bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses
Authors: Quigley Lisa , O'Sullivan Orla , Beresford Tom P. , Ross R. Paul , Fitzgerald Gerald F. , Cotter Paul D. 
Published: June 2012

ABSTRACT

Here, high-throughput sequencing was employed to reveal the highly diverse bacterial populations present in 62 Irish artisanal cheeses and, in some cases, associated cheese rinds. Using this approach, we revealed the presence of several genera not previously associated with cheese, including
Faecalibacterium
,
Prevotella
, and
Helcococcus
and, for the first time, detected the presence of
Arthrobacter
and
Brachybacterium
in goats' milk cheese. Our analysis confirmed many previously observed patterns, such as the dominance of typical cheese bacteria, the fact that the microbiota of raw and pasteurized milk cheeses differ, and that the level of cheese maturation has a significant influence on
Lactobacillus
populations. It was also noted that cheeses containing adjunct ingredients had lower proportions of
Lactococcus
species. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods.
Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite
Authors: Shelobolina Evgenya , Xu Huifang , Konishi Hiromi , Kukkadapu Ravi , Wu Tao , Blöthe Marco , Roden Eric 
Published: June 2012

ABSTRACT

Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. Here we show that the lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458–1460, 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay-sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Mössbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 1.5 × 10
7
cells were produced per μmol of Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including a decrease in the unit cell b dimension toward dioctahedral levels and Fe and K release. Structural Fe(II) oxidation may involve either direct enzymatic oxidation, followed by solid-state mineral transformation, or indirect oxidation as a result of the formation of aqueous Fe, followed by electron transfer from Fe(II) in the mineral to Fe(III) in solution. Although it is not possible to distinguish between these two mechanisms with available data, the complete absence of aqueous Fe in oxidation experiments favors the former alternative. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms are directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere.
Real-Time PCR Detection of Paenibacillus spp. in Raw Milk To Predict Shelf Life Performance of Pasteurized Fluid Milk Products
Authors: Ranieri Matthew L. , Ivy Reid A. , Mitchell W. Robert , Call Emma , Masiello Stephanie N. , Wiedmann Martin , Boor Kathryn J. 
Published: June 2012

ABSTRACT

Psychrotolerant sporeformers, specifically
Paenibacillus
spp., are important spoilage bacteria for pasteurized, refrigerated foods such as fluid milk. While
Paenibacillus
spp. have been isolated from farm environments, raw milk, processing plant environments, and pasteurized fluid milk, no information on the number of
Paenibacillus
spp. that need to be present in raw milk to cause pasteurized milk spoilage was available. A real-time PCR assay targeting the 16S rRNA gene was designed to detect
Paenibacillus
spp. in fluid milk and to discriminate between
Paenibacillus
and other closely related spore-forming bacteria. Specificity was confirmed using 16
Paenibacillus
and 17
Bacillus
isolates. All 16
Paenibacillus
isolates were detected with a mean cycle threshold (

C
T

) of 19.14 ± 0.54. While 14/17
Bacillus
isolates showed no signal (

C
T

> 40), 3
Bacillus
isolates showed very weak positive signals (

C
T

= 38.66 ± 0.65). The assay provided a detection limit of approximately 3.25 × 10
1
CFU/ml using total genomic DNA extracted from raw milk samples inoculated with
Paenibacillus
. Application of the TaqMan PCR to colony lysates obtained from heat-treated and enriched raw milk provided fast and accurate detection of
Paenibacillus
. Heat-treated milk samples where
Paenibacillus
(≥1 CFU/ml) was detected by this colony TaqMan PCR showed high bacterial counts (>4.30 log CFU/ml) after refrigerated storage (6°C) for 21 days. We thus developed a tool for rapid detection of
Paenibacillus
that has the potential to identify raw milk with microbial spoilage potential as a pasteurized product.
Directed Evolution of Xylose Isomerase for Improved Xylose Catabolism and Fermentation in the Yeast Saccharomyces cerevisiae
Authors: Lee Sun-Mi , Jellison Taylor , Alper Hal S. 
Published: June 2012

