1</td><td>0</td><td>1</td></tr><tr><td>Xanthobacter sp.</td><td>Even-bias</td><td>147</td><td>32</td><td>134</td><td>17</td><td>14</td><td>2</td><td>13</td><td>0</td></tr><tr><td>Zymomonas mobilis (strain CP4 / ZM4 / ATCC 31821)</td><td>Even-bias</td><td>56</td><td>16</td><td>32</td><td>4</td><td>16</td><td>4</td><td>2</td><td>0</td></tr></tbody></table>

Downloaded from www.jbc.org at AGRICULTURAL RESEARCH AGENCY, NIGERIA, ON OCTOBER 9, 2010
<table><caption>Supplemental Table1A Daniels *et al.* 2009</caption><tr><td>Escherichia coli (strain K12)</td><td>Even-bias</td><td>150</td><td>27</td><td>114</td><td>12</td><td>54</td><td>9</td><td>30</td><td>4</td></tr><tr><td>Francisella tularensis (subsp. tularensis, strain FSC 198)</td><td>Even-bias</td><td>37</td><td>10</td><td>22</td><td>4</td><td>25</td><td>1</td><td>13</td><td>2</td></tr><tr><td>Haemophilus ducreyi (strain ATCC 700724 / 35000HP)</td><td>Even-bias</td><td>51</td><td>8</td><td>34</td><td>3</td><td>2</td><td>0</td><td>0</td><td>0</td></tr><tr><td>Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)</td><td>Even-bias</td><td>62</td><td>5</td><td>31</td><td>4</td><td>9</td><td>3</td><td>4</td><td>0</td></tr><tr><td>Haemophilus somnus (strain 129Pt)</td><td>Even-bias</td><td>46</td><td>3</td><td>18</td><td>1</td><td>19</td><td>2</td><td>12</td><td>0</td></tr><tr><td>Hahella chejuensis (strain KCTC 2396)</td><td>Even-bias</td><td>237</td><td>56</td><td>165</td><td>23</td><td>74</td><td>13</td><td>52</td><td>6</td></tr><tr><td>Halorhodospira halophila (strain DSM 244 / SL1)</td><td>Even-bias</td><td>106</td><td>11</td><td>23</td><td>3</td><td>36</td><td>2</td><td>12</td><td>1</td></tr><tr><td>Idiomarina loihiensis (strain L2-TR / DSM 15497 / ATCC BAA-735)</td><td>Even-bias</td><td>146</td><td>15</td><td>67</td><td>4</td><td>57</td><td>2</td><td>18</td><td>0</td></tr><tr><td>Klebsiella pneumoniae (subsp. pneumoniae, strain ATCC 700721 / MGH 78578)</td><td>Even-bias</td><td>184</td><td>18</td><td>107</td><td>4</td><td>47</td><td>3</td><td>21</td><td>3</td></tr><tr><td>Legionella pneumophila (strain Paris)</td><td>Even-bias</td><td>88</td><td>27</td><td>59</td><td>18</td><td>33</td><td>9</td><td>12</td><td>1</td></tr><tr><td>Marinobacter aquaeolei (strain DSM 11845 / ATCC 700491 / VT8) / VT8)</td><td>Even-bias</td><td>158</td><td>21</td><td>93</td><td>17</td><td>66</td><td>3</td><td>24</td><td>1</td></tr><tr><td>Marinomonas sp. MWYL1</td><td>Even-bias</td><td>162</td><td>17</td><td>92</td><td>10</td><td>56</td><td>2</td><td>21</td><td>1</td></tr><tr><td>Methylococcus capsulatus (strain Bath / NCIMB 11132)</td><td>Even-bias</td><td>79</td><td>26</td><td>32</td><td>9</td><td>27</td><td>10</td><td>15</td><td>1</td></tr><tr><td>Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)</td><td>Even-bias</td><td>84</td><td>24</td><td>45</td><td>12</td><td>46</td><td>3</td><td>11</td><td>1</td></tr><tr><td>Pasteurella multocida (strain Pm70)</td><td>Even-bias</td><td>65</td><td>8</td><td>41</td><td>5</td><td>33</td><td>3</td><td>23</td><td>1</td></tr><tr><td>Photobacterium profundum (strain SS9)</td><td>Even-bias</td><td>254</td><td>32</td><td>138</td><td>19</td><td>1</td><td>0</td><td>0</td><td>1</td></tr><tr><td>Photorhabdus luminescens laumondii (strain TT01)</td><td>Even-bias</td><td>91</td><td>8</td><td>78</td><td>6</td><td>38</td><td>9</td><td>14</td><td>1</td></tr><tr><td>Pseudoalteromonas atlantica (strain T6c / BAA-1087)</td><td>Even-bias</td><td>211</td><td>46</td><td>119</td><td>16</td><td>69</td><td>16</td><td>56</td><td>1</td></tr><tr><td>Pseudoalteromonas haloplanktis (strain TAC 125)</td><td>Even-bias</td><td>166</td><td>21</td><td>94</td><td>7</td><td>75</td><td>7</td><td>33</td><td>1</td></tr><tr><td>Pseudomonas aeruginosa (strain LMG 12228 / ATCC 15692 / PRS 101 / 1C / PAO1)</td><td>Even-bias</td><td>235</td><td>36</td><td>149</td><td>15</td><td>80</td><td>10</td><td>52</td><td>1</td></tr><tr><td>Pseudomonas entomophila (strain L48)</td><td>Even-bias</td><td>221</td><td>33</td><td>114</td><td>17</td><td>74</td><td>11</td><td>39</td><td>1</td></tr><tr><td>Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)</td><td>Even-bias</td><td>232</td><td>46</td><td>142</td><td>17</td><td>83</td><td>11</td><td>46</td><td>1</td></tr><tr><td>Pseudomonas mendocina (strain ymp)</td><td>Even-bias</td><td>216</td><td>39</td><td>104</td><td>13</td><td>69</td><td>8</td><td>38</td><td>1</td></tr><tr><td>Pseudomonas putida (strain F1 / ATCC 700007)</td><td>Even-bias</td><td>230</td><td>26</td><td>124</td><td>11</td><td>68</td><td>15</td><td>37</td><td>1</td></tr><tr><td>Pseudomonas stutzeri (strain A1501)</td><td>Even-bias</td><td>128</td><td>26</td><td>90</td><td>7</td><td>48</td><td>6</td><td>25</td><td>1</td></tr><tr><td>Pseudomonas syringae (pathovar phaseolicola, strain 1448A / Race 6)</td><td>Even-bias</td><td>177</td><td>29</td><td>98</td><td>12</td><td>68</td><td>9</td><td>29</td><td>1</td></tr><tr><td>Psychrobacter arcticum (strain 273-4)</td><td>Even-bias</td><td>45</td><td>12</td><td>21</td><td>2</td><td>32</td><td>1</td><td>20</td><td>1</td></tr><tr><td>Psychrobacter cryohalolentis (strain K5)</td><td>Even-bias</td><td>59</td><td>13</td><td>25</td><td>4</td><td>42</td><td>1</td><td>31</td><td>1</td></tr><tr><td>Psychrobacter sp. (strain PRwf-1)</td><td>Even-bias</td><td>65</td><td>11</td><td>31</td><td>0</td><td>41</td><td>2</td><td>31</td><td>1</td></tr><tr><td>Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)</td><td>Even-bias</td><td>177</td><td>53</td><td>116</td><td>19</td><td>74</td><td>13</td><td>57</td><td>1</td></tr><tr><td>Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)</td><td>Even-bias</td><td>120</td><td>25</td><td>85</td><td>9</td><td>43</td><td>6</td><td>23</td><td>1</td></tr><tr><td>Salmonella choleraesuis (strain SC-B67)</td><td>Even-bias</td><td>142</td><td>25</td><td>113</td><td>14</td><td>46</td><td>8</td><td>25</td><td>1</td></tr><tr><td>Salmonella paratyphi A (strain SARB42 / ATCC 9150)</td><td>Even-bias</td><td>138</td><td>22</td><td>109</td><td>12</td><td>42</td><td>8</td><td>25</td><td>1</td></tr><tr><td>Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)</td><td>Even-bias</td><td>145</td><td>22</td><td>111</td><td>11</td><td>40</td><td>10</td><td>23</td><td>1</td></tr><tr><td>Salmonella typhi (strain ATCC 700931 / Ty2)</td><td>Even-bias</td><td>149</td><td>27</td><td>114</td><td>14</td><td>46</td><td>10</td><td>25</td><td>1</td></tr><tr><td>Salmonella typhimurium (strain ATCC 700720 / SGSC1412 / LT2)</td><td>Even-bias</td><td>161</td><td>25</td><td>118</td><td>10</td><td>45</td><td>10</td><td>26</td><td>1</td></tr><tr><td>Serratia proteamaculans (strain 568)</td><td>Even-bias</td><td>178</td><td>31</td><td>132</td><td>7</td><td>62</td><td>4</td><td>27</td><td>1</td></tr><tr><td>Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)</td><td>Even-bias</td><td>199</td><td>35</td><td>101</td><td>13</td><td>60</td><td>11</td><td>30</td><td>1</td></tr><tr><td>Shewanella baltica (strain OS155 / ATCC BAA-1091)</td><td>Even-bias</td><td>202</td><td>30</td><td>101</td><td>11</td><td>57</td><td>13</td><td>30</td><td>1</td></tr><tr><td>Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)</td><td>Even-bias</td><td>196</td><td>32</td><td>94</td><td>7</td><td>66</td><td>6</td><td>30</td><td>1</td></tr><tr><td>Shewanella frigidimarina (strain NCIMB 400)</td><td>Even-bias</td><td>199</td><td>31</td><td>93</td><td>14</td><td>67</td><td>11</td><td>32</td><td>1</td></tr><tr><td>Shewanella loihica (strain BAA-1088 / PV-4)</td><td>Even-bias</td><td>212</td><td>33</td><td>114</td><td>11</td><td>65</td><td>13</td><td>33</td><td>1</td></tr><tr><td>Shewanella oneidensis (strain MR-1)</td><td>Even-bias</td><td>171</td><td>29</td><td>105</td><td>13</td><td>62</td><td>10</td><td>29</td><td>1</td></tr><tr><td>Shewanella pealeana ATCC 700345</td><td>Even-bias</td><td>226</td><td>25</td><td>125</td><td>17</td><td>71</td><td>14</td><td>37</td><td>1</td></tr><tr><td>Shewanella putrefaciens (strain CN-32/ATCC BAA-453)</td><td>Even-bias</td><td>191</td><td>21</td><td>84</td><td>10</td><td>64</td><td>12</td><td>24</td><td>1</td></tr><tr><td>Shewanella sediminis HAW-EB3</td><td>Even-bias</td><td>226</td><td>44</td><td>111</td><td>16</td><td>82</td><td>15</td><td>27</td><td>1</td></tr><tr><td>Shewanella sp. (strain ANA-3)</td><td>Even-bias</td><td>215</td><td>27</td><td>120</td><td>14</td><td>69</td><td>10</td><td>37</td><td>1</td></tr><tr><td>Shigella boydii (serovar 4, strain Sb227)</td><td>Even-bias</td><td>106</td><td>27</td><td>68</td><td>7</td><td>37</td><td>7</td><td>19</td><td>1</td></tr><tr><td>Shigella dysenteriae (serovar 1, strain Sd97 / Sd197)</td><td>Even-bias</td><td>101</td><td>25</td><td>68</td><td>7</td><td>34</td><td>8</td><td>15</td><td>1</td></tr><tr><td>Shigella flexneri (serovar2a, strain 2457T/ATCC 700930)</td><td>Even-bias</td><td>104</td><td>19</td><td>71</td><td>11</td><td>43</td><td>9</td><td>18</td><td>1</td></tr><tr><td>Shigella sonnei (strain Ss046)</td><td>Even-bias</td><td>120</td><td>23</td><td>77</td><td>12</td><td>41</td><td>11</td><td>19</td><td>1</td></tr><tr><td>Sodalis glossinidius (strain morsitans)</td><td>Even-bias</td><td>48</td><td>21</td><td>37</td><td>3</td><td>21</td><td>10</td><td>5</td><td>0</td></tr><tr><td>Vesicomyosocius okutanii (subsp. Calyptogena okutanii, strain HA)</td><td>Even-bias</td><td>17</td><td>5</td><td>12</td><td>2</td><td>6</td><td>2</td><td>1</td><td>3</td></tr><tr><td>Vibrio cholerae (strain ATCC 39541 / O395)</td><td>Even-bias</td><td>141</td><td>25</td><td>68</td><td>7</td><td>42</td><td>2</td><td>23</td><td>1</td></tr></table>
<table><caption>Supplemental Table1A Daniels *et al.* 2009</caption><thead><tr><th>Gram-positive Bacteria</th><th>Actinobacteria</th><th>Anaerobic</th><th>Anaerobic</th></tr></thead><tbody><tr><td></td><td></td><td>Vibrio fischeri (strain ATCC 700601 / ES114)</td><td>Even-bias</td><td>171</td><td>19</td><td>86</td><td>5</td><td>68</td><td>5</td><td>49</td><td>2</td></tr><tr><td></td><td></td><td>Vibrio harveyi (strain ATCC BAA-1116 / BB120)</td><td>Even-bias</td><td>196</td><td>36</td><td>118</td><td>9</td><td>60</td><td>6</td><td>54</td><td>9</td></tr><tr><td></td><td></td><td>Vibrio parahaemolyticus (serovar O3:K6, strain RIMD 2210633)</td><td>Even-bias</td><td>201</td><td>30</td><td>110</td><td>9</td><td>69</td><td>3</td><td>52</td><td>4</td></tr><tr><td></td><td></td><td>Vibrio vulnificus (strain CMCP6)</td><td>Even-bias</td><td>170</td><td>19</td><td>92</td><td>6</td><td>49</td><td>1</td><td>32</td><td>2</td></tr><tr><td></td><td></td><td>Wigglesworthia glossinidia brevipalpis</td><td>&lt;25 proteins</td><td>2</td><td>0</td><td>2</td><td>0</td><td>3</td><td>4</td><td>0</td><td>0</td></tr><tr><td></td><td></td><td>Xanthomonas axonopodis citri (strain 306)</td><td>Even-bias</td><td>173</td><td>44</td><td>113</td><td>11</td><td>48</td><td>10</td><td>38</td><td>2</td></tr><tr><td></td><td></td><td>Xanthomonas campestris (strain ATCC 33913)</td><td>Even-bias</td><td>168</td><td>43</td><td>112</td><td>19</td><td>47</td><td>9</td><td>47</td><td>0</td></tr><tr><td></td><td></td><td>Xanthomonas oryzae (pathovar oryzae, MAFF 311018)</td><td>Even-bias</td><td>146</td><td>39</td><td>87</td><td>26</td><td>47</td><td>7</td><td>37</td><td>1</td></tr><tr><td></td><td></td><td>Xylella fastidiosa (strain 9a5c)</td><td>Even-bias</td><td>58</td><td>18</td><td>24</td><td>11</td><td>27</td><td>6</td><td>12</td><td>0</td></tr><tr><td></td><td></td><td>Xylella fastidiosa (strain Temecula1 / ATCC 700964)</td><td>Even-bias</td><td>49</td><td>15</td><td>28</td><td>11</td><td>27</td><td>6</td><td>13</td><td>1</td></tr><tr><td></td><td></td><td>Yersinia enterocolitica (serovar O:8 / strain 8081)</td><td>Even-bias</td><td>139</td><td>15</td><td>98</td><td>7</td><td>55</td><td>4</td><td>17</td><td>0</td></tr><tr><td></td><td></td><td>Yersinia pestis (biovar Antiqua Antiqua, strain Antiqua)</td><td>Even-bias</td><td>154</td><td>19</td><td>106</td><td>6</td><td>54</td><td>3</td><td>14</td><td>1</td></tr><tr><td></td><td></td><td>Yersinia pseudotuberculosis (serovar I, strain IP32953)</td><td>Even-bias</td><td>162</td><td>21</td><td>108</td><td>4</td><td>53</td><td>5</td><td>17</td><td>1</td></tr><tr><td></td><td></td><td>Alkalilimnicola ehrlichei (strain MLHE-1)</td><td>Even-bias</td><td>108</td><td>17</td><td>48</td><td>8</td><td>36</td><td>1</td><td>15</td><td>0</td></tr><tr><td></td><td></td><td>Carsonella ruddii (strain PV)</td><td>&lt;25 proteins</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td></td><td></td><td>Mannheimia succiniciproducens (strain MBEL55E)</td><td>Even-bias</td><td>63</td><td>9</td><td>30</td><td>2</td><td>35</td><td>2</td><td>18</td><td>0</td></tr><tr><td></td><td></td><td>Psychromonas ingrahamii (strain 37)</td><td>Even-bias</td><td>123</td><td>18</td><td>68</td><td>7</td><td>42</td><td>5</td><td>19</td><td>0</td></tr><tr><td></td><td></td><td>Ruthia magnifica magnifica (subsp. Calyptogena)</td><td>Even-bias</td><td>22</td><td>4</td><td>10</td><td>3</td><td>10</td><td>0</td><td>2</td><td>0</td></tr><tr><td></td><td></td><td>Thiomicrospira crunogena (strain XCL-2)</td><td>Even-bias</td><td>100</td><td>19</td><td>39</td><td>3</td><td>27</td><td>3</td><td>18</td><td>0</td></tr><tr><td></td><td></td><td>Acidothermus