bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison between Cultured Small-Intestinal and Fecal Microbiotas in Beagle Dogs
Authors: Mentula Silja , Harmoinen Jaana , Heikkilä Matti , Westermarck Elias , Rautio Merja , Huovinen Pentti , Könönen Eija 
Published: August 2005

ABSTRACT

The microbiota of the small intestine is poorly known because of difficulties in sampling. In this study, we examined whether the organisms cultured from the jejunum and feces resemble each other. Small-intestinal fluid samples were collected from 22 beagle dogs with a permanent jejunal fistula in parallel with fecal samples. In addition, corresponding samples from seven of the dogs were collected during a 4-week period (days 4, 10, 14, and 28) to examine the stability of the microbiota. In the jejunal samples, aerobic/facultative and anaerobic bacteria were equally represented, whereas anaerobes dominated in the fecal samples. Despite lower numbers of bacteria in the jejunum (range, 10
2
to 10
6
CFU/g) than in feces (range, 10
8
to 10
11
CFU/g), some microbial groups were more prevalent in the small intestine: staphylococci, 64% versus 36%; nonfermentative gram-negative rods, 27% versus 9%; and yeasts, 27% versus 5%, respectively. In contrast, part of the fecal dominant microbiota (bile-resistant
Bacteroides
spp.,
Clostridium hiranonis
-like organisms, and lactobacilli) was practically absent in the jejunum. Many species were seldom isolated simultaneously from both sample types, regardless of their overall prevalence. In conclusion, the small intestine contains a few bacterial species at a time with vastly fluctuating counts, opposite to the results obtained for the colon, where the major bacterial groups remain relatively constant over time. Qualitative and quantitative differences between the corresponding jejunal and fecal samples indicate the inability of fecal samples to represent the microbiotas present in the upper gut.
Development and Assessment of a Real-Time PCR Assay for Rapid and Sensitive Detection of a Novel Thermotolerant Bacterium,
Lactobacillus thermotolerans
, in Chicken Feces
Authors: Selim Abu Sadeque Md , Boonkumklao Piyanuch , Sone Teruo , Assavanig Apinya , Wada Masaru , Yokota Atsushi 
Published: August 2005

ABSTRACT

A new real-time PCR assay was successfully developed using a TaqMan fluorescence probe for specific detection and enumeration of a novel bacterium,
Lactobacillus thermotolerans
, in chicken feces. The specific primers and probe were designed based on the
L. thermotolerans
16S rRNA gene sequences, and these sequences were compared to those of all available 16S rRNA genes in the GenBank database. The assay, targeting 16S rRNA gene, was evaluated using DNA from a pure culture of
L. thermotolerans
, DNA from the closely related bacteria
Lactobacillus mucosae
DSM 13345
T
and
Lactobacillus fermentum
JCM 1173
T
, and DNA from other lactic acid bacteria in quantitative experiments. Serial dilutions of
L. thermotolerans
DNA were used as external standards for calibration. The minimum detection limit of this technique was 1.84 × 10
3
cells/ml of an
L. thermotolerans
pure culture. The assay was then applied to chicken feces in two different trials. In the first trial, the cell population was 10
4
cells/g feces on day 4 and 10
5
cells/g feces on days 11 to 18. However, cell populations of 10
6
to 10
7
cells/g feces were detected in the second trial. The total bacterial count, measured by 4′,6-diamidino-2-phenylindole (DAPI) staining, was approximately 10
11
cells/g feces. These results suggest that in general,
L. thermotolerans
is a normal member of the chicken gut microbiota, although it is present at relatively low levels in the feces.
Bacteriophages May Bias Outcome of Bacterial Enrichment Cultures
Authors: Muniesa Maite , Blanch Anicet R. , Lucena Francisco , Jofre Juan 
Published: August 2005

ABSTRACTEnrichment cultures are widely used for the isolation of bacteria in clinical, biotechnological, and environmental studies. However, competition, relative growth rates, or inhibitory effects may alter the outcome of enrichment cultures, causing the phenomenon known as enrichment bias. Bacteriophages are a major component in many microbial systems, and it abounds in natural settings. This abundance means that bacteriophages are likely to be present in many laboratory enrichment cultures. Our hypothesis was that bacteriophages present in the sample might bias the enriched subpopulation, since it can infect and lyse the target bacteria during the enrichment step once the bacteria reach a given density. Here we show that the presence of bacteriophages inSalmonellaandShigellaenrichment cultures produced a significant reduction (more than 1 log unit) in the number of these bacteria compared with samples in which bacteriophages had been reduced by filtration through 0.45-μm non-protein-binding membranes. Furthermore, our data indicate that theSalmonellabiotypes isolated after the enrichment culture change if bacteriophages are present, thus distorting the results of the analysis.
Effects of Bacteria on
Artemia franciscana
Cultured in Different