ABSTRACT

The heterologous expression of a highly functional xylose isomerase pathway in
Saccharomyces cerevisiae
would have significant advantages for ethanol yield, since the pathway bypasses cofactor requirements found in the traditionally used oxidoreductase pathways. However, nearly all reported xylose isomerase-based pathways in
S. cerevisiae
suffer from poor ethanol productivity, low xylose consumption rates, and poor cell growth compared with an oxidoreductase pathway and, additionally, often require adaptive strain evolution. Here, we report on the directed evolution of the
Piromyces
sp. xylose isomerase (encoded by
xylA
) for use in yeast. After three rounds of mutagenesis and growth-based screening, we isolated a variant containing six mutations (E15D, E114G, E129D, T142S, A177T, and V433I) that exhibited a 77% increase in enzymatic activity. When expressed in a minimally engineered yeast host containing a
gre3
knockout and
tal1
and
XKS1
overexpression, the strain expressing this mutant enzyme improved its aerobic growth rate by 61-fold and both ethanol production and xylose consumption rates by nearly 8-fold. Moreover, the mutant enzyme enabled ethanol production by these yeasts under oxygen-limited fermentation conditions, unlike the wild-type enzyme. Under microaerobic conditions, the ethanol production rates of the strain expressing the mutant xylose isomerase were considerably higher than previously reported values for yeast harboring a xylose isomerase pathway and were also comparable to those of the strains harboring an oxidoreductase pathway. Consequently, this study shows the potential to evolve a xylose isomerase pathway for more efficient xylose utilization.
Ketoglutarate Transport Protein KgtP Is Secreted through the Type III Secretion System and Contributes to Virulence in Xanthomonas oryzae pv. oryzae
Authors: Guo Wei , Cai Lu-Lu , Zou Hua-Song , Ma Wen-Xiu , Liu Xi-Ling , Zou Li-Fang , Li Yu-Rong , Chen Xiao-Bin , Chen Gong-You 
Published: June 2012

ABSTRACT

The phytopathogenic prokaryote
Xanthomonas oryzae
pv. oryzae is the causal agent of bacterial leaf blight (BB) of rice and utilizes a type III secretion system (T3SS) to deliver T3SS effectors into rice cells. In this report, we show that the ketoglutarate transport protein (KgtP) is secreted in an HpaB-independent manner through the T3SS of
X. oryzae
pv. oryzae PXO99
A
and localizes to the host cell membrane for α-ketoglutaric acid export.
kgtP
contained an imperfect PIP box (plant-inducible promoter) in the promoter region and was positively regulated by HrpX and HrpG. A
kgtP
deletion mutant was impaired in bacterial virulence and growth
in planta
; furthermore, the mutant showed reduced growth in minimal media containing α-ketoglutaric acid or sodium succinate as the sole carbon source. The reduced virulence and the deficiency in α-ketoglutaric acid utilization by the
kgtP
mutant were restored to wild-type levels by the presence of
kgtP
in
trans
. The expression of
OsIDH
, which is responsible for the synthesis of α-ketoglutaric acid in rice, was enhanced when KgtP was present in the pathogen. To our knowledge, this is the first report demonstrating that KgtP, which is regulated by HrpG and HrpX and secreted by the T3SS in
Xanthomonas oryzae
pv. oryzae, transports α-ketoglutaric acid when the pathogen infects rice.
Complete Genome Sequence of the Strong Mutator Salmonella enterica subsp. enterica Serotype Heidelberg Strain B182
Authors: Le Bars Hervé , Bousarghin Latifa , Bonnaure-Mallet Martine , Jolivet-Gougeon Anne , Barloy-Hubler Frédérique 
Published: June 2012