cellulolyticus (strain ATCC 43068 / 11B)</td><td>Even-bias</td><td>18</td><td>8</td><td>20</td><td>7</td><td>4</td><td>3</td><td>14</td><td>0</td></tr><tr><td></td><td></td><td>Arthrobacter aurescens (strain TC1)</td><td>Even-bias</td><td>38</td><td>16</td><td>44</td><td>8</td><td>32</td><td>4</td><td>39</td><td>0</td></tr><tr><td></td><td></td><td>Clavibacter michiganensis (subsp. michiganensis, strain NCPPB 382)</td><td>Even-bias</td><td>41</td><td>16</td><td>41</td><td>4</td><td>28</td><td>2</td><td>26</td><td>0</td></tr><tr><td></td><td></td><td>Corynebacterium diphtheriae (biovar gravis, strain NCTC 13129 / ATCC 700971)</td><td>Even-bias</td><td>19</td><td>8</td><td>33</td><td>5</td><td>15</td><td>3</td><td>21</td><td>0</td></tr><tr><td></td><td></td><td>Corynebacterium efficiens (strain DSM 44549 / NBRC 100395 / JCM 11189 / YS-314 / AJ 12310)</td><td>Even-bias</td><td>28</td><td>7</td><td>40</td><td>5</td><td>15</td><td>2</td><td>14</td><td>0</td></tr><tr><td></td><td></td><td>Corynebacterium glutamicum (strain R)</td><td>Even-bias</td><td>28</td><td>11</td><td>32</td><td>9</td><td>33</td><td>4</td><td>30</td><td>0</td></tr><tr><td></td><td></td><td>Corynebacterium jeikeium (strain K411)</td><td>Even-bias</td><td>32</td><td>6</td><td>32</td><td>10</td><td>14</td><td>2</td><td>17</td><td>0</td></tr><tr><td></td><td></td><td>Frankia alni (strain ACN14a)</td><td>Even-bias</td><td>40</td><td>13</td><td>50</td><td>8</td><td>13</td><td>1</td><td>11</td><td>0</td></tr><tr><td></td><td></td><td>Kineococcus radiotolerans SRS30216</td><td>Even-bias</td><td>60</td><td>19</td><td>63</td><td>4</td><td>19</td><td>7</td><td>26</td><td>0</td></tr><tr><td></td><td></td><td>Leifsonia xyli xyli (strain CTCB07)</td><td>Even-bias</td><td>17</td><td>13</td><td>18</td><td>2</td><td>12</td><td>3</td><td>12</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium avium (strain 104)</td><td>Even-bias</td><td>29</td><td>20</td><td>76</td><td>9</td><td>24</td><td>7</td><td>23</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium bovis (strain ATCC BAA-935)</td><td>Even-bias</td><td>24</td><td>23</td><td>43</td><td>12</td><td>11</td><td>5</td><td>21</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium gilvum PYR-GCK</td><td>Even-bias</td><td>56</td><td>15</td><td>104</td><td>8</td><td>28</td><td>2</td><td>40</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium leprae (strain TN)</td><td>Even-bias</td><td>14</td><td>8</td><td>26</td><td>6</td><td>4</td><td>4</td><td>6</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)</td><td>Even-bias</td><td>26</td><td>26</td><td>62</td><td>16</td><td>22</td><td>9</td><td>16</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium smegmatis (strain ATCC 700084 / mc(2) / mc(2)155)</td><td>Even-bias</td><td>70</td><td>21</td><td>94</td><td>13</td><td>45</td><td>7</td><td>56</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)</td><td>Even-bias</td><td>26</td><td>21</td><td>48</td><td>12</td><td>12</td><td>5</td><td>21</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium ulcerans (strain Agy99)</td><td>Even-bias</td><td>34</td><td>20</td><td>54</td><td>15</td><td>14</td><td>5</td><td>25</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium vanbaalenii (strain DSM 7251 / PYR-1)</td><td>Even-bias</td><td>63</td><td>25</td><td>125</td><td>13</td><td>34</td><td>3</td><td>38</td><td>0</td></tr><tr><td></td><td></td><td>Nocardia farcinica (strain IFM 10152)</td><td>Even-bias</td><td>40</td><td>22</td><td>72</td><td>16</td><td>25</td><td>7</td><td>43</td><td>0</td></tr><tr><td></td><td></td><td>Nocardioïdés sp. (strain BAA-499 / JS614)</td><td>Even-bias</td><td>52</td><td>23</td><td>81</td><td>10</td><td>29</td><td>2</td><td>39</td><td>0</td></tr><tr><td></td><td></td><td>Renibacterium salmoninarum (strain ATCC 33209)</td><td>Even-bias</td><td>29</td><td>18</td><td>24</td><td>9</td><td>16</td><td>10</td><td>16</td><td>0</td></tr><tr><td></td><td></td><td>Rhodococcus sp. (strain RHA1)</td><td>Even-bias</td><td>65</td><td>27</td><td>85</td><td>14</td><td>53</td><td>8</td><td>54</td><td>0</td></tr><tr><td></td><td></td><td>Rubrobacter xylanophilus (strain DSM 9941 / NBRC 16129)</td><td>Even-bias</td><td>39</td><td>18</td><td>19</td><td>5</td><td>20</td><td>3</td><td>9</td><td>0</td></tr><tr><td></td><td></td><td>Saccharopolyspora erythraea (strain NRRL 23338)</td><td>Even-bias</td><td>62</td><td>21</td><td>89</td><td>20</td><td>23</td><td>6</td><td>32</td><td>0</td></tr><tr><td></td><td></td><td>Salinispora arenicola CNS-205</td><td>Even-bias</td><td>37</td><td>15</td><td>47</td><td>8</td><td>15</td><td>9</td><td>29</td><td>0</td></tr><tr><td></td><td></td><td>Salinispora tropica CNB-440</td><td>Even-bias</td><td>27</td><td>19</td><td>32</td><td>6</td><td>13</td><td>7</td><td>26</td><td>0</td></tr><tr><td></td><td></td><td>Streptomyces avermitilis (strain DSM 46492 / NRRL 8165 / NCIMB 12804 / ATCC 31267 / JCM 5070)</td><td>Even-bias</td><td>68</td><td>48</td><td>99</td><td>36</td><td>38</td><td>7</td><td>42</td><td>6</td></tr><tr><td></td><td></td><td>Streptomyces coelicolor (strain ATCC BAA-471 / M145 / A3(2))</td><td>Even-bias</td><td>75</td><td>40</td><td>108</td><td>37</td><td>49</td><td>12</td><td>57</td><td>3</td></tr><tr><td></td><td></td><td>Thermobifida fusca (strain YX)</td><td>Even-bias</td><td>25</td><td>13</td><td>34</td><td>4</td><td>17</td><td>6</td><td>17</td><td>0</td></tr><tr><td></td><td></td><td>Tropheryma whipplei (strain Twist)</td><td>Even-bias</td><td>6</td><td>1</td><td>8</td><td>1</td><td>4</td><td>0</td><td>2</td><td>0</td></tr><tr><td></td><td></td><td>Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083)</td><td>Exclusionary</td><td>14</td><td>9</td><td>8</td><td>5</td><td>5</td><td>5</td><td>5</td><td>2</td></tr><tr><td></td><td></td><td>Bifidobacterium longum (strain NCC 2705)</td><td>Exclusionary</td><td>8</td><td>9</td><td>6</td><td>6</td><td>12</td><td>4</td><td>5</td><td>4</td></tr><tr><td></td><td></td><td>Propionibacterium acnes (strain DSM 16379 / KPA171202)</td><td>Even-bias</td><td>9</td><td>8</td><td>30</td><td>4</td><td>14</td><td>8</td><td>13</td><td>5</td></tr></tbody></table>
<table><caption>Supplemental Table1A Daniels *et al.* 2009</caption><thead><tr><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td rowspan="10">Anaerobic</td><td>Streptococcus agalactiae la (serovar la, strain A909 / CDC SS700 / ATCC 27591)</td><td>Exclusionary</td><td>59</td><td>15</td><td>4</td><td>1</td><td>30</td><td>1</td><td>0</td><td>0</td></tr><tr><td>Streptococcus agalactiae III (serovar III, strain NEM316)</td><td>Exclusionary</td><td>56</td><td>18</td><td>5</td><td>1</td><td>27</td><td>3</td><td>0</td><td>0</td></tr><tr><td>Streptococcus agalactiae V (serovar V, strain 2603 V/R / ATCC BAA-611)</td><td>Exclusionary</td><td>57</td><td>15</td><td>3</td><td>0</td><td>27</td><td>1</td><td>0</td><td>0</td></tr><tr><td>Streptococcus gordonii (strain Challis / ATCC 35105 / CH1 / DL1 / V288)</td><td>Remaining</td><td>52</td><td>5</td><td>8</td><td>2</td><td>47</td><td>5</td><td>2</td><td>1</td></tr><tr><td>Streptococcus mutans (serovar c, strain ATCC 700610 / UA159)</td><td>Exclusionary</td><td>40</td><td>10</td><td>6</td><td>1</td><td>22</td><td>1</td><td>0</td><td>0</td></tr><tr><td>Streptococcus pneumoniae (serovar 2, strain D39 / NCTC 7466)</td><td>Even-bias</td><td>31</td><td>2</td><td>4</td><td>0</td><td>27</td><td>0</td><td>2</td><td>1</td></tr><tr><td>Streptococcus pneumoniae (strain ATCC BAA-255 / R6)</td><td>Even-bias</td><td>32</td><td>5</td><td>4</td><td>0</td><td>25</td><td>0</td><td>3</td><td>1</td></tr><tr><td>Streptococcus pneumoniae (strain TIGR4 / ATCC BAA-334)</td><td>Even-bias</td><td>35</td><td>3</td><td>4</td><td>0</td><td>28</td><td>0</td><td>2</td><td>1</td></tr><tr><td>Streptococcus pyogenes M1 (serovar M1, strain MGAS5005 / ATCC BAA-947)</td><td>Exclusionary</td><td>40</td><td>16</td><td>8</td><td>4</td><td>21</td><td>2</td><td>2</td><td></td></tr><tr><td>Streptococcus sanguinis (strain SK36)</td><td>Exclusionary</td><td>61</td><td>8</td><td>2</td><td>2</td><td>38</td><td>7</td><td>3</td><td></td></tr><tr><td>Streptococcus suis (strain 05ZYH33)</td><td>Exclusionary</td><td>38</td><td>6</td><td>5</td><td>2</td><td>26</td><td>5</td><td>1</td><td></td></tr><tr><td>Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9)</td><td>Exclusionary</td><td>35</td><td>7</td><td>1</td><td>0</td><td>13</td><td>6</td><td>0</td><td></td></tr><tr><td>Symbiobacterium thermophilum (strain IAM 14863 / T)</td><td>Even-bias</td><td>100</td><td>16</td><td>29</td><td>4</td><td>0</td><td>0</td><td>0</td><td></td></tr><tr><td>Ureaplasma parvum (serovar 3, strain ATCC 700970)</td><td>Even-bias</td><td>11</td><td>7</td><td>6</td><td>3</td><td>15</td><td>2</td><td>4</td><td></td></tr><tr><td>Alkaliphilus metalliredigens (strain QYMF)</td><td>Exclusionary</td><td>185</td><td>39</td><td>11</td><td>3</td><td>0</td><td>0</td><td>0</td><td></td></tr><tr><td>Alkaliphilus oremlandii (strain OhILAs)</td><td>Exclusionary</td><td>115</td><td>30</td><td>14</td><td>5</td><td>10</td><td>8</td><td>0</td><td></td></tr><tr><td>Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903)</td><td>Remaining</td><td>27</td><td>37</td><td>36</td><td>18</td><td>3</td><td>8</td><td>6</td><td></td></tr><tr><td>Carboxydothermus hydrogenoformans (strain Z-2901 / DSM 6008)</td><td>Exclusionary</td><td>45</td><td>25</td><td>11</td><td>10</td><td>0</td><td>0</td><td>0</td><td></td></tr><tr><td>Clostridium acetobutylicum (strain DSM 792 / JCM 1419 / LMG 5710 / ATCC 824 / VKM B-1787)</td><td>Remaining</td><td>30</td><td>36</td><td>20</td><td>18</td><td>22</td><td>22</td><td>21</td><td></td></tr><tr><td>Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)</td><td>Exclusionary</td><td>51</td><td>43</td><td>33</td><td>23</td><td>28</td><td>25</td><td>16</td><td></td></tr><tr><td>Clostridium botulinum (strain ATCC 19397 / Type A)</td><td>Remaining</td><td>42</td><td>42</td><td>32</td><td>19</td><td>0</td><td>0</td><td>0</td><td></td></tr><tr><td>Clostridium difficile (strain 630)</td><td>Exclusionary</td><td>46</td><td>35</td><td>32</td><td>11</td><td>1</td><td>0</td><td>0</td><td></td></tr><tr><td>Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NCIMB 10680)</td><td>Remaining</td><td>23</td><td>33</td><td>20</td><td>15</td><td>15</td><td>23</td><td>12</td><td></td></tr><tr><td>Clostridium novyi (strain NT)</td><td>Remaining</td><td>9</td><td>14</td><td>15</td><td>9</td><td>15</td><td>12</td><td>12</td><td></td></tr><tr><td>Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)</td><td>Exclusionary</td><td>50</td><td>48</td><td>18</td><td>13</td><td>5</td><td>6</td><td>2</td><td></td></tr><tr><td>Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)</td><td>Remaining</td><td>13</td><td>21</td><td>25</td><td>23</td><td>24</td><td>24</td><td>32</td><td></td></tr><tr><td>Clostridium tetani (strain Massachusetts / E88)</td><td>Even-bias</td><td>24</td><td>21</td><td>21</td><td>10</td><td>22</td><td>15</td><td>16</td><td></td></tr><tr><td>Clostridium thermocellum (strain ATCC 27405 / DSM 1237)</td><td>Remaining</td><td>37</td><td>39</td><td>40</td><td>22</td><td>18</td><td>18</td><td>17</td><td></td></tr><tr><td>Desulfotomaculum reducens (strain MI-1)</td><td>Exclusionary</td><td>42</td><td>30</td><td>32</td><td>10</td><td>28</td><td>14</td><td>3</td><td></td></tr><tr><td>Moorella thermoacetica (strain ATCC 39073)</td><td>Exclusionary</td><td>44</td><td>25</td><td>11</td><td>5</td><td>16</td><td>6</td><td>6</td><td></td></tr><tr><td>Mycoplasma mycoides SC (subsp. mycoides, strain PG1)</td><td>Exclusionary</td><td>10</td><td>11</td><td>1</td><td>0</td><td>23</td><td>4</td><td>0</td><td></td></tr><tr><td>Mycoplasma penetrans (strain HF-2)</td><td>Exclusionary</td><td>19</td><td>10</td><td>1</td><td>1</td><td>14</td><td>3</td><td>0</td><td></td></tr></tbody></table>

Downloaded from www.jbc.org at: NIA Institut Nationale de la Recherche Agronomique et des Aliments de l'Organisme N°10808 on October 7, 2010
<table><caption>Exported protein signal peptides (secreted proteins and lipoproteins)</caption><thead><tr><th rowspan="2"></th><th rowspan="2">Species</th><th colspan="3">Number of secreted protein signal peptides</th><th colspan="3">Number of lipoprotein signal peptides</th></tr><tr><th>0 Cys</th><th>1 Cys</th><th>2 Cys</th><th>0 Cys</th><th>1 Cys</th><th>2 Cys</th></tr></thead><tbody><tr><td rowspan="13">Gram-negative Bacteria</td><td>Acidiphilium cryptum (strain JF-5)</td><td>179</td><td>61</td><td>6</td><td>35</td><td>7</td><td>1</td></tr><tr><td>Agrobacterium tumefaciens (strain C58 / ATCC 33970)</td><td>354</td><td>89</td><td>15</td><td>34</td><td>8</td><td>0</td></tr><tr><td>Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571)</td><td>257</td><td>78</td><td>18</td><td>19</td><td>6</td><td>0</td></tr><tr><td>Bartonella bacilliformis (strain ATCC 35685 / KC583)</td><td>32</td><td>21</td><td>5</td><td>6</td><td>7</td><td>1</td></tr><tr><td>Bartonella henselae (strain Houston 1 / ATCC 49882)</td><td>47</td><td>23</td><td>10</td><td>17</td><td>4</td><td>2</td></tr><tr><td>Bartonella quintana (strain Toulouse)</td><td>42</td><td>16</td><td>7</td><td>14</td><td>6</td><td>2</td></tr><tr><td>Bartonella tribocorum CIP 105476</td><td>54</td><td>23</td><td>10</td><td>15</td><td>11</td><td>1</td></tr><tr><td>Bradyrhizobium japonicum (strain USDA 110)</td><td>497</td><td>171</td><td>41</td><td>33</td><td>10</td><td>1</td></tr><tr><td>Brucella abortus (strain 2308)</td><td>172</td><td>54</td><td>11</td><td>27</td><td>8</td><td>0</td></tr><tr><td>Brucella canis ATCC 23365</td><td>191</td><td>52</td><td>12</td><td>30</td><td>9</td><td>0</td></tr><tr><td>Brucella melitensis (biovar 1, strain NCTC 10094 / ATCC 23456 / 16M)</td><td>125</td><td>42</td><td>10</td><td>18</td><td>5</td><td>0</td></tr><tr><td>Brucella suis ATCC 23445</td><td>187</td><td>53</td><td>12</td><td>27</td><td>8</td><td>0</td></tr><tr><td>Caulobacter crescentus (strain CB15 / ATCC 19089)</td><td>279</td><td>86</td><td>4</td><td>58</td><td>10</td><td>0</td></tr><tr><td>Dinoroseobacter shibae DFL 12</td><td>268</td><td>88</td><td>16</td><td>40</td><td>11</td><td>0</td></tr><tr><td>Ehrlichia canis (strain Jake)</td><td>18</td><td>19</td><td>4</td><td>6</td><td>6</td><td>0</td></tr><tr><td>Ehrlichia chaffeensis (strain Arkansas)</td><td>17</td><td>13</td><td>4</td><td>2</td><td>6</td><td>1</td></tr><tr><td>Ehrlichia ruminantium (strain Gardel)</td><td>16</td><td>14</td><td>3</td><td>4</td><td>3</td><td>1</td></tr><tr><td>Erythroblasts (strain HTCC2594)</td><td>198</td><td>49</td><td>9</td><td>75</td><td>18</td><td>1</td></tr><tr><td>Gluconacetobacter diazotrophicus PAI 5</td><td>162</td><td>68</td><td>21</td><td>28</td><td>11</td><td>1</td></tr><tr><td>Gluconobacter oxydans (strain 621H)</td><td>142</td><td>79</td><td>18</td><td>39</td><td>18</td><td>3</td></tr><tr><td>Granulobacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1)</td><td>95</td><td>39</td><td>13</td><td>18</td><td>11</td><td>2</td></tr><tr><td>Hyphomonas neptunium (strain ATCC 15444)</td><td>212</td><td>91</td><td>12</td><td>152</td><td>30</td><td>4</td></tr><tr><td>Jannaschia sp. (strain CCS1)</td><td>312</td><td>89</td><td>27</td><td>42</td><td>8</td><td>1</td></tr><tr><td>Magnetospirillum magneticum (strain AMB-1 / ATCC 700264)</td><td>228</td><td>58</td><td>15</td><td>54</td><td>11</td><td>2</td></tr><tr><td>Maricaulis maris (strain MCS10)</td><td>267</td><td>72</td><td>20</td><td>96</td><td>20</td><td>4</td></tr><tr><td>Mesorhizobium sp. (strain BNC1)</td><td>307</td><td>92</td><td>14</td><td>36</td><td>9</td><td>3</td></tr><tr><td>Methylobacterium extorquens PAI1</td><td>368</td><td>99</td><td>14</td><td>27</td><td>11</td><td>0</td></tr><tr><td>Neorickettsia sennetsu (strain Miyayama)</td><td>18</td><td>11</td><td>5</td><td>2</td><td>1</td><td>1</td></tr><tr><td>Nitrobacter hamburgensis (strain X14 / DSM 10229)</td><td>287</td><td>85</td><td>32</td><td>27</td><td>12</td><td>1</td></tr><tr><td>Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391)</td><td>204</td><td>63</td><td>16</td><td>23</td><td>8</td><td>0</td></tr><tr><td>Novosphingobium aromaticivorans (strain DSM 12444)</td><td>276</td><td>76</td><td>18</td><td>67</td><td>9</td><td>3</td></tr><tr><td>Orientia tsutsugamushi (strain Boryong)</td><td>28</td><td>10</td><td>1</td><td>4</td><td>0</td><td>0</td></tr><tr><td>Paracoccus denitrificans (strain Pd 1222)</td><td>346</td><td>85</td><td>17</td><td>50</td><td>7</td><td>0</td></tr><tr><td>Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)</td><td>196</td><td>66</td><td>8</td><td>40</td><td>11</td><td>1</td></tr><tr><td>Pelagibacter ubique (strain HTCC1062)</td><td>63</td><td>7</td><td>0</td><td>15</td><td>0</td><td>1</td></tr><tr><td>Rhizobium etli (strain CFN 42 / ATCC 51251)</td><td>364</td><td>94</td><td>10</td><td>45</td><td>7</td><td>2</td></tr><tr><td>Rhizobium leguminosarum bv. viciae (strain 3841)</td><td>458</td><td>118</td><td>18</td><td>49</td><td>5</td><td>0</td></tr><tr><td>Rhizobium loti (strain MAFF303099)</td><td>382</td><td>107</td><td>17</td><td>38</td><td>10</td><td>2</td></tr><tr><td>Rhizobium meliloti (strain 1021)</td><td>410</td><td>90</td><td>20</td><td>38</td><td>6</td><td>0</td></tr><tr><td>Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)</td><td>270</td><td>63</td><td>12</td><td>41</td><td>14</td><td>1</td></tr><tr><td>Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)</td><td>350</td><td>93</td><td>23</td><td>34</td><td>11</td><td>0</td></tr><tr><td>Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255)</td><td>195</td><td>58</td><td>13</td><td>40</td><td>14</td><td>0</td></tr><tr><td>Roseobacter denitrificans (strain OCh 114 / ATCC 33942)</td><td>254</td><td>93</td><td>18</td><td>33</td><td>11</td><td>0</td></tr><tr><td>Silicibacter pomeroyi (strain ATCC 700808 / DSS-3 / DSM 15171)</td><td>263</td><td>65</td><td>11</td><td>38</td><td>11</td><td>0</td></tr><tr><td>Silicibacter sp. (strain TM1040)</td><td>224</td><td>74</td><td>20</td><td>41</td><td>9</td><td>0</td></tr><tr><td>Sinorhizobium medicae (strain WSM419)</td><td>409</td><td>117</td><td>24</td><td>43</td><td>13</td><td>3</td></tr><tr><td>Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)</td><td>410</td><td>99</td><td>15</td><td>61</td><td>6</td><td>1</td></tr><tr><td>Sphingopyxis alaskensis</td><td>264</td><td>63</td><td>13</td><td>83</td><td>8</td><td>1</td></tr><tr><td>Wolbachia pipientis wMel</td><td>18</td><td>12</td><td>1</td><td>3</td><td>3</td><td>0</td></tr><tr><td>Wolbachia sp. (subsp. Brugia malayi, strain TRS)</td><td>12</td><td>11</td><td>1</td><td>5</td><td>0</td><td>0</td></tr><tr><td>Xanthobacter sp.</td><td>334</td><td>69</td><td>17</td><td>30</td><td>6</td><td>1</td></tr><tr><td>Zymomonas mobilis (strain CP4 / ZM4 / ATCC 31821)</td><td>77</td><td>44</td><td>9</td><td>20</td><td>3</td><td>2</td></tr></tbody></table>
<table><caption>Supplemental Table1B Daniels *et al.* 2009</caption><thead><tr><th></th><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td>Escherichia coli (strain K12)</td><td>254</td><td>89</td><td>31</td><td>74</td><td>30</td><td>2</td></tr><tr><td>Francisella tularensis (subsp. tularensis, strain FSC 198)</td><td>64</td><td>29</td><td>5</td><td>36</td><td>12</td><td>0</td></tr><tr><td>Haemophilus ducreyi (strain ATCC 700724 / 35000HP)</td><td>70</td><td>39</td><td>9</td><td>2</td><td>1</td><td>0</td></tr><tr><td>Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)</td><td>74</td><td>45</td><td>4</td><td>15</td><td>0</td><td>1</td></tr><tr><td>Haemophilus somnus (strain 129Pt)</td><td>69</td><td>19</td><td>2</td><td>31</td><td>4</td><td>1</td></tr><tr><td>Hahella chejuensis (strain KCTC 2396)</td><td>368</td><td>205</td><td>62</td><td>131</td><td>47</td><td>6</td></tr><tr><td>Halorhodospira halophila (strain DSM 244 / SL1)</td><td>118</td><td>35</td><td>10</td><td>46</td><td>10</td><td>2</td></tr><tr><td>Idiomarina lohiiensis (strain L2-TR / DSM 15497 / ATCC BAA-735)</td><td>216</td><td>57</td><td>5</td><td>82</td><td>6</td><td>1</td></tr><tr><td>Klebsiella pneumoniae (subsp. pneumoniae, strain ATCC 700721 / MGH 78578)</td><td>272</td><td>83</td><td>13</td><td>61</td><td>22</td><td>1</td></tr><tr><td>Legionella pneumophila (strain Paris)</td><td>168</td><td>85</td><td>21</td><td>31</td><td>25</td><td>2</td></tr><tr><td>Marinobacter aquaeolei (strain DSM 11845 / ATCC 700491 / VT8) / VT8)</td><td>250</td><td>67</td><td>21</td><td>101</td><td>16</td><td>1</td></tr><tr><td>Marinomonas sp. MWYL1</td><td>215</td><td>85</td><td>21</td><td>63</td><td>23</td><td>1</td></tr><tr><td>Methylococcus capsulatus (strain Bath / NCIMB 11132)</td><td>132</td><td>57</td><td>18</td><td>40</td><td>14</td><td>2</td></tr><tr><td>Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)</td><td>153</td><td>51</td><td>7</td><td>41</td><td>20</td><td>4</td></tr><tr><td>Pasteurella multocida (strain Pm70)</td><td>102</td><td>35</td><td>8</td><td>49</td><td>11</td><td>2</td></tr><tr><td>Photobacterium profundum (strain SS9)</td><td>319</td><td>172</td><td>36</td><td>1</td><td>0</td><td>0</td></tr><tr><td>Photorhabdus luminescens laumondii (strain TT01)</td><td>172</td><td>51</td><td>9</td><td>57</td><td>16</td><td>1</td></tr><tr><td>Pseudoalteromonas atlantica (strain T6c / BAA-1087)</td><td>282</td><td>141</td><td>49</td><td>132</td><td>30</td><td>8</td></tr><tr><td>Pseudoalteromonas haloplanktis (strain TAC 125)</td><td>217</td><td>100</td><td>16</td><td>106</td><td>33</td><td>3</td></tr><tr><td>Pseudomonas aeruginosa (strain LMG 12228 / ATCC 15692 / PRS 101 / 1C / PAO1)</td><td>325</td><td>177</td><td>45</td><td>118</td><td>39</td><td>4</td></tr><tr><td>Pseudomonas entomophila (strain L48)</td><td>296</td><td>136</td><td>38</td><td>100</td><td>32</td><td>8</td></tr><tr><td>Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)</td><td>315</td><td>166</td><td>59</td><td>118</td><td>37</td><td>6</td></tr><tr><td>Pseudomonas mendocina (strain ymp)</td><td>295</td><td>128</td><td>37</td><td>97</td><td>25</td><td>6</td></tr><tr><td>Pseudomonas putida (strain F1 / ATCC 700007)</td><td>299</td><td>133</td><td>36</td><td>91</td><td>30</td><td>6</td></tr><tr><td>Pseudomonas stutzeri (strain A1501)</td><td>196</td><td>80</td><td>20</td><td>63</td><td>17</td><td>6</td></tr><tr><td>Pseudomonas syringae (pathovar phaseolicola, strain 1448A / Race 6)</td><td>235</td><td>113</td><td>23</td><td>84</td><td>25</td><td>6</td></tr><tr><td>Psychrobacter arcticum (strain 273-4)</td><td>71</td><td>21</td><td>3</td><td>56</td><td>4</td><td>2</td></tr><tr><td>Psychrobacter cryohalolentis (strain K5)</td><td>92</td><td>27</td><td>7</td><td>80</td><td>12</td><td>1</td></tr><tr><td>Psychrobacter sp. (strain PRwf-1)</td><td>91</td><td>25</td><td>10</td><td>74</td><td>12</td><td>1</td></tr><tr><td>Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)</td><td>264</td><td>161</td><td>66</td><td>129</td><td>66</td><td>13</td></tr><tr><td>Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)</td><td>219</td><td>65</td><td>9</td><td>63</td><td>21</td><td>1</td></tr><tr><td>Salmonella choleraesuis (strain SC-B67)</td><td>258</td><td>84</td><td>19</td><td>66</td><td>22</td><td>3</td></tr><tr><td>Salmonella paratyphi A (strain SARB42 / ATCC 9150)</td><td>261</td><td>76</td><td>16</td><td>62</td><td>23</td><td>2</td></tr><tr><td>Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)</td><td>270</td><td>80</td><td>15</td><td>60</td><td>26</td><td>3</td></tr><tr><td>Salmonella typhi (strain ATCC 700931 / Ty2)</td><td>268</td><td>86</td><td>20</td><td>65</td><td>25</td><td>2</td></tr><tr><td>Salmonella typhimurium (strain ATCC 700720 / SGSC1412 / LT2)</td><td>291</td><td>79</td><td>21</td><td>68</td><td>21</td><td>4</td></tr><tr><td>Serratia proteamaculans (strain 568)</td><td>290</td><td>109</td><td>28</td><td>78</td><td>21</td><td>0</td></tr><tr><td>Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)</td><td>313</td><td>103</td><td>27</td><td>114</td><td>24</td><td>4</td></tr><tr><td>Shewanella baltica (strain OS155 / ATCC BAA-1091)</td><td>274</td><td>136</td><td>28</td><td>85</td><td>41</td><td>6</td></tr><tr><td>Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)</td><td>257</td><td>117</td><td>30</td><td>95</td><td>23</td><td>10</td></tr><tr><td>Shewanella frigidimarina (strain NCIMB 400)</td><td>277</td><td>115</td><td>34</td><td>115</td><td>28</td><td>3</td></tr><tr><td>Shewanella loihica (strain BAA-1088 / PV-4)</td><td>313</td><td>115</td><td>27</td><td>123</td><td>27</td><td>5</td></tr><tr><td>Shewanella oneidensis (strain MR-1)</td><td>270</td><td>112</td><td>29</td><td>96</td><td>34</td><td>2</td></tr><tr><td>Shewanella pealeana ATCC 700345</td><td>328</td><td>130</td><td>29</td><td>140</td><td>28</td><td>5</td></tr><tr><td>Shewanella putrefaciens (strain CN-32/ATCC BAA-453)</td><td>252</td><td>114</td><td>25</td><td>90</td><td>33</td><td>7</td></tr><tr><td>Shewanella sediminis HAW-EB3</td><td>332</td><td>141</td><td>30</td><td>140</td><td>39</td><td>6</td></tr><tr><td>Shewanella sp. (strain ANA-3)</td><td>292</td><td>149</td><td>34</td><td>110</td><td>33</td><td>7</td></tr><tr><td>Shigella boydii (serovar 4, strain Sb227)</td><td>167</td><td>64</td><td>17</td><td>56</td><td>15</td><td>1</td></tr><tr><td>Shigella dysenteriae (serovar 1, strain Sd97 / Sd197)</td><td>163</td><td>53</td><td>14</td><td>52</td><td>17</td><td>1</td></tr><tr><td>Shigella flexneri (serovar2a, strain 2457T/ATCC 700930)</td><td>178</td><td>59</td><td>15</td><td>54</td><td>23</td><td>2</td></tr><tr><td>Shigella sonnei (strain Ss046)</td><td>199</td><td>66</td><td>19</td><td>57</td><td>20</td><td>3</td></tr><tr><td>Sodalis glossinidius (strain morsitans)</td><td>91</td><td>26</td><td>5</td><td>32</td><td>9</td><td>0</td></tr><tr><td>Vesicomyosocius okutanii (subsp. Calyptogena okutanii, strain HA)</td><td>33</td><td>9</td><td>0</td><td>12</td><td>1</td><td>0</td></tr><tr><td>Vibrio cholerae (strain ATCC 39541 / O395)</td><td>204</td><td>74</td><td>13</td><td>62</td><td>16</td><td>1</td></tr></tbody></table>