ABSTRACT

In bacteria, normal mutation frequencies are mostly around 10
−10
per base pair. However, there exists natural isolates, called “mutators,” that exhibit permanent mutation occurrences up to 1,000-fold greater than usual. As mutations play essential roles, particularly in the evolution of antibiotic resistance, bacteria showing elevated mutation rates could have an important responsibility in the emergence of antibiotic resistance, especially in the clinical background. In this announcement, we report the first complete genome sequence of the
Salmonella enterica
subsp.
enterica
serotype Heidelberg B182 mutator strain, isolated from bovine feces (France), which consists of a 4,750,465-bp circular chromosome (cB182_4750; GC, 52.2%) and one circular plasmid of 37,581 bp (pB182_37; GC, 42.8%).
Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17, Which Forms Biofilms on Hydrophobic Organic Compounds
Authors: Grimaud Regis , Ghiglione Jean-François , Cagnon Christine , Lauga Béatrice , Vaysse Pierre-Joseph , Rodriguez-Blanco Arturo , Mangenot Sophie , Cruveiller Stephane , Barbe Valérie , Duran Robert , Wu Long-Fei , Talla Emmanuel , Bonin Patricia , Michotey Valerie 
Published: June 2012

ABSTRACT

Marinobacter hydrocarbonoclasticus
SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.
The MscS and MscL Families of Mechanosensitive Channels Act as Microbial Emergency Release Valves
Authors: Booth Ian R. , Blount Paul 
Published: June 2012

ABSTRACTSingle-celled organisms must survive exposure to environmental extremes. Perhaps one of the most variable and potentially life-threatening changes that can occur is that of a rapid and acute decrease in external osmolarity. This easily translates into several atmospheres of additional pressure that can build up within the cell. Without a protective mechanism against such pressures, the cell will lyse. Hence, most microbes appear to possess members of one or both families of bacterial mechanosensitive channels, MscS and MscL, which can act as biological emergency release valves that allow cytoplasmic solutes to be jettisoned rapidly from the cell. While this is undoubtedly a function of these proteins, the discovery of the presence of MscS homologues in plant organelles and MscL in fungus and mycoplasma genomes may complicate this simplistic interpretation of the physiology underlying these proteins. Here we compare and contrast these two mechanosensitive channel families, discuss their potential physiological roles, and review some of the most relevant data that underlie the current models for their structure and function.
Enzymology and Structure of the GH13_31 Glucan 1,6-α-Glucosidase That Confers Isomaltooligosaccharide Utilization in the Probiotic Lactobacillus acidophilus NCFM
Authors: Møller Marie S. , Fredslund Folmer , Majumder Avishek , Nakai Hiroyuki , Poulsen Jens-Christian N. , Lo Leggio Leila , Svensson Birte , Abou Hachem Maher 
Published: June 2012

ABSTRACT

Isomaltooligosaccharides (IMO) have been suggested as promising prebiotics that stimulate the growth of probiotic bacteria. Genomes of probiotic lactobacilli from the acidophilus group, as represented by
Lactobacillus acidophilus
NCFM, encode α-1,6 glucosidases of the family GH13_31 (glycoside hydrolase family 13 subfamily 31) that confer degradation of IMO. These genes reside frequently within maltooligosaccharide utilization operons, which include an ATP-binding cassette transporter and α-glucan active enzymes, e.g., maltogenic amylases and maltose phosphorylases, and they also occur separated from any carbohydrate transport or catabolism genes on the genomes of some acidophilus complex members, as in
L. acidophilus
NCFM. Besides the isolated locus encoding a GH13_31 enzyme, the ABC transporter and another GH13 in the maltooligosaccharide operon were induced in response to IMO or maltotetraose, as determined by reverse transcription-PCR (RT-PCR) transcriptional analysis, suggesting coregulation of α-1,6- and α-1,4-glucooligosaccharide utilization loci in
L. acidophilus
NCFM. The
L. acidophilus
NCFM GH13_31 (
La
GH13_31) was produced recombinantly and shown to be a glucan 1,6-α-glucosidase active on IMO and dextran and product-inhibited by glucose. The catalytic efficiency of
La
GH13_31 on dextran and the dextran/panose (trisaccharide) efficiency ratio were the highest reported for this class of enzymes, suggesting higher affinity at distal substrate binding sites. The crystal structure of
La
GH13_31 was determined to a resolution of 2.05 Å and revealed additional substrate contacts at the +2 subsite in
La
GH13_31 compared to the GH13_31 from
Streptococcus mutans
(
Sm
GH13_31), providing a possible structural rationale to the relatively high affinity for dextran. A comprehensive phylogenetic and activity motif analysis mapped IMO utilization enzymes from gut microbiota to rationalize preferential utilization of IMO by gut residents.
Type IV Pilus Assembly in Pseudomonas aeruginosa over a Broad Range of Cyclic di-GMP Concentrations
Authors: Jain Ruchi , Behrens Anna-Janina , Kaever Volkhard , Kazmierczak Barbara I. 
Published: June 2012