<table><caption>Supplemental Table1B Daniels *et al.* 2009</caption><thead><tr><th>Gram-positive Bacteria</th><th>Actinobacteria</th><th>Aerobic</th><th>Anaerobic</th></tr></thead><tbody><tr><td></td><td></td><td>Vibrio fischeri (strain ATCC 700601 / ES114)</td><td>241</td><td>84</td><td>13</td><td>121</td><td>17</td><td>3</td></tr><tr><td></td><td></td><td>Vibrio harveyi (strain ATCC BAA-1116 / BB120)</td><td>322</td><td>114</td><td>16</td><td>124</td><td>22</td><td>0</td></tr><tr><td></td><td></td><td>Vibrio parahaemolyticus (serovar O3:K6, strain RIMD 2210633)</td><td>316</td><td>93</td><td>21</td><td>129</td><td>21</td><td>1</td></tr><tr><td></td><td></td><td>Vibrio vulnificus (strain CMCP6)</td><td>265</td><td>82</td><td>13</td><td>90</td><td>12</td><td>0</td></tr><tr><td></td><td></td><td>Wigglesworthia glossinidia brevipalpis</td><td>4</td><td>1</td><td>0</td><td>6</td><td>1</td><td>0</td></tr><tr><td></td><td></td><td>Xanthomonas axonopodis citri (strain 306)</td><td>247</td><td>138</td><td>47</td><td>79</td><td>35</td><td>7</td></tr><tr><td></td><td></td><td>Xanthomonas campestris (strain ATCC 33913)</td><td>249</td><td>141</td><td>47</td><td>80</td><td>33</td><td>10</td></tr><tr><td></td><td></td><td>Xanthomonas oryzae (pathovar oryzae, MAFF 311018)</td><td>213</td><td>132</td><td>39</td><td>66</td><td>34</td><td>5</td></tr><tr><td></td><td></td><td>Xylella fastidiosa (strain 9a5c)</td><td>91</td><td>39</td><td>9</td><td>33</td><td>13</td><td>2</td></tr><tr><td></td><td></td><td>Xylella fastidiosa (strain Temecula1 / ATCC 700964)</td><td>80</td><td>38</td><td>10</td><td>29</td><td>16</td><td>5</td></tr><tr><td></td><td></td><td>Yersinia enterocolitica (serovar O:8 / strain 8081)</td><td>227</td><td>79</td><td>11</td><td>66</td><td>16</td><td>1</td></tr><tr><td></td><td></td><td>Yersinia pestis (biovar Antiqua Antiqua, strain Antiqua)</td><td>243</td><td>78</td><td>15</td><td>54</td><td>21</td><td>0</td></tr><tr><td></td><td></td><td>Yersinia pseudotuberculosis (serovar I, strain IP32953)</td><td>253</td><td>83</td><td>15</td><td>59</td><td>20</td><td>1</td></tr><tr><td></td><td></td><td>Alkalilimnicola ehrlichei (strain MLHE-1)</td><td>153</td><td>54</td><td>10</td><td>50</td><td>7</td><td>0</td></tr><tr><td></td><td></td><td>Carsonella ruddii (strain PV)</td><td>0</td><td>0</td><td>0</td><td>1</td><td>0</td><td>0</td></tr><tr><td></td><td></td><td>Mannheimia succinicirciproducens (strain MBEL55E)</td><td>95</td><td>24</td><td>6</td><td>55</td><td>3</td><td>2</td></tr><tr><td></td><td></td><td>Psychromonas ingrahamii (strain 37)</td><td>163</td><td>79</td><td>13</td><td>65</td><td>10</td><td>2</td></tr><tr><td></td><td></td><td>Ruthia magnifica magnifica (subsp. Calyptogena)</td><td>38</td><td>7</td><td>2</td><td>13</td><td>1</td><td>0</td></tr><tr><td></td><td></td><td>Thiomicrospira crunogena (strain XCL-2)</td><td>144</td><td>30</td><td>3</td><td>52</td><td>6</td><td>0</td></tr><tr><td></td><td></td><td>Acidothermus cellulolyticus (strain ATCC 43068 / 11B)</td><td>68</td><td>15</td><td>1</td><td>25</td><td>8</td><td>0</td></tr><tr><td></td><td></td><td>Arthrobacter aureiscens (strain TC1)</td><td>103</td><td>38</td><td>10</td><td>78</td><td>7</td><td>3</td></tr><tr><td></td><td></td><td>Clavibacter michiganensis (subsp. michiganensis, strain NCPPB 382)</td><td>95</td><td>33</td><td>3</td><td>63</td><td>3</td><td>0</td></tr><tr><td></td><td></td><td>Corynebacterium diphtheriae (biovar gravis, strain NCTC 13129 / ATCC 700971)</td><td>55</td><td>24</td><td>4</td><td>28</td><td>14</td><td>2</td></tr><tr><td></td><td></td><td>Corynebacterium efficiens (strain DSM 44549 / NBRC 100395 / JCM 11189 / YS-314 / AJ 12310)</td><td>73</td><td>24</td><td>2</td><td>34</td><td>2</td><td>0</td></tr><tr><td></td><td></td><td>Corynebacterium glutamicum (strain R)</td><td>72</td><td>19</td><td>1</td><td>72</td><td>9</td><td>0</td></tr><tr><td></td><td></td><td>Corynebacterium jeikeium (strain K411)</td><td>74</td><td>20</td><td>1</td><td>30</td><td>7</td><td>1</td></tr><tr><td></td><td></td><td>Frankia alni (strain ACN14a)</td><td>118</td><td>30</td><td>3</td><td>34</td><td>4</td><td>2</td></tr><tr><td></td><td></td><td>Kineococcus radiotolerans SRS30216</td><td>138</td><td>40</td><td>5</td><td>60</td><td>5</td><td>0</td></tr><tr><td></td><td></td><td>Leifsonia xyli xyli (strain CTCB07)</td><td>52</td><td>18</td><td>0</td><td>29</td><td>1</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium avium (strain 104)</td><td>135</td><td>47</td><td>11</td><td>51</td><td>14</td><td>1</td></tr><tr><td></td><td></td><td>Mycobacterium bovis (strain ATCC BAA-935)</td><td>102</td><td>25</td><td>13</td><td>43</td><td>16</td><td>3</td></tr><tr><td></td><td></td><td>Mycobacterium gilvum PYR-GCK</td><td>163</td><td>60</td><td>12</td><td>77</td><td>15</td><td>1</td></tr><tr><td></td><td></td><td>Mycobacterium leprae (strain TN)</td><td>40</td><td>23</td><td>5</td><td>12</td><td>9</td><td>0</td></tr><tr><td></td><td></td><td>Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)</td><td>116</td><td>50</td><td>17</td><td>43</td><td>15</td><td>3</td></tr><tr><td></td><td></td><td>Mycobacterium smegmatis (strain ATCC 700084 / mc(2 / mc(2)155)</td><td>187</td><td>54</td><td>11</td><td>116</td><td>17</td><td>6</td></tr><tr><td></td><td></td><td>Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)</td><td>102</td><td>30</td><td>13</td><td>45</td><td>16</td><td>3</td></tr><tr><td></td><td></td><td>Mycobacterium ulcerans (strain Agy99)</td><td>120</td><td>36</td><td>6</td><td>53</td><td>17</td><td>2</td></tr><tr><td></td><td></td><td>Mycobacterium vanbaalenii (strain DSM 7251 / PYR-1)</td><td>207</td><td>74</td><td>14</td><td>77</td><td>32</td><td>2</td></tr><tr><td></td><td></td><td>Nocardia farcinica (strain IFM 10152)</td><td>139</td><td>55</td><td>8</td><td>71</td><td>18</td><td>0</td></tr><tr><td></td><td></td><td>Nocardioides sp. (strain BAA-499 / JS614)</td><td>202</td><td>44</td><td>4</td><td>85</td><td>7</td><td>1</td></tr><tr><td></td><td></td><td>Renibacterium salmoninarum (strain ATCC 33209)</td><td>69</td><td>25</td><td>4</td><td>42</td><td>4</td><td>1</td></tr><tr><td></td><td></td><td>Rhodococcus sp. (strain RHA1)</td><td>176</td><td>64</td><td>13</td><td>116</td><td>37</td><td>0</td></tr><tr><td></td><td></td><td>Rubrobacter xylanophilus (strain DSM 9941 / NBRC 16129)</td><td>64</td><td>19</td><td>8</td><td>28</td><td>7</td><td>2</td></tr><tr><td></td><td></td><td>Saccharopolyspora erythraea (strain NRRL 23338)</td><td>204</td><td>66</td><td>12</td><td>69</td><td>10</td><td>2</td></tr><tr><td></td><td></td><td>Salinispora arenicola CNS-205</td><td>162</td><td>20</td><td>5</td><td>63</td><td>4</td><td>0</td></tr><tr><td></td><td></td><td>Salinispora tropica CNB-440</td><td>124</td><td>23</td><td>6</td><td>56</td><td>3</td><td>0</td></tr><tr><td></td><td></td><td>Streptomyces avermitilis (strain DSM 46492 / NRRL 8165 / NCIMB 12804 / ATCC 31267 / JCM 5070)</td><td>296</td><td>91</td><td>14</td><td>88</td><td>21</td><td>3</td></tr><tr><td></td><td></td><td>Streptomyces coelicolor (strain ATCC BAA-471 / M145 / A3(2))</td><td>326</td><td>84</td><td>14</td><td>116</td><td>26</td><td>3</td></tr><tr><td></td><td></td><td>Thermobifida fusca (strain YX)</td><td>75</td><td>30</td><td>4</td><td>39</td><td>11</td><td>2</td></tr><tr><td></td><td></td><td>Tropheryma whipplei (strain Twist)</td><td>13</td><td>7</td><td>2</td><td>7</td><td>1</td><td>0</td></tr><tr><td></td><td></td><td>Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083)</td><td>23</td><td>13</td><td>5</td><td>13</td><td>4</td><td>1</td></tr><tr><td></td><td></td><td>Bifidobacterium longum (strain NCC 2705)</td><td>16</td><td>12</td><td>6</td><td>18</td><td>4</td><td>4</td></tr><tr><td></td><td></td><td>Propionibacterium acnes (strain DSM 16379 / KPA171202)</td><td>46</td><td>20</td><td>5</td><td>36</td><td>11</td><td>3</td></tr></tbody></table>
<table><caption>Supplemental Table1B Daniels *et al.* 2009</caption><tbody><tr><td></td><td>Streptococcus agalactiae la (serovar la, strain A909 / CDC SS700 / ATCC 27591)</td><td>59</td><td>18</td><td>3</td><td>21</td><td>8</td><td>2</td></tr><tr><td></td><td>Streptococcus agalactiae III (serovar III, strain NEM316)</td><td>59</td><td>21</td><td>2</td><td>22</td><td>6</td><td>2</td></tr><tr><td></td><td>Streptococcus agalactiae V (serovar V, strain 2603 V/R / ATCC BAA-611)</td><td>55</td><td>18</td><td>2</td><td>18</td><td>9</td><td>1</td></tr><tr><td></td><td>Streptococcus gordonii (strain Challis / ATCC 35105 / CH1 / DL1 / V288)</td><td>55</td><td>12</td><td>0</td><td>41</td><td>12</td><td>2</td></tr><tr><td></td><td>Streptococcus mutans (serovar c, strain ATCC 700610 / UA159)</td><td>44</td><td>12</td><td>3</td><td>22</td><td>2</td><td>0</td></tr><tr><td></td><td>Streptococcus pneumoniae (serovar 2, strain D39 / NCTC 7466)</td><td>32</td><td>5</td><td>1</td><td>22</td><td>7</td><td>1</td></tr><tr><td></td><td>Streptococcus pneumoniae (strain ATCC BAA-255 / R6)</td><td>35</td><td>5</td><td>1</td><td>21</td><td>7</td><td>1</td></tr><tr><td></td><td>Streptococcus pneumoniae (strain TIGR4 / ATCC BAA-334)</td><td>36</td><td>4</td><td>2</td><td>23</td><td>7</td><td>1</td></tr><tr><td></td><td>Streptococcus pyogenes M1 (serovar M1, strain MGAS5005 / ATCC BAA-947)</td><td>49</td><td>16</td><td>3</td><td>20</td><td>6</td><td>0</td></tr><tr><td></td><td>Streptococcus sanguinis (strain SK36)</td><td>66</td><td>11</td><td>0</td><td>39</td><td>7</td><td>2</td></tr><tr><td></td><td>Streptococcus suis (strain 05ZYH33)</td><td>39</td><td>10</td><td>2</td><td>26</td><td>5</td><td>2</td></tr><tr><td></td><td>Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9)</td><td>40</td><td>2</td><td>1</td><td>14</td><td>4</td><td>1</td></tr><tr><td></td><td>Symbiobacterium thermophilum (strain IAM 14863 / T)</td><td>89</td><td>73</td><td>12</td><td>0</td><td>0</td><td>0</td></tr><tr><td></td><td>Ureaplasma parvum (serovar 3, strain ATCC 700970)</td><td>20</td><td>6</td><td>3</td><td>20</td><td>1</td><td>1</td></tr><tr><td></td><td>Alkaliphilus metalliredigens (strain QYMF)</td><td>103</td><td>121</td><td>19</td><td>0</td><td>0</td><td>0</td></tr><tr><td></td><td>Alkaliphilus oremlandii (strain OhILAs)</td><td>83</td><td>72</td><td>16</td><td>17</td><td>2</td><td>0</td></tr><tr><td></td><td>Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903)</td><td>109</td><td>39</td><td>2</td><td>17</td><td>6</td><td>0</td></tr><tr><td></td><td>Carboxydothermus hydrogenoformans (strain Z-2901 / DSM 6008)</td><td>76</td><td>31</td><td>2</td><td>0</td><td>0</td><td>0</td></tr><tr><td></td><td>Clostridium acetobutylicum (strain DSM 792 / JCM 1419 / LMG 5710 / ATCC 824 / VKM B-1787)</td><td>117</td><td>39</td><td>9</td><td>61</td><td>19</td><td>4</td></tr><tr><td></td><td>Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)</td><td>120</td><td>47</td><td>5</td><td>65</td><td>22</td><td>1</td></tr><tr><td></td><td>Clostridium botulinum (strain ATCC 19397 / Type A)</td><td>77</td><td>64</td><td>17</td><td>0</td><td>0</td><td>0</td></tr><tr><td></td><td>Clostridium difficile (strain 630)</td><td>66</td><td>53</td><td>19</td><td>1</td><td>0</td><td>0</td></tr><tr><td></td><td>Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NCIMB 10680)</td><td>80</td><td>28</td><td>8</td><td>39</td><td>11</td><td>5</td></tr><tr><td></td><td>Clostridium novyi (strain NT)</td><td>51</td><td>18</td><td>3</td><td>27</td><td>19</td><td>7</td></tr><tr><td></td><td>Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)</td><td>77</td><td>63</td><td>11</td><td>11</td><td>1</td><td>1</td></tr><tr><td></td><td>Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)</td><td>83</td><td>41</td><td>14</td><td>108</td><td>42</td><td>20</td></tr><tr><td></td><td>Clostridium tetani (strain Massachusetts / E88)</td><td>62</td><td>30</td><td>4</td><td>49</td><td>13</td><td>2</td></tr><tr><td></td><td>Clostridium thermocellum (strain ATCC 27405 / DSM 1237)</td><td>113</td><td>71</td><td>13</td><td>55</td><td>18</td><td>3</td></tr><tr><td></td><td>Desulfotomaculum reducens (strain MI-1)</td><td>92</td><td>38</td><td>4</td><td>44</td><td>6</td><td>3</td></tr><tr><td></td><td>Moorella thermoacetica (strain ATCC 39073)</td><td>78</td><td>15</td><td>2</td><td>25</td><td>3</td><td>0</td></tr><tr><td></td><td>Mycoplasma mycoides SC (subsp. mycoides, strain PG1)</td><td>18</td><td>6</td><td>0</td><td>26</td><td>1</td><td>0</td></tr><tr><td></td><td>Mycoplasma penetrans (strain HF-2)</td><td>24</td><td>7</td><td>0</td><td>17</td><td>0</td><td>0</td></tr></tbody></table>
<table><caption>Transmembrane protein loops (cytoplasmic and extra-cytoplasmic)</caption><thead><tr><th rowspan="2"></th><th rowspan="2">Species</th><th colspan="4">Number of extra-cytoplasmic TM-protein loops</th><th colspan="4">Number of cytoplasmic TM-protein loops</th></tr><tr><th>0 Cys</th><th>1 Cys</th><th>2 Cys</th><th>3 Cys</th><th>0 Cys</th><th>1 Cys</th><th>2 Cys</th><th>3 Cys</th></tr></thead><tbody><tr><td rowspan="10">Gram-negative Bacteria</td><td>Acidiphilium cryptum (strain JF-5)</td><td>526</td><td>69</td><td>38</td><td>17</td><td>413</td><td>117</td><td>59</td><td>31</td></tr><tr><td>Agrobacterium tumefaciens (strain C58 / ATCC 33970)</td><td>840</td><td>59</td><td>70</td><td>9</td><td>719</td><td>160</td><td>62</td><td>19</td></tr><tr><td>Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571)</td><td>806</td><td>87</td><td>80</td><td>15</td><td>601</td><td>220</td><td>90</td><td>61</td></tr><tr><td>Bartonella bacilliformis (strain ATCC 35685 / KC583)</td><td>154</td><td>21</td><td>8</td><td>2</td><td>106</td><td>57</td><td>18</td><td>3</td></tr><tr><td>Bartonella henselae (strain Houston 1 / ATCC 49882)</td><td>189</td><td>34</td><td>17</td><td>5</td><td>140</td><td>59</td><td>27</td><td>14</td></tr><tr><td>Bartonella quintana (strain Toulouse)</td><td>174</td><td>32</td><td>16</td><td>3</td><td>115</td><td>66</td><td>34</td><td>11</td></tr><tr><td>Bartonella tribocorum CIP 105476</td><td>238</td><td>36</td><td>17</td><td>3</td><td>174</td><td>71</td><td>28</td><td>13</td></tr><tr><td>Bradyrhizobium japonicum (strain USDA 110)</td><td>1211</td><td>144</td><td>126</td><td>29</td><td>916</td><td>311</td><td>154</td><td>83</td></tr><tr><td>Brucella abortus (strain 2308)</td><td>450</td><td>43</td><td>24</td><td>6</td><td>358</td><td>109</td><td>37</td><td>12</td></tr><tr><td>Brucella canis ATCC 23365</td><td>493</td><td>42</td><td>25</td><td>8</td><td>382</td><td>115</td><td>38</td><td>18</td></tr><tr><td>Brucella melitensis (biovar 1, strain NCTC 10094 / ATCC 23456 / 16M)</td><td>488</td><td>48</td><td>30</td><td>10</td><td>373</td><td>123</td><td>44</td><td>17</td></tr><tr><td rowspan="10">Alpha proteobacteria</td><td>Brucella suis ATCC 23445</td><td>492</td><td>46</td><td>24</td><td>8</td><td>377</td><td>115</td><td>40</td><td>21</td></tr><tr><td>Caulobacter crescentus (strain CB15 / ATCC 19089)</td><td>551</td><td>69</td><td>49</td><td>10</td><td>465</td><td>118</td><td>55</td><td>29</td></tr><tr><td>Dinoroseobacter shibae DFL 12</td><td>609</td><td>34</td><td>55</td><td>10</td><td>502</td><td>131</td><td>40</td><td>18</td></tr><tr><td>Ehrlichia canis (strain Jake)</td><td>128</td><td>37</td><td>13</td><td>6</td><td>61</td><td>35</td><td>42</td><td>18</td></tr><tr><td>Ehrlichia chaffeensis (strain Arkansas)</td><td>114</td><td>29</td><td>20</td><td>5</td><td>64</td><td>36</td><td>33</td><td>12</td></tr><tr><td>Ehrlichia ruminantium (strain Gardel)</td><td>145</td><td>37</td><td>27</td><td>9</td><td>77</td><td>50</td><td>37</td><td>23</td></tr><tr><td>Erythrobacter litoralis (strain HTCC2594)</td><td>442</td><td>26</td><td>34</td><td>5</td><td>369</td><td>69</td><td>37</td><td>21</td></tr><tr><td>Gluconacetobacter diazotrophicus PAI 5</td><td>472</td><td>91</td><td>34</td><td>16</td><td>334</td><td>159</td><td>66</td><td>31</td></tr><tr><td>Gluconobacter oxydans (strain 621H)</td><td>334</td><td>68</td><td>32</td><td>15</td><td>254</td><td>104</td><td>47</td><td>33</td></tr><tr><td>Granulobacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1)</td><td>353</td><td>64</td><td>36</td><td>7</td><td>241</td><td>105</td><td>68</td><td>31</td></tr><tr><td>Hyphomonas neptunium (strain ATCC 15444)</td><td>526</td><td>36</td><td>49</td><td>11</td><td>440</td><td>111</td><td>49</td><td>15</td></tr><tr><td>Jannaschia sp. (strain CCS1)</td><td>719</td><td>51</td><td>69</td><td>10</td><td>630</td><td>134</td><td>48</td><td>18</td></tr><tr><td>Magnetospirillum magneticum (strain AMB-1 / ATCC 700264)</td><td>620</td><td>79</td><td>65</td><td>19</td><td>442</td><td>142</td><td>99</td><td>62</td></tr><tr><td>Maricaulis maris (strain MCS10)</td><td>567</td><td>27</td><td>46</td><td>3</td><td>475</td><td>96</td><td>43</td><td>15</td></tr><tr><td>Mesorhizobium sp. (strain BNC1)</td><td>678</td><td>52</td><td>46</td><td>8</td><td>577</td><td>121</td><td>41</td><td>29</td></tr><tr><td>Methylobacterium extorquens PA1</td><td>713</td><td>71</td><td>62</td><td>13</td><td>594</td><td>147</td><td>82</td><td>25</td></tr><tr><td>Neorickettsia sennetsu (strain Miyayama)</td><td>102</td><td>30</td><td>17</td><td>3</td><td>54</td><td>30</td><td>37</td><td>13</td></tr><tr><td>Nitrobacter hamburgensis (strain X14 / DSM 10229)</td><td>587</td><td>61</td><td>41</td><td>16</td><td>450</td><td>144</td><td>58</td><td>33</td></tr><tr><td>Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391)</td><td>406</td><td>26</td><td>39</td><td>6</td><td>318</td><td>102</td><td>32</td><td>16</td></tr><tr><td>Novosphingobium aromaticivorans (strain DSM 12444)</td><td>479</td><td>44</td><td>40</td><td>8</td><td>382</td><td>105</td><td>45</td><td>17</td></tr><tr><td>Orientia tsutsugamushi (strain Boryong)</td><td>101</td><td>41</td><td>20</td><td>3</td><td>67</td><td>56</td><td>23</td><td>17</td></tr><tr><td>Paracoccus denitrificans (strain Pd 1222)</td><td>730</td><td>60</td><td>60</td><td>11</td><td>596</td><td>149</td><td>68</td><td>18</td></tr><tr><td>Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)</td><td>537</td><td>51</td><td>48</td><td>3</td><td>453</td><td>109</td><td>35</td><td>23</td></tr><tr><td>Pelagibacter ubique (strain HTCC1062)</td><td>207</td><td>16</td><td>18</td><td>6</td><td>186</td><td>38</td><td>14</td><td>6</td></tr><tr><td>Rhizobium etli (strain CFN 42 / ATCC 51251)</td><td>887</td><td>97</td><td>80</td><td>18</td><td>737</td><td>205</td><td>90</td><td>36</td></tr><tr><td>Rhizobium leguminosarum bv. viciae (strain 3841)</td><td>1044</td><td>108</td><td>87</td><td>18</td><td>897</td><td>199</td><td>99</td><td>36</td></tr><tr><td>Rhizobium loti (strain MAFF303099)</td><td>1012</td><td>97</td><td>94</td><td>17</td><td>809</td><td>205</td><td>121</td><td>47</td></tr><tr><td>Rhizobium meliloti (strain 1021)</td><td>949</td><td>69</td><td>57</td><td>13</td><td>757</td><td>203</td><td>60</td><td>34</td></tr><tr><td>Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)</td><td>650</td><td>46</td><td>56</td><td>5</td><td>540</td><td>124</td><td>45</td><td>20</td></tr><tr><td>Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)</td><td>758</td><td>88</td><td>64</td><td>10</td><td>608</td><td>165</td><td>90</td><td>27</td></tr><tr><td>Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255)</td><td>634</td><td>67</td><td>47</td><td>15</td><td>496</td><td>133</td><td>68</td><td>35</td></tr><tr><td>Roseobacter denitrificans (strain OCh 114 / ATCC 33942)</td><td>665</td><td>45</td><td>49</td><td>8</td><td>507</td><td>160</td><td>53</td><td>23</td></tr><tr><td>Silicibacter pomeroyi (strain ATCC 700808 / DSS-3 / DSM 15171)</td><td>647</td><td>52</td><td>66</td><td>19</td><td>532</td><td>148</td><td>63</td><td>19</td></tr><tr><td>Silicibacter sp. (strain TM1040)</td><td>565</td><td>49</td><td>38</td><td>14</td><td>452</td><td>120</td><td>47</td><td>24</td></tr><tr><td>Sinorhizobium medicae (strain WSM419)</td><td>935</td><td>77</td><td>70</td><td>11</td><td>777</td><td>204</td><td>65</td><td>31</td></tr><tr><td>Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)</td><td>640</td><td>59</td><td>67</td><td>17</td><td>514</td><td>146</td><td>83</td><td>33</td></tr><tr><td>Sphingopyxis alaskensis</td><td>463</td><td>50</td><td>41</td><td>11</td><td>395</td><td>78</td><td>49</td><td>23</td></tr><tr><td>Wolbachia pipientis wMel</td><td>153</td><td>31</td><td>9</td><td>6</td><td>79</td><td>47</td><td>37</td><td>13</td></tr><tr><td>Wolbachia sp. (subsp. Brugia malayi, strain TRS)</td><td>110</td><td>25</td><td>12</td><td>3</td><td>64</td><td>36</td><td>26</td><td>8</td></tr><tr><td>Xanthobacter sp.</td><td>705</td><td>76</td><td>54</td><td>9</td><td>569</td><td>146</td><td>78</td><td>25</td></tr><tr><td>Zymomonas mobilis (strain CP4 / ZM4 / ATCC 31821)</td><td>236</td><td>38</td><td>26</td><td>2</td><td>174</td><td>71</td><td>30</td><td>12</td></tr></tbody></table>
<table><caption>Supplemental Table1C Daniels *et al.* 2009</caption><thead><tr><th>Firmicutes</th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td rowspan="24">Aerobic</td><td>Acholeplasma laidlawii (strain PG-8A)</td><td>293</td><td>12</td><td>1</td><td>0</td><td>257</td><td>32</td><td>6</td><td>5</td></tr><tr><td>Bacillus amyloliquefaciens (strain FZB42)</td><td>656</td><td>50</td><td>17</td><td>3</td><td>506</td><td>139</td><td>39</td><td>27</td></tr><tr><td>Bacillus anthracis (strain Ames, isolate Porton)</td><td>939</td><td>59</td><td>23</td><td>6</td><td>742</td><td>181</td><td>54</td><td>27</td></tr><tr><td>Bacillus cereus (strain ATCC 10987)</td><td>984</td><td>67</td><td>32</td><td>8</td><td>760</td><td>201</td><td>70</td><td>32</td></tr><tr><td>Bacillus clausii (strain KSM-K16)</td><td>752</td><td>44</td><td>24</td><td>4</td><td>595</td><td>144</td><td>42</td><td>22</td></tr><tr><td>Bacillus halodurans (strain C-125 / ATCC BAA-125 / JCM 9153 / FERM 7344 / DSM 18197)</td><td>726</td><td>40</td><td>16</td><td>2</td><td>585</td><td>127</td><td>39</td><td>15</td></tr><tr><td>Bacillus licheniformis (strain DSM 13 / ATCC 14580, sub_strain Goettingen)</td><td>767</td><td>46</td><td>24</td><td>9</td><td>591</td><td>155</td><td>48</td><td>24</td></tr><tr><td>Bacillus pumilus (strain SAFR-032)</td><td>656</td><td>40</td><td>12</td><td>6</td><td>516</td><td>118</td><td>39</td><td>21</td></tr><tr><td>Bacillus subtilis (strain 168)</td><td>730</td><td>59</td><td>22</td><td>5</td><td>574</td><td>142</td><td>51</td><td>27</td></tr><tr><td>Bacillus thuringiensis (strain Al Hakam)</td><td>863</td><td>74</td><td>24</td><td>3</td><td>615</td><td>211</td><td>83</td><td>29</td></tr><tr><td>Bacillus weihenstephanensis KBAB4</td><td>931</td><td>65</td><td>26</td><td>3</td><td>715</td><td>185</td><td>60</td><td>31</td></tr><tr><td>Desulfitobacterium hafniense (strain Y51)</td><td>785</td><td>119</td><td>39</td><td>20</td><td>580</td><td>191</td><td>99</td><td>49</td></tr><tr><td>Enterococcus faecalis (strain V583 / ATCC 700802)</td><td>563</td><td>41</td><td>11</td><td>3</td><td>452</td><td>113</td><td>28</td><td>17</td></tr><tr><td>Geobacillus kaustophilus (strain HTA426)</td><td>546</td><td>48</td><td>25</td><td>7</td><td>443</td><td>111</td><td>43</td><td>21</td></tr><tr><td>Geobacillus thermodenitrificans (strain NG80-2)</td><td>610</td><td>65</td><td>21</td><td>6</td><td>480</td><td>126</td><td>58</td><td>18</td></tr><tr><td>Lactobacillus acidophilus (strain NCFM)</td><td>329</td><td>40</td><td>13</td><td>0</td><td>279</td><td>72</td><td>20</td><td>6</td></tr><tr><td>Lactobacillus brevis (strain ATCC 367 / JCM 1170)</td><td>424</td><td>24</td><td>2</td><td>0</td><td>373</td><td>56</td><td>10</td><td>3</td></tr><tr><td>Lactobacillus casei (strain ATCC 334)</td><td>527</td><td>36</td><td>5</td><td>3</td><td>480</td><td>56</td><td>24</td><td>6</td></tr><tr><td>Lactobacillus delbrueckii (subsp. bulgaricus, strain ATCC BAA-365)</td><td>259</td><td>36</td><td>4</td><td>2</td><td>212</td><td>61</td><td>19</td><td>6</td></tr><tr><td>Lactobacillus gasseri (strain ATCC 33323 / DSM 20243)</td><td>317</td><td>43</td><td>10</td><td>0</td><td>272</td><td>63</td><td>19</td><td>7</td></tr><tr><td>Lactobacillus helveticus (strain DPC 4571)</td><td>253</td><td>29</td><td>2</td><td>0</td><td>222</td><td>41</td><td>14</td><td>2</td></tr><tr><td>Lactobacillus johnsonii (strain NCC 533)</td><td>368</td><td>44</td><td>6</td><td>4</td><td>316</td><td>69</td><td>22</td><td>8</td></tr><tr><td>Lactobacillus plantarum (strain WCFS1 / ATCC BAA-793 / NCIMB 8826)</td><td>574</td><td>46</td><td>8</td><td>3</td><td>481</td><td>99</td><td>31</td><td>9</td></tr><tr><td>Lactobacillus reuteri (strain ATCC 23272 / DSM 20016 / F275)</td><td>308</td><td>23</td><td>5</td><td>5</td><td>267</td><td>50</td><td>14</td><td>4</td></tr><tr><td>Lactobacillus sakei (subsp. sakei, strain 23K)</td><td>25</td><td>5</td><td>0</td><td>0</td><td>28</td><td>2</td><td>0</td><td>0</td></tr><tr><td>Lactobacillus salivarius (subsp. salivarius, strain UCC118)</td><td>337</td><td>30</td><td>3</td><td>1</td><td>283</td><td>55</td><td>17</td><td>3</td></tr><tr><td>Lactococcus lactis (subsp. lactis, strain IL1403)</td><td>409</td><td>27</td><td>1</td><td>2</td><td>346</td><td>58</td><td>23</td><td>8</td></tr><tr><td>Leuconostoc mesenteroides (subsp. mesenteroides, strain ATCC 8293 / NCDO 523)</td><td>390</td><td>13</td><td>7</td><td>2</td><td>373</td><td>26</td><td>11</td><td>2</td></tr><tr><td>Listeria innocua (serovar 6a, strain CLIP 11262)</td><td>514</td><td>39</td><td>11</td><td>0</td><td>451</td><td>72</td><td>25</td><td>10</td></tr><tr><td>Listeria monocytogenes (serovar 1/2a, strain EGD-e / ATCC BAA-679)</td><td>511</td><td>42</td><td>12</td><td>0</td><td>451</td><td>74</td><td>29</td><td>8</td></tr><tr><td>Listeria welshimeri (serovar 6b, strain ATCC 35897 / DSM 20650 / SLCC5334)</td><td>508</td><td>42</td><td>8</td><td>1</td><td>447</td><td>68</td><td>28</td><td>8</td></tr><tr><td>Mesoplasma florum (strain ATCC 33453 / NCTC 11704 / L1 / NBRC 100688)</td><td>122</td><td>15</td><td>3</td><td>0</td><td>95</td><td>25</td><td>6</td><td>10</td></tr><tr><td>Mycoplasma agalactiae</td><td>107</td><td>21</td><td>3</td><td>0</td><td>94</td><td>22</td><td>10</td><td>3</td></tr><tr><td>Mycoplasma capricolum (subsp. capricolum, strain California kid / ATCC 27343 / NCTC 10154)</td><td>138</td><td>13</td><td>4</td><td>1</td><td>99</td><td>34</td><td>10</td><td>4</td></tr><tr><td>Mycoplasma gallisepticum (strain R(low))</td><td>125</td><td>12</td><td>2</td><td>1</td><td>93</td><td>28</td><td>9</td><td>6</td></tr><tr><td>Mycoplasma genitalium (strain ATCC 33530 / NCTC 10195 / G-37)</td><td>74</td><td>8</td><td>3</td><td>1</td><td>48</td><td>25</td><td>6</td><td>5</td></tr><tr><td>Mycoplasma hyopneumoniae (strain J / ATCC 25934 / NCTC 10110)</td><td>110</td><td>11</td><td>4</td><td>1</td><td>97</td><td>17</td><td>9</td><td>3</td></tr><tr><td>Mycoplasma mobile (strain 163K / NCTC 11711 / ATCC 43663)</td><td>113</td><td>3</td><td>1</td><td>1</td><td>95</td><td>16</td><td>6</td><td>1</td></tr><tr><td>Mycoplasma pneumoniae (strain M129 / ATCC 29342)</td><td>97</td><td>13</td><td>2</td><td>2</td><td>63</td><td>30</td><td>11</td><td>7</td></tr><tr><td>Mycoplasma pulmonis (strain UAB CTIP)</td><td>138</td><td>9</td><td>1</td><td>1</td><td>115</td><td>26</td><td>4</td><td>3</td></tr><tr><td>Mycoplasma synoviae (strain 53)</td><td>106</td><td>5</td><td>3</td><td>0</td><td>90</td><td>18</td><td>5</td><td>0</td></tr><tr><td>Oceanobacillus iheyensis (strain KCTC 3954 / DSM 14371 / JCM 11309 / HTE831)</td><td>690</td><td>29</td><td>15</td><td>3</td><td>592</td><td>94</td><td>29</td><td>12</td></tr><tr><td>Oenococcus oeni (strain BAA-331 / PSU-1)</td><td>317</td><td>20</td><td>4</td><td>1</td><td>290</td><td>38</td><td>9</td><td>3</td></tr><tr><td>Onion yellows phytoplasma (strain OY-M)</td><td>45</td><td>35</td><td>10</td><td>5</td><td>55</td><td>27</td><td>7</td><td>6</td></tr><tr><td>Pediococcus pentosaceus (strain ATCC25745 / 183-1w)</td><td>319</td><td>17</td><td>4</td><td>0</td><td>282</td><td>40</td><td>10</td><td>1</td></tr><tr><td>Pelotomaculum thermopropionicum (strain DSM 13744 / JCM 10971 / SI)</td><td>310</td><td>67</td><td>22</td><td>8</td><td>224</td><td>97</td><td>44</td><td>20</td></tr><tr><td>Staphylococcus aureus (strain Mu50 / ATCC 700699)</td><td>479</td><td>32</td><td>11</td><td>3</td><td>405</td><td>78</td><td>22</td><td>13</td></tr><tr><td>Staphylococcus epidermidis (strain ATCC 12228)</td><td>424</td><td>38</td><td>5</td><td>2</td><td>351</td><td>81</td><td>22</td><td>3</td></tr><tr><td>Staphylococcus haemolyticus (strain JCSC1435)</td><td>465</td><td>24</td><td>3</td><td>1</td><td>380</td><td>72</td><td>27</td><td>5</td></tr><tr><td>Staphylococcus saprophyticus (subsp. saprophyticus, strain ATCC 15305 / DSM 20229)</td><td>433</td><td>18</td><td>4</td><td>1</td><td>362</td><td>62</td><td>19</td><td>4</td></tr></tbody></table>