ABSTRACTPseudomonas aeruginosais a Gram-negative, opportunistic pathogen that utilizes polar type IV pili (T4P) for twitching motility and adhesion in the environment and during infection. Pilus assembly requires FimX, a GGDEF/EAL domain protein that binds and hydrolyzes cyclic di-GMP (c-di-GMP). Bacteria lacking FimX are deficient in twitching motility and microcolony formation. We carried out an extragenic suppressor screen in PA103ΔfimXbacteria to identify additional regulators of pilus assembly. Multiple suppressor mutations were mapped to PA0171, PA1121 (yfiR), and PA3703 (wspF), three genes previously associated with small-colony-variant phenotypes. Multiple independent techniques confirmed that suppressors assembled functional surface pili, though at both polar and nonpolar sites. Whole-cell c-di-GMP levels were elevated in suppressor strains, in agreement with previous studies that had shown that the disrupted genes encoded negative regulators of diguanylate cyclases. Overexpression of the regulated diguanylate cyclases was sufficient to suppress the ΔfimXpilus assembly defect, as was overexpression of an unrelated diguanylate cyclase fromCaulobacter crescentus. Furthermore, under natural conditions of high c-di-GMP, PA103ΔfimXformed robust biofilms that showed T4P staining and were structurally distinct from those formed by nonpiliated bacteria. These results are the first demonstration thatP. aeruginosaassembles a surface organelle, type IV pili, over a broad range of c-di-GMP concentrations. Assembly of pili at low c-di-GMP concentrations requires a polarly localized c-di-GMP binding protein and phosphodiesterase, FimX; this requirement for FimX is bypassed at high c-di-GMP concentrations. Thus,P. aeruginosacan assemble the same surface organelle in distinct ways for motility or adhesion under very different environmental conditions.
Synthesis of Long-Chain Chitooligosaccharides by a Hypertransglycosylating Processive Endochitinase of Serratia proteamaculans 568
Authors: Purushotham Pallinti , Podile Appa Rao 
Published: June 2012

ABSTRACT

We describe the heterologous expression and characterization of a 407-residue single-domain glycosyl hydrolase family 18 chitinase (
Sp
ChiD) from Gram-negative
Serratia proteamaculans
568 that has unprecedented catalytic properties.
Sp
ChiD was optimally active at pH 6.0 and 40°C, where it showed a

K
m

of 83 mg ml
−1
, a
k
cat
of 3.9 × 10
2
h
−1
, and a
k
cat
/

K
m

of 4.7 h mg
−1
ml
−1
on colloidal chitin. On chitobiose, the

K
m

,
k
cat
, and
k
cat
/

K
m

were 203 μM, 1.3 × 10
2
h
−1
, and 0.62 h
−1
μM
−1
, respectively. Hydrolytic activity on chitooligosaccharides (CHOS) and colloidal chitin indicated that
Sp
ChiD was an endo-acting processive enzyme, with the unique ability to convert released chitobiose to
N
-acetylglucosamine, the major end product.
Sp
ChiD showed hyper transglycosylation (TG) with trimer-hexamer CHOS substrates, generating considerable amounts of long-chain CHOS. The TG activity of
Sp
ChiD was dependent on both the length and concentration of the oligomeric substrate and also on the enzyme concentration. The length and amount of accumulated TG products increased with increases in the length of the substrate and its concentration and decreased with increases in the enzyme concentration. The
Sp
ChiD bound to insoluble and soluble chitin substrates despite the absence of accessory domains. Sequence alignments and structural modeling indicated that
Sp
ChiD would have a deep substrate-binding groove lined with aromatic residues, which is characteristic of processive enzymes.
Sp
ChiD shows a combination of properties that seems rare among family 18 chitinases and that may resemble the properties of human chitotriosidase.
Cell Biology of Cnidarian-Dinoflagellate Symbiosis
Authors: Davy Simon K. , Allemand Denis , Weis Virginia M. 
Published: June 2012

SUMMARYThe symbiosis between cnidarians (e.g., corals or sea anemones) and intracellular dinoflagellate algae of the genusSymbiodiniumis of immense ecological importance. In particular, this symbiosis promotes the growth and survival of reef corals in nutrient-poor tropical waters; indeed, coral reefs could not exist without this symbiosis. However, our fundamental understanding of the cnidarian-dinoflagellate symbiosis and of its links to coral calcification remains poor. Here we review what we currently know about the cell biology of cnidarian-dinoflagellate symbiosis. In doing so, we aim to refocus attention on fundamental cellular aspects that have been somewhat neglected since the early to mid-1980s, when a more ecological approach began to dominate. We review the four major processes that we believe underlie the various phases of establishment and persistence in the cnidarian/coral-dinoflagellate symbiosis: (i) recognition and phagocytosis, (ii) regulation of host-symbiont biomass, (iii) metabolic exchange and nutrient trafficking, and (iv) calcification. Where appropriate, we draw upon examples from a range of cnidarian-alga symbioses, including the symbiosis between greenHydraand its intracellular chlorophyte symbiont, which has considerable potential to inform our understanding of the cnidarian-dinoflagellate symbiosis. Ultimately, we provide a comprehensive overview of the history of the field, its current status, and where it should be going in the future.
A cohort study comparing cardiovascular risk factors in rural Māori, urban Māori and non-Māori communities in New Zealand
Authors: Cameron Vicky A , Faatoese Allamanda F , Gillies Matea W , Robertson Paul J , Huria Tania M , Doughty Rob N , Whalley Gillian A , Richards Mark A , Troughton Richard W , Tikao-Mason Karen N , Wells Elisabeth J , Sheerin Ian G , Pitama Suzanne G 
Published: June 2012

ObjectivesTo understand health disparities in cardiovascular disease (CVD) in the indigenous Māori of New Zealand, diagnosed and undiagnosed CVD risk factors were compared in rural Māori in an area remote from health services with urban Māori and non-Māori in a city well served with health services.DesignProspective cohort study.SettingHauora Manawa is a cohort study of diagnosed and previously undiagnosed CVD, diabetes and risk factors, based on random selection from electoral rolls of the rural Wairoa District and Christchurch City, New Zealand.ParticipantsScreening clinics were attended by 252 rural Māori, 243 urban Māori and 256 urban non-Māori, aged 20–64 years.Main outcome measuresThe study documented personal and family medical history, blood pressure, anthropometrics, fasting lipids, insulin, glucose, HbA1c and urate to identify risk factors in common and those that differ among the three communities.ResultsMean age (SD) was 45.7 (11.5) versus 42.6 (11.2) versus 43.6 (11.5) years in rural Māori, urban Māori and non-Māori, respectively. Age-adjusted rates of diagnosed cardiac disease were not significantly different across the cohorts (7.5% vs 5.8% vs 2.8%, p=0.073). However, rural Māori had significantly higher levels of type-2 diabetes (10.7% vs 3.7% vs 2.4%, p<0.001), diagnosed hypertension (25.0% vs 14.9% vs 10.7%, p<0.001), treated dyslipidaemia (15.7% vs 7.1% vs 2.8%, p<0.001), current smoking (42.8% vs 30.5% vs 15.2%, p<0.001) and age-adjusted body mass index (30.7 (7.3) vs 29.1 (6.4) vs 26.1 (4.5) kg/m2, p<0.001). Similarly high rates of previously undocumented elevated blood pressure (22.2% vs 23.5% vs 17.6%, p=0.235) and high cholesterol (42.1% vs 54.3% vs 42.2%, p=0.008) were observed across all cohorts.ConclusionsSupporting integrated rural healthcare to provide screening and management of CVD risk factors would reduce health disparities in this indigenous population.