<table><caption>Supplemental Table1C Daniels *et al.* 2009</caption><thead><tr><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td rowspan="18">Anaerobic</td><td>Streptococcus agalactiae la (serovar la, strain A909 / CDC SS700 / ATCC 27591)</td><td>378</td><td>34</td><td>4</td><td>4</td><td>314</td><td>71</td><td>17</td><td>8</td></tr><tr><td>Streptococcus agalactiae III (serovar III, strain NEM316)</td><td>396</td><td>30</td><td>4</td><td>5</td><td>327</td><td>79</td><td>21</td><td>5</td></tr><tr><td>Streptococcus agalactiae V (serovar V, strain 2603 V/R / ATCC BAA-611)</td><td>369</td><td>27</td><td>6</td><td>7</td><td>303</td><td>73</td><td>17</td><td>8</td></tr><tr><td>Streptococcus gordonii (strain Challis / ATCC 35105 / CH1 / DL1 / V288)</td><td>421</td><td>22</td><td>7</td><td>1</td><td>326</td><td>87</td><td>18</td><td>11</td></tr><tr><td>Streptococcus mutans (serovar c, strain ATCC 700610 / UA159)</td><td>355</td><td>23</td><td>6</td><td>3</td><td>286</td><td>78</td><td>14</td><td>4</td></tr><tr><td>Streptococcus pneumoniae (serovar 2, strain D39 / NCTC 7466)</td><td>357</td><td>30</td><td>4</td><td>3</td><td>300</td><td>62</td><td>21</td><td>8</td></tr><tr><td>Streptococcus pneumoniae (strain ATCC BAA-255 / R6)</td><td>353</td><td>35</td><td>5</td><td>4</td><td>294</td><td>65</td><td>26</td><td>7</td></tr><tr><td>Streptococcus pneumoniae (strain TIGR4 / ATCC BAA-334)</td><td>343</td><td>31</td><td>4</td><td>5</td><td>282</td><td>61</td><td>30</td><td>6</td></tr><tr><td>Streptococcus pyogenes M1 (serovar M1, strain MGAS5005 / ATCC BAA-947)</td><td>295</td><td>27</td><td>8</td><td>3</td><td>241</td><td>59</td><td>19</td><td>6</td></tr><tr><td>Streptococcus sanguinis (strain SK36)</td><td>459</td><td>29</td><td>7</td><td>2</td><td>377</td><td>76</td><td>27</td><td>9</td></tr><tr><td>Streptococcus suis (strain 05ZYH33)</td><td>376</td><td>41</td><td>7</td><td>4</td><td>308</td><td>81</td><td>25</td><td>13</td></tr><tr><td>Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9)</td><td>277</td><td>22</td><td>7</td><td>0</td><td>238</td><td>38</td><td>14</td><td>8</td></tr><tr><td>Symbiobacterium thermophilum (strain IAM 14863 / T)</td><td>577</td><td>62</td><td>24</td><td>11</td><td>484</td><td>108</td><td>46</td><td>20</td></tr><tr><td>Ureaplasma parvum (serovar 3, strain ATCC 700970)</td><td>94</td><td>9</td><td>5</td><td>1</td><td>76</td><td>20</td><td>8</td><td>3</td></tr><tr><td>Alkaliphilus metalliredigens (strain QYMF)</td><td>775</td><td>68</td><td>11</td><td>9</td><td>569</td><td>166</td><td>62</td><td>27</td></tr><tr><td>Alkaliphilus oremlandii (strain OhILAs)</td><td>518</td><td>54</td><td>15</td><td>6</td><td>390</td><td>111</td><td>44</td><td>30</td></tr><tr><td>Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903)</td><td>343</td><td>70</td><td>14</td><td>10</td><td>262</td><td>91</td><td>42</td><td>14</td></tr><tr><td>Carboxydothermus hydrogenoformans (strain Z-2901 / DSM 6008)</td><td>353</td><td>32</td><td>17</td><td>5</td><td>314</td><td>53</td><td>17</td><td>10</td></tr><tr><td>Clostridium acetobutylicum (strain DSM 792 / JCM 1419 / LMG 5710 / ATCC 824 / VKM B-1787)</td><td>527</td><td>111</td><td>39</td><td>28</td><td>399</td><td>175</td><td>68</td><td>35</td></tr><tr><td>Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)</td><td>683</td><td>135</td><td>42</td><td>11</td><td>491</td><td>208</td><td>75</td><td>47</td></tr><tr><td>Clostridium botulinum (strain ATCC 19397 / Type A)</td><td>512</td><td>88</td><td>33</td><td>12</td><td>336</td><td>181</td><td>66</td><td>33</td></tr><tr><td>Clostridium difficile (strain 630)</td><td>516</td><td>122</td><td>31</td><td>13</td><td>343</td><td>179</td><td>75</td><td>36</td></tr><tr><td>Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NCIMB 10680)</td><td>475</td><td>116</td><td>30</td><td>17</td><td>350</td><td>151</td><td>51</td><td>36</td></tr><tr><td>Clostridium novyi (strain NT)</td><td>305</td><td>77</td><td>23</td><td>15</td><td>206</td><td>103</td><td>58</td><td>27</td></tr><tr><td>Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)</td><td>501</td><td>72</td><td>38</td><td>14</td><td>351</td><td>158</td><td>56</td><td>30</td></tr><tr><td>Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)</td><td>580</td><td>141</td><td>46</td><td>31</td><td>393</td><td>204</td><td>83</td><td>53</td></tr><tr><td>Clostridium tetani (strain Massachusetts / E88)</td><td>368</td><td>89</td><td>35</td><td>16</td><td>277</td><td>141</td><td>52</td><td>19</td></tr><tr><td>Clostridium thermocellum (strain ATCC 27405 / DSM 1237)</td><td>380</td><td>97</td><td>39</td><td>19</td><td>280</td><td>113</td><td>63</td><td>34</td></tr><tr><td>Desulfotomaculum reducens (strain MI-1)</td><td>463</td><td>68</td><td>18</td><td>10</td><td>325</td><td>121</td><td>53</td><td>22</td></tr><tr><td>Moorella thermoacetica (strain ATCC 39073)</td><td>383</td><td>51</td><td>13</td><td>4</td><td>287</td><td>90</td><td>32</td><td>16</td></tr><tr><td>Mycoplasma mycoides SC (subsp. mycoides, strain PG1)</td><td>143</td><td>19</td><td>3</td><td>1</td><td>110</td><td>32</td><td>10</td><td>7</td></tr><tr><td>Mycoplasma penetrans (strain HF-2)</td><td>138</td><td>40</td><td>12</td><td>2</td><td>113</td><td>42</td><td>20</td><td>7</td></tr></tbody></table>
<table><caption>**Cytoplasmic proteins**</caption><thead><tr><th rowspan="2"></th><th rowspan="2">Species</th><th rowspan="2">Trend</th><th colspan="4">Number of cytoplasmic proteins</th></tr><tr><th>0 Cys</th><th>1 Cys</th><th>2 Cys</th><th>3 Cys</th></tr></thead><tbody><tr><td rowspan="10">Gram-negative Bacteria</td><td>Acidiphilium cryptum (strain JF-5)</td><td>Semi-normal</td><td>277</td><td>342</td><td>347</td><td>297</td></tr><tr><td>Agrobacterium tumefaciens (strain C58 / ATCC 33970)</td><td>Semi-normal</td><td>476</td><td>577</td><td>551</td><td>416</td></tr><tr><td>Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571)</td><td>Semi-normal</td><td>393</td><td>460</td><td>467</td><td>375</td></tr><tr><td>Bartonella bacilliformis (strain ATCC 35685 / KC583)</td><td>Semi-normal</td><td>89</td><td>109</td><td>101</td><td>92</td></tr><tr><td>Bartonella henselae (strain Houston 1 / ATCC 49882)</td><td>Semi-normal</td><td>95</td><td>126</td><td>113</td><td>117</td></tr><tr><td>Bartonella quintana (strain Toulouse)</td><td>Semi-normal</td><td>61</td><td>101</td><td>92</td><td>97</td></tr><tr><td>Bartonella tribocorum CIP 105476</td><td>Semi-normal</td><td>112</td><td>154</td><td>121</td><td>139</td></tr><tr><td>Bradyrhizobium japonicum (strain USDA 110)</td><td>Semi-normal</td><td>580</td><td>710</td><td>778</td><td>572</td></tr><tr><td>Brucella abortus (strain 2308)</td><td>Semi-normal</td><td>268</td><td>335</td><td>297</td><td>254</td></tr><tr><td>Brucella canis ATCC 23365</td><td>Semi-normal</td><td>259</td><td>338</td><td>312</td><td>258</td></tr><tr><td rowspan="10">Alpha proteobacteria</td><td>Brucella melitensis (biovar 1, strain NCTC 10094 / ATCC 23456 / 16M)</td><td>Semi-normal</td><td>323</td><td>357</td><td>345</td><td>277</td></tr><tr><td>Brucella suis ATCC 23445</td><td>Semi-normal</td><td>268</td><td>329</td><td>312</td><td>255</td></tr><tr><td>Caulobacter crescentus (strain CB15 / ATCC 19089)</td><td>Semi-normal</td><td>359</td><td>440</td><td>378</td><td>279</td></tr><tr><td>Dinoroseobacter shibae DFL 12</td><td>Semi-normal</td><td>280</td><td>336</td><td>331</td><td>307</td></tr><tr><td>Ehrlichia canis (strain Jake)</td><td>Semi-normal</td><td>25</td><td>64</td><td>66</td><td>79</td></tr><tr><td>Ehrlichia chaffeensis (strain Arkansas)</td><td>Semi-normal</td><td>22</td><td>62</td><td>68</td><td>63</td></tr><tr><td>Ehrlichia ruminantium (strain Gardel)</td><td>Semi-normal</td><td>26</td><td>64</td><td>63</td><td>56</td></tr><tr><td>Erythrobacter litoralis (strain HTCC2594)</td><td>Semi-normal</td><td>281</td><td>304</td><td>290</td><td>229</td></tr><tr><td>Gluconacetobacter diazotrophicus PAI 5</td><td>Semi-normal</td><td>256</td><td>297</td><td>317</td><td>270</td></tr><tr><td>Gluconobacter oxydans (strain 621H)</td><td>Semi-normal</td><td>218</td><td>223</td><td>241</td><td>194</td></tr><tr><td>Granulobacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1)</td><td>Semi-normal</td><td>188</td><td>225</td><td>241</td><td>196</td></tr><tr><td rowspan="10">Aerobic</td><td>Hyphomonas neptunium (strain ATCC 15444)</td><td>Semi-normal</td><td>290</td><td>349</td><td>342</td><td>313</td></tr><tr><td>Jannaschia sp. (strain CCS1)</td><td>Semi-normal</td><td>332</td><td>416</td><td>431</td><td>375</td></tr><tr><td>Magnetospirillum magneticum (strain AMB-1 / ATCC 700264)</td><td>Semi-normal</td><td>335</td><td>388</td><td>365</td><td>313</td></tr><tr><td>Maricaulis maris (strain MCS10)</td><td>Semi-normal</td><td>248</td><td>272</td><td>295</td><td>230</td></tr><tr><td>Mesorhizobium sp. (strain BNC1)</td><td>Semi-normal</td><td>416</td><td>474</td><td>444</td><td>380</td></tr><tr><td>Methylobacterium extorquens PA1</td><td>Exclusionary</td><td>464</td><td>462</td><td>450</td><td>344</td></tr><tr><td>Neorickettsia sennetsu (strain Miyayama)</td><td>Semi-normal</td><td>18</td><td>55</td><td>60</td><td>51</td></tr><tr><td>Nitrobacter hamburgensis (strain X14 / DSM 10229)</td><td>Semi-normal</td><td>406</td><td>420</td><td>402</td><td>308</td></tr><tr><td>Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391)</td><td>Semi-normal</td><td>331</td><td>348</td><td>292</td><td>221</td></tr><tr><td>Novosphingobium aromaticivorans (strain DSM 12444)</td><td>Semi-normal</td><td>269</td><td>332</td><td>308</td><td>264</td></tr><tr><td>Orientia tsutsugamushi (strain Boryong)</td><td>Semi-normal</td><td>37</td><td>42</td><td>66</td><td>57</td></tr><tr><td>Paracoccus denitrificans (strain Pd 1222)</td><td>Semi-normal</td><td>434</td><td>493</td><td>466</td><td>402</td></tr><tr><td>Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)</td><td>Semi-normal</td><td>331</td><td>396</td><td>374</td><td>311</td></tr><tr><td rowspan="10">Pelagibacter ubique (strain HTCC1062)</td><td>Rhizobium etli (strain CFN 42 / ATCC 51251)</td><td>Semi-normal</td><td>112</td><td>154</td><td>127</td><td>120</td></tr><tr><td>Rhizobium leguminosarum bv. viciae (strain 3841)</td><td>Semi-normal</td><td>544</td><td>611</td><td>633</td><td>501</td></tr><tr><td>Rhizobium loti (strain MAFF303099)</td><td>Semi-normal</td><td>657</td><td>729</td><td>724</td><td>549</td></tr><tr><td>Rhizobium meliloti (strain 1021)</td><td>Semi-normal</td><td>628</td><td>794</td><td>664</td><td>561</td></tr><tr><td>Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)</td><td>Semi-normal</td><td>507</td><td>582</td><td>578</td><td>504</td></tr><tr><td>Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)</td><td>Semi-normal</td><td>340</td><td>408</td><td>413</td><td>300</td></tr><tr><td>Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255)</td><td>Semi-normal</td><td>325</td><td>360</td><td>345</td><td>292</td></tr><tr><td>Roseobacter denitrificans (strain OCh 114 / ATCC 33942)</td><td>Semi-normal</td><td>286</td><td>377</td><td>328</td><td>336</td></tr><tr><td>Silicibacter pomeroyi (strain ATCC 700808 / DSS-3 / DSM 15171)</td><td>Semi-normal</td><td>297</td><td>411</td><td>413</td><td>348</td></tr><tr><td>Silicibacter sp. (strain TM1040)</td><td>Semi-normal</td><td>336</td><td>373</td><td>404</td><td>365</td></tr><tr><td>Sinorhizobium medicae (strain WSM419)</td><td>Semi-normal</td><td>490</td><td>606</td><td>547</td><td>512</td></tr><tr><td>Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)</td><td>Semi-normal</td><td>482</td><td>545</td><td>505</td><td>419</td></tr><tr><td rowspan="5">Wolbachia</td><td>Sphingopyxis alaskensis</td><td>Semi-normal</td><td>308</td><td>346</td><td>316</td><td>232</td></tr><tr><td>Wolbachia pipientis wMel</td><td>Semi-normal</td><td>69</td><td>70</td><td>96</td><td>84</td></tr><tr><td>Wolbachia sp. (subsp. Brugia malayi, strain TRS)</td><td>Semi-normal</td><td>46</td><td>65</td><td>75</td><td>57</td></tr><tr><td>Xanthobacter sp.</td><td>Semi-normal</td><td>421</td><td>510</td><td>419</td><td>351</td></tr><tr><td>Zymomonas mobilis (strain CP4 / ZM4 / ATCC 31821)</td><td>Exclusionary</td><td>201</td><td>195</td><td>188</td><td>148</td></tr></tbody></table>
<table><caption>Supplemental Table1D Daniels *et al.* 2009</caption><thead><tr><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td rowspan="20">Beta Proteobacteria</td><td rowspan="10">Anaerobic</td><td>Anaplasma marginale (strain St. Maries)</td><td>Semi-normal</td><td>9</td><td>39</td><td>55</td><td>53</td></tr><tr><td>Anaplasma phagocytophilum (strain HZ)</td><td>Semi-normal</td><td>17</td><td>44</td><td>53</td><td>65</td></tr><tr><td>Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512)</td><td>Semi-normal</td><td>244</td><td>308</td><td>282</td><td>252</td></tr><tr><td>Ochrobactrum anthropi (strain ATCC 49188 / DSM 6882 / NCTC 12168)</td><td>Semi-normal</td><td>463</td><td>547</td><td>457</td><td>361</td></tr><tr><td>Rickettsia akari (strain Hartford)</td><td>Semi-normal</td><td>89</td><td>106</td><td>109</td><td>73</td></tr><tr><td>Rickettsia bellii (strain OSU 85-389)</td><td>Semi-normal</td><td>126</td><td>180</td><td>133</td><td>116</td></tr><tr><td>Rickettsia canadensis (strain McKiel)</td><td>Semi-normal</td><td>62</td><td>72</td><td>91</td><td>79</td></tr><tr><td>Rickettsia conorii (strain ATCC VR-613 / Malish 7)</td><td>Semi-normal</td><td>150</td><td>152</td><td>129</td><td>90</td></tr><tr><td>Rickettsia felis (strain ATCC VR-1525 / URRWXCal2)</td><td>Semi-normal</td><td>142</td><td>165</td><td>145</td><td>119</td></tr><tr><td>Rickettsia massiliae (strain Mtu5)</td><td>Semi-normal</td><td>83</td><td>95</td><td>96</td><td>71</td></tr><tr><td>Rickettsia prowazekii (strain Madrid E)</td><td>Semi-normal</td><td>52</td><td>78</td><td>74</td><td>72</td></tr><tr><td>Rickettsia rickettsii lowa</td><td>Exclusionary</td><td>125</td><td>118</td><td>111</td><td>82</td></tr><tr><td>Rickettsia typhi (strain Wilmington / ATCC VR-144)</td><td>Semi-normal</td><td>52</td><td>67</td><td>81</td><td>55</td></tr><tr><td>Acidovorax avenae (subsp. citrulli, strain AAC00-1)</td><td>Semi-normal</td><td>313</td><td>389</td><td>388</td><td>356</td></tr><tr><td>Acidovorax sp. (strain JS42)</td><td>Semi-normal</td><td>298</td><td>301</td><td>328</td><td>307</td></tr><tr><td>Bordetella avium (strain 197N)</td><td>Semi-normal</td><td>262</td><td>291</td><td>325</td><td>263</td></tr><tr><td>Bordetella bronchiseptica (strain NCTC 13252 / RB50 / ATCC BAA-588)</td><td>Semi-normal</td><td>325</td><td>362</td><td>450</td><td>346</td></tr><tr><td>Bordetella parapertussis (strain NCTC 13253 / ATCC BAA-587 / 12822)</td><td>Semi-normal</td><td>258</td><td>307</td><td>375</td><td>291</td></tr><tr><td>Bordetella pertussis (strain ATCC BAA-589 / Tohama I / NCTC 13251)</td><td>Semi-normal</td><td>245</td><td>261</td><td>291</td><td>253</td></tr><tr><td>Bordetella petrii</td><td>Semi-normal</td><td>322</td><td>372</td><td>429</td><td>368</td></tr><tr><td>Burkholderia cenocepacia (strain AU 1054)</td><td>Semi-normal</td><td>447</td><td>562</td><td>561</td><td>502</td></tr><tr><td>Burkholderia cepacia (strain ATCC 53795 / AMMD)</td><td>Semi-normal</td><td>464</td><td>555</td><td>564</td><td>505</td></tr><tr><td>Burkholderia mallei (strain ATCC 23344)</td><td>Semi-normal</td><td>304</td><td>390</td><td>449</td><td>377</td></tr><tr><td>Burkholderia multivorans ATCC 17616</td><td>Semi-normal</td><td>424</td><td>503</td><td>511</td><td>473</td></tr><tr><td>Burkholderia pseudomallei (strain 668)</td><td>Semi-normal</td><td>385</td><td>501</td><td>532</td><td>479</td></tr><tr><td>Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301)</td><td>Semi-normal</td><td>328</td><td>413</td><td>474</td><td>420</td></tr><tr><td>Burkholderia vietnamiensis (strain R1808 / G4 / LMG 22486) / LMG 22486)</td><td>Semi-normal</td><td>535</td><td>694</td><td>652</td><td>582</td></tr><tr><td>Burkholderia xenovorans (strain LB400)</td><td>Semi-normal</td><td>534</td><td>716</td><td>754</td><td>680</td></tr><tr><td>Chromobacterium violaceum (strain IFO 12614 / ATCC 12472 / DSM 30191 / NCIB 9131 / JCM 1249)</td><td>Semi-normal</td><td>280</td><td>362</td><td>385</td><td>371</td></tr><tr><td>Dechloromonas aromatica (strain RCB)</td><td>Semi-normal</td><td>250</td><td>293</td><td>337</td><td>288</td></tr><tr><td>Delftia acidovorans SPH-1</td><td>Semi-normal</td><td>391</td><td>469</td><td>507</td><td>437</td></tr><tr><td>Janthinobacterium sp. (strain Marseille)</td><td>Semi-normal</td><td>261</td><td>347</td><td>371</td><td>257</td></tr><tr><td>Methylibium petroleiphilum (strain PM1)</td><td>Semi-normal</td><td>304</td><td>397</td><td>383</td><td>330</td></tr><tr><td>Methylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875)</td><td>Semi-normal</td><td>235</td><td>249</td><td>240</td><td>207</td></tr><tr><td>Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)</td><td>Semi-normal</td><td>136</td><td>161</td><td>190</td><td>161</td></tr><tr><td>Neisseria meningitidis (serogroup C, serovar 2a, strain ATCC 700532 / FAM18)</td><td>Semi-normal</td><td>130</td><td>174</td><td>185</td><td>159</td></tr><tr><td>Nitrosomonas europaea (strain IFO 14298 / ATCC 19718)</td><td>Semi-normal</td><td>185</td><td>207</td><td>189</td><td>222</td></tr><tr><td>Nitrosomonas eutropha (strain C71)</td><td>Semi-normal</td><td>175</td><td>203</td><td>211</td><td>199</td></tr><tr><td>Nitrosospira multiformis (strain ATCC 25196 / NCIMB 11849)</td><td>Exclusionary</td><td>230</td><td>226</td><td>212</td><td>215</td></tr><tr><td>Polaromonas naphthalenivorans (strain CJ2)</td><td>Semi-normal</td><td>335</td><td>398</td><td>438</td><td>369</td></tr><tr><td>Polaromonas sp. (strain JS666 / ATCC BAA-500)</td><td>Semi-normal</td><td>364</td><td>479</td><td>502</td><td>443</td></tr><tr><td>Polynucleobacter sp. (strain QLW-P1DMWA-1)</td><td>Semi-normal</td><td>162</td><td>185</td><td>188</td><td>184</td></tr><tr><td>Ralstonia eutropha (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)</td><td>Semi-normal</td><td>390</td><td>510</td><td>535</td><td>498</td></tr><tr><td>Ralstonia metallidurans (strain CH34 / ATCC 43123)</td><td>Semi-normal</td><td>383</td><td>494</td><td>550</td><td>477</td></tr><tr><td>Ralstonia solanacearum (strain GMI1000)</td><td>Semi-normal</td><td>342</td><td>452</td><td>391</td><td>386</td></tr><tr><td>Thiobacillus denitrificans (strain ATCC 25259)</td><td>Semi-normal</td><td>210</td><td>261</td><td>262</td><td>228</td></tr><tr><td>Verminephrobacter eiseniae (strain EF01-2)</td><td>Semi-normal</td><td>221</td><td>329</td><td>329</td><td>368</td></tr><tr><td rowspan="2">Anaerobic</td><td>Herminiimonas arsenicoxydans (strain ULPAs1)</td><td>Semi-normal</td><td>253</td><td>295</td><td>291</td><td>248</td></tr><tr><td>Rhodoferax ferrireducens (strain DSM 15236 / ATCC BAA-621 / T118)</td><td>Semi-normal</td><td>269</td><td>342</td><td>357</td><td>359</td></tr></tbody></table>
<table><caption>Supplemental Table1D Daniels *et al.* 2009</caption><thead><tr><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td>Escherichia coli (strain K12)</td><td>Semi-normal</td><td>247</td><td>295</td><td>312</td><td>338</td></tr><tr><td>Francisella tularensis (subsp. tularensis, strain FSC 198)</td><td>Semi-normal</td><td>85</td><td>134</td><td>156</td><td>113</td></tr><tr><td>Haemophilus ducreyi (strain ATCC 700724 / 35000HP)</td><td>Semi-normal</td><td>128</td><td>151</td><td>135</td><td>131</td></tr><tr><td>Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)</td><td>Semi-normal</td><td>137</td><td>150</td><td>169</td><td>147</td></tr><tr><td>Haemophilus somnus (strain 129Pt)</td><td>Semi-normal</td><td>127</td><td>184</td><td>158</td><td>160</td></tr><tr><td>Hahella chejuensis (strain KCTC 2396)</td><td>Semi-normal</td><td>387</td><td>467</td><td>513</td><td>509</td></tr><tr><td>Halorhodospira halophila (strain DSM 244 / SL1)</td><td>Semi-normal</td><td>170</td><td>202</td><td>233</td><td>212</td></tr><tr><td>Idiomarina loihiensis (strain L2-TR / DSM 15497 / ATCC BAA-735)</td><td>Semi-normal</td><td>212</td><td>237</td><td>221</td><td>210</td></tr><tr><td>Klebsiella pneumoniae (subsp. pneumoniae, strain ATCC 700721 / MGH 78578)</td><td>Semi-normal</td><td>282</td><td>384</td><td>454</td><td>403</td></tr><tr><td>Legionella pneumophila (strain Paris)</td><td>Semi-normal</td><td>169</td><td>202</td><td>196</td><td>201</td></tr><tr><td>Marinobacter aquaeolei (strain DSM 11845 / ATCC 700491 / VT8) / VT8)</td><td>Semi-normal</td><td>303</td><td>321</td><td>389</td><td>304</td></tr><tr><td>Marinomonas sp. MWYL1</td><td>Semi-normal</td><td>246</td><td>354</td><td>390</td><td>395</td></tr><tr><td>Methylococcus capsulatus (strain Bath / NCIMB 11132)</td><td>Semi-normal</td><td>185</td><td>223</td><td>243</td><td>226</td></tr><tr><td>Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)</td><td>Semi-normal</td><td>202</td><td>249</td><td>237</td><td>235</td></tr><tr><td>Pasteurella multocida (strain Pm70)</td><td>Semi-normal</td><td>121</td><td>148</td><td>166</td><td>166</td></tr><tr><td>Photobacterium profundum (strain SS9)</td><td>Semi-normal</td><td>300</td><td>368</td><td>422</td><td>375</td></tr><tr><td>Photohabdus luminescens laumondii (strain TT01)</td><td>Semi-normal</td><td>337</td><td>367</td><td>363</td><td>310</td></tr><tr><td>Pseudoalteromonas atlantica (strain T6c / BAA-1087)</td><td>Semi-normal</td><td>235</td><td>320</td><td>347</td><td>297</td></tr><tr><td>Pseudoalteromonas haloplanktis (strain TAC 125)</td><td>Semi-normal</td><td>211</td><td>246</td><td>269</td><td>289</td></tr><tr><td>Pseudomonas aeruginosa (strain LMG 12228 / ATCC 15692 / PRS 101 / 1C / PAO1)</td><td>Semi-normal</td><td>324</td><td>438</td><td>479</td><td>388</td></tr><tr><td>Pseudomonas entomophila (strain L48)</td><td>Semi-normal</td><td>293</td><td>388</td><td>423</td><td>392</td></tr><tr><td>Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)</td><td>Semi-normal</td><td>326</td><td>451</td><td>502</td><td>444</td></tr><tr><td>Pseudomonas mendocina (strain ymp)</td><td>Semi-normal</td><td>269</td><td>337</td><td>361</td><td>374</td></tr><tr><td>Pseudomonas putida (strain F1 / ATCC 700007)</td><td>Semi-normal</td><td>299</td><td>357</td><td>410</td><td>385</td></tr><tr><td>Pseudomonas stutzeri (strain A1501)</td><td>Semi-normal</td><td>216</td><td>282</td><td>346</td><td>293</td></tr><tr><td>Pseudomonas syringae (pathovar phaseolicola, strain 1448A / Race 6)</td><td>Semi-normal</td><td>292</td><td>416</td><td>425</td><td>420</td></tr><tr><td>Psychrobacter arcticum (strain 273-4)</td><td>Semi-normal</td><td>179</td><td>218</td><td>204</td><td>181</td></tr><tr><td>Psychrobacter cryohalolentis (strain K5)</td><td>Semi-normal</td><td>173</td><td>221</td><td>232</td><td>223</td></tr><tr><td>Psychrobacter sp. (strain PRwf-1)</td><td>Semi-normal</td><td>185</td><td>242</td><td>227</td><td>182</td></tr><tr><td>Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)</td><td>Semi-normal</td><td>204</td><td>278</td><td>305</td><td>258</td></tr><tr><td>Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)</td><td>Semi-normal</td><td>243</td><td>353</td><td>334</td><td>309</td></tr><tr><td>Salmonella choleraesuis (strain SC-B67)</td><td>Semi-normal</td><td>249</td><td>350</td><td>354</td><td>340</td></tr><tr><td>Salmonella paratyphi A (strain SARB42 / ATCC 9150)</td><td>Semi-normal</td><td>239</td><td>295</td><td>295</td><td>309</td></tr><tr><td>Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)</td><td>Semi-normal</td><td>257</td><td>344</td><td>359</td><td>326</td></tr><tr><td>Salmonella typhi (strain ATCC 700931 / Ty2)</td><td>Semi-normal</td><td>244</td><td>324</td><td>319</td><td>312</td></tr><tr><td>Salmonella typhimurium (strain ATCC 700720 / SGSC1412 / LT2)</td><td>Semi-normal</td><td>251</td><td>338</td><td>340</td><td>337</td></tr><tr><td>Serratia proteamaculans (strain 568)</td><td>Semi-normal</td><td>314</td><td>398</td><td>413</td><td>342</td></tr><tr><td>Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)</td><td>Semi-normal</td><td>187</td><td>239</td><td>279</td><td>252</td></tr><tr><td>Shewanella baltica (strain OS155 / ATCC BAA-1091)</td><td>Semi-normal</td><td>252</td><td>324</td><td>304</td><td>319</td></tr><tr><td>Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)</td><td>Semi-normal</td><td>232</td><td>285</td><td>315</td><td>269</td></tr><tr><td>Shewanella frigidimarina (strain NCIMB 400)</td><td>Semi-normal</td><td>234</td><td>293</td><td>292</td><td>279</td></tr><tr><td>Shewanella loihica (strain BAA-1088 / PV-4)</td><td>Semi-normal</td><td>198</td><td>256</td><td>278</td><td>274</td></tr><tr><td>Shewanella oneidensis (strain MR-1)</td><td>Semi-normal</td><td>282</td><td>308</td><td>320</td><td>309</td></tr><tr><td>Shewanella pealeana ATCC 700345</td><td>Semi-normal</td><td>211</td><td>256</td><td>325</td><td>285</td></tr><tr><td>Shewanella putrefaciens (strain CN-32/ATCC BAA-453)</td><td>Semi-normal</td><td>223</td><td>289</td><td>302</td><td>290</td></tr><tr><td>Shewanella sediminis HAW-EB3</td><td>Semi-normal</td><td>239</td><td>284</td><td>308</td><td>318</td></tr><tr><td>Shewanella sp. (strain ANA-3)</td><td>Semi-normal</td><td>250</td><td>315</td><td>320</td><td>312</td></tr><tr><td>Shigella boydii (serovar 4, strain Sb227)</td><td>Semi-normal</td><td>238</td><td>292</td><td>317</td><td>275</td></tr><tr><td>Shigella dysenteriae (serovar 1, strain Sd97 / Sd197)</td><td>Semi-normal</td><td>248</td><td>291</td><td>294</td><td>276</td></tr><tr><td>Shigella flexneri (serovar2a, strain 2457T/ATCC 700930)</td><td>Semi-normal</td><td>242</td><td>291</td><td>299</td><td>293</td></tr><tr><td>Shigella sonnei (strain Ss046)</td><td>Semi-normal</td><td>263</td><td>279</td><td>305</td><td>289</td></tr><tr><td>Sodalis glossinidius (strain morsitans)</td><td>Semi-normal</td><td>177</td><td>215</td><td>253</td><td>219</td></tr><tr><td>Vesicomyosocius okutanii (subsp. Calyptogena okutanii, strain HA)</td><td>Semi-normal</td><td>75</td><td>88</td><td>84</td><td>104</td></tr><tr><td>Vibrio cholerae (strain ATCC 39541 / O395)</td><td>Semi-normal</td><td>217</td><td>257</td><td>303</td><td>263</td></tr></tbody></table>
<table><caption>Supplemental Table1D Daniels *et al.* 2009</caption><thead><tr><th></th><th></th><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td rowspan="22">Firmicutes</td><td rowspan="18">Aerobic</td><td>Acholeplasma laidlawii (strain PG-8A)</td><td>Exclusionary</td><td>324</td><td>225</td><td>161</td><td>76</td></tr><tr><td>Bacillus amyloliquefaciens (strain FZB42)</td><td>Semi-normal</td><td>399</td><td>412</td><td>370</td><td>283</td></tr><tr><td>Bacillus anthracis (strain Ames, isolate Porton)</td><td>Semi-normal</td><td>491</td><td>529</td><td>472</td><td>375</td></tr><tr><td>Bacillus cereus (strain ATCC 10987)</td><td>Semi-normal</td><td>466</td><td>559</td><td>517</td><td>399</td></tr><tr><td>Bacillus clausii (strain KSM-K16)</td><td>Semi-normal</td><td>440</td><td>467</td><td>436</td><td>330</td></tr><tr><td>Bacillus halodurans (strain C-125 / ATCC BAA-125 / JCM 9153 / FERM 7344 / DSM 18197)</td><td>Semi-normal</td><td>427</td><td>473</td><td>403</td><td>336</td></tr><tr><td>Bacillus licheniformis (strain DSM 13 / ATCC 14580, sub_strain Goettingen)</td><td>Semi-normal</td><td>465</td><td>481</td><td>416</td><td>331</td></tr><tr><td>Bacillus pumilus (strain SAFR-032)</td><td>Semi-normal</td><td>425</td><td>439</td><td>408</td><td>279</td></tr><tr><td>Bacillus subtilis (strain 168)</td><td>Semi-normal</td><td>458</td><td>467</td><td>406</td><td>328</td></tr><tr><td>Bacillus thuringiensis (strain Al Hakam)</td><td>Semi-normal</td><td>436</td><td>523</td><td>496</td><td>392</td></tr><tr><td>Bacillus weihenstephanensis KBAB4</td><td>Semi-normal</td><td>457</td><td>539</td><td>486</td><td>363</td></tr><tr><td>Desulfitobacterium hafniense (strain Y51)</td><td>Semi-normal</td><td>333</td><td>429</td><td>432</td><td>350</td></tr><tr><td>Enterococcus faecalis (strain V583 / ATCC 700802)</td><td>Exclusionary</td><td>490</td><td>403</td><td>303</td><td>193</td></tr><tr><td>Geobacillus kaustophilus (strain HTA426)</td><td>Exclusionary</td><td>355</td><td>348</td><td>317</td><td>297</td></tr><tr><td>Geobacillus thermodenitrificans (strain NG80-2)</td><td>Semi-normal</td><td>347</td><td>365</td><td>354</td><td>292</td></tr><tr><td>Lactobacillus acidophilus (strain NCFM)</td><td>Exclusionary</td><td>329</td><td>257</td><td>173</td><td>122</td></tr><tr><td>Lactobacillus brevis (strain ATCC 367 / JCM 1170)</td><td>Exclusionary</td><td>544</td><td>304</td><td>172</td><td>121</td></tr><tr><td>Lactobacillus casei (strain ATCC 334)</td><td>Exclusionary</td><td>775</td><td>310</td><td>180</td><td>105</td></tr><tr><td>Lactobacillus delbrueckii (subsp. bulgaricus, strain ATCC BAA-365)</td><td>Exclusionary</td><td>254</td><td>202</td><td>165</td><td>115</td></tr><tr><td>Lactobacillus gasseri (strain ATCC 33323 / DSM 20243)</td><td>Exclusionary</td><td>330</td><td>249</td><td>189</td><td>102</td></tr><tr><td>Lactobacillus helveticus (strain DPC 4571)</td><td>Exclusionary</td><td>282</td><td>237</td><td>151</td><td>107</td></tr><tr><td>Lactobacillus johnsonii (strain NCC 533)</td><td>Exclusionary</td><td>362</td><td>258</td><td>191</td><td>111</td></tr><tr><td>Lactobacillus plantarum (strain WCFS1 / ATCC BAA-793 / NCIMB 8826)</td><td>Exclusionary</td><td>612</td><td>393</td><td>300</td><td>173</td></tr><tr><td>Lactobacillus reuteri (strain ATCC 23272 / DSM 20016 / F275)</td><td>Exclusionary</td><td>404</td><td>264</td><td>195</td><td>110</td></tr><tr><td>Lactobacillus sakei (subsp. sakei, strain 23K)</td><td>Exclusionary</td><td>505</td><td>321</td><td>229</td><td>130</td></tr><tr><td>Lactobacillus salivarius (subsp. salivarius, strain UCC118)</td><td>Exclusionary</td><td>423</td><td>269</td><td>206</td><td>143</td></tr><tr><td>Lactococcus lactis (subsp. lactis, strain IL1403)</td><td>Exclusionary</td><td>543</td><td>314</td><td>199</td><td>113</td></tr><tr><td>Leuconostoc mesenteroides (subsp. mesenteroides, strain ATCC 8293 / NCDO 523)</td><td>Exclusionary</td><td>793</td><td>200</td><td>80</td><td>62</td></tr><tr><td>Listeria innocua (serovar 6a, strain CLIP 11262)</td><td>Exclusionary</td><td>522</td><td>417</td><td>363</td><td>214</td></tr><tr><td>Listeria monocytogenes (serovar 1/2a, strain EGD-e / ATCC BAA-679)</td><td>Exclusionary</td><td>482</td><td>387</td><td>347</td><td>211</td></tr><tr><td>Listeria welshimeri (serovar 6b, strain ATCC 35897 / DSM 20650 / SLCC5334)</td><td>Exclusionary</td><td>461</td><td>365</td><td>344</td><td>193</td></tr><tr><td>Mesoplasma florum (strain ATCC 33453 / NCTC 11704 / L1 / NBRC 100688)</td><td>Exclusionary</td><td>103</td><td>92</td><td>75</td><td>64</td></tr><tr><td>Mycoplasma agalactiae</td><td>Semi-normal</td><td>94</td><td>98</td><td>69</td><td>59</td></tr><tr><td>Mycoplasma capricolum (subsp. capricolum, strain California kid / ATCC 27343 / NCTC 10154)</td><td>Remaining</td><td>115</td><td>76</td><td>79</td><td>57</td></tr><tr><td>Mycoplasma gallisepticum (strain R(low))</td><td>Remaining</td><td>88</td><td>72</td><td>82</td><td>56</td></tr><tr><td>Mycoplasma genitalium (strain ATCC 33530 / NCTC 10195 / G-37)</td><td>Remaining</td><td>50</td><td>44</td><td>44</td><td>56</td></tr><tr><td>Mycoplasma hyopneumoniae (strain J / ATCC 25934 / NCTC 10110)</td><td>Exclusionary</td><td>102</td><td>91</td><td>74</td><td>47</td></tr><tr><td>Mycoplasma mobile (strain 163K / NCTC 11711 / ATCC 43663)</td><td>Exclusionary</td><td>170</td><td>122</td><td>54</td><td>34</td></tr><tr><td>Mycoplasma pneumoniae (strain M129 / ATCC 29342)</td><td>Semi-normal</td><td>55</td><td>61</td><td>66</td><td>56</td></tr><tr><td>Mycoplasma pulmonis (strain UAB CTIP)</td><td>Exclusionary</td><td>145</td><td>132</td><td>90</td><td>34</td></tr><tr><td>Mycoplasma synoviae (strain 53)</td><td>Remaining</td><td>110</td><td>87</td><td>96</td><td>46</td></tr><tr><td>Oceanobacillus iheyensis (strain KCTC 3954 / DSM 14371 / JCM 11309 / HTE831)</td><td>Exclusionary</td><td>474</td><td>454</td><td>385</td><td>265</td></tr><tr><td>Oenococcus oeni (strain BAA-331 / PSU-1)</td><td>Exclusionary</td><td>539</td><td>224</td><td>110</td><td>56</td></tr><tr><td>Onion yellows phytoplasma (strain OY-M)</td><td>Semi-normal</td><td>50</td><td>58</td><td>45</td><td>43</td></tr><tr><td>Pediococcus pentosaceus (strain ATCC25745 / 183-1w)</td><td>Exclusionary</td><td>493</td><td>235</td><td>154</td><td>86</td></tr><tr><td>Pelotomaculum thermopropionicum (strain DSM 13744 / JCM 10971 / SI)</td><td>Semi-normal</td><td>222</td><td>251</td><td>249</td><td>230</td></tr><tr><td>Staphylococcus aureus (strain Mu50 / ATCC 700699)</td><td>Exclusionary</td><td>380</td><td>371</td><td>285</td><td>201</td></tr><tr><td>Staphylococcus epidermidis (strain ATCC 12228)</td><td>Exclusionary</td><td>328</td><td>319</td><td>252</td><td>174</td></tr><tr><td>Staphylococcus haemolyticus (strain JCSC1435)</td><td>Exclusionary</td><td>419</td><td>366</td><td>261</td><td>200</td></tr><tr><td>Staphylococcus saprophyticus (subsp. saprophyticus, strain ATCC 15305 / DSM 20229)</td><td>Exclusionary</td><td>396</td><td>349</td><td>266</td><td>202</td></tr></tbody></table>
<table><caption>Supplemental Table1D Daniels *et al.* 2009</caption><tbody><tr><td></td><td>Streptococcus agalactiae la (serovar la, strain A909 / CDC SS700 / ATCC 27591)</td><td>Exclusionary</td><td>392</td><td>280</td><td>186</td><td>139</td></tr><tr><td></td><td>Streptococcus agalactiae III (serovar III, strain NEM316)</td><td>Exclusionary</td><td>392</td><td>265</td><td>187</td><td>137</td></tr><tr><td></td><td>Streptococcus agalactiae V (serovar V, strain 2603 V/R / ATCC BAA-611)</td><td>Exclusionary</td><td>386</td><td>267</td><td>190</td><td>134</td></tr><tr><td></td><td>Streptococcus gordonii (strain Challis / ATCC 35105 / CH1 / DL1 / V288)</td><td>Exclusionary</td><td>392</td><td>253</td><td>204</td><td>149</td></tr><tr><td></td><td>Streptococcus mutans (serovar c, strain ATCC 700610 / UA159)</td><td>Exclusionary</td><td>393</td><td>248</td><td>188</td><td>137</td></tr><tr><td></td><td>Streptococcus pneumoniae (serovar 2, strain D39 / NCTC 7466)</td><td>Exclusionary</td><td>361</td><td>262</td><td>194</td><td>137</td></tr><tr><td></td><td>Streptococcus pneumoniae (strain ATCC BAA-255 / R6)</td><td>Exclusionary</td><td>362</td><td>254</td><td>204</td><td>130</td></tr><tr><td></td><td>Streptococcus pneumoniae (strain TIGR4 / ATCC BAA-334)</td><td>Exclusionary</td><td>358</td><td>245</td><td>190</td><td>130</td></tr><tr><td></td><td>Streptococcus pyogenes M1 (serovar M1, strain MGAS5005 / ATCC BAA-947)</td><td>Exclusionary</td><td>348</td><td>227</td><td>153</td><td>129</td></tr><tr><td></td><td>Streptococcus sanguinis (strain SK36)</td><td>Exclusionary</td><td>419</td><td>299</td><td>225</td><td>167</td></tr><tr><td></td><td>Streptococcus suis (strain 05ZYH33)</td><td>Exclusionary</td><td>392</td><td>277</td><td>224</td><td>133</td></tr><tr><td></td><td>Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9)</td><td>Exclusionary</td><td>335</td><td>243</td><td>152</td><td>106</td></tr><tr><td></td><td>Symbiobacterium thermophilum (strain IAM 14863 / T)</td><td>Semi-normal</td><td>305</td><td>314</td><td>320</td><td>261</td></tr><tr><td></td><td>Ureaplasma parvum (serovar 3, strain ATCC 700970)</td><td>Exclusionary</td><td>87</td><td>73</td><td>56</td><td>55</td></tr><tr><td rowspan="10">Anaerobic</td><td>Alkaliphilus metalliredigens (strain QYMF)</td><td>Remaining</td><td>390</td><td>387</td><td>424</td><td>326</td></tr><tr><td>Alkaliphilus oremlandii (strain OhILAs)</td><td>Semi-normal</td><td>260</td><td>264</td><td>261</td><td>225</td></tr><tr><td>Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903)</td><td>Remaining</td><td>201</td><td>200</td><td>223</td><td>181</td></tr><tr><td>Carboxydothermus hydrogenoformans (strain Z-2901 / DSM 6008)</td><td>Exclusionary</td><td>337</td><td>309</td><td>267</td><td>175</td></tr><tr><td>Clostridium acetobutylicum (strain DSM 792 / JCM 1419 / LMG 5710 / ATCC 824 / VKM B-1787)</td><td>Semi-normal</td><td>231</td><td>297</td><td>329</td><td>285</td></tr><tr><td>Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)</td><td>Semi-normal</td><td>277</td><td>369</td><td>456</td><td>411</td></tr><tr><td>Clostridium botulinum (strain ATCC 19397 / Type A)</td><td>Semi-normal</td><td>196</td><td>249</td><td>284</td><td>269</td></tr><tr><td>Clostridium difficile (strain 630)</td><td>Semi-normal</td><td>198</td><td>275</td><td>317</td><td>275</td></tr><tr><td>Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NCIMB 10680)</td><td>Semi-normal</td><td>253</td><td>302</td><td>301</td><td>250</td></tr><tr><td>Clostridium novyi (strain NT)</td><td>Semi-normal</td><td>146</td><td>190</td><td>176</td><td>170</td></tr><tr><td></td><td>Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)</td><td>Semi-normal</td><td>144</td><td>244</td><td>240</td><td>193</td></tr><tr><td></td><td>Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)</td><td>Semi-normal</td><td>178</td><td>247</td><td>312</td><td>281</td></tr><tr><td></td><td>Clostridium tetani (strain Massachusetts / E88)</td><td>Semi-normal</td><td>136</td><td>194</td><td>220</td><td>195</td></tr><tr><td></td><td>Clostridium thermocellum (strain ATCC 27405 / DSM 1237)</td><td>Semi-normal</td><td>213</td><td>281</td><td>234</td><td>219</td></tr><tr><td></td><td>Desulfotomaculum reducens (strain MI-1)</td><td>Semi-normal</td><td>284</td><td>301</td><td>283</td><td>241</td></tr><tr><td></td><td>Moorella thermoacetica (strain ATCC 39073)</td><td>Semi-normal</td><td>257</td><td>259</td><td>226</td><td>185</td></tr><tr><td></td><td>Mycoplasma mycoides SC (subsp. mycoides, strain PG1)</td><td>Exclusionary</td><td>132</td><td>90</td><td>88</td><td>59</td></tr><tr><td></td><td>Mycoplasma penetrans (strain HF-2)</td><td>Semi-normal</td><td>71</td><td>86</td><td>82</td><td>97</td></tr></tbody></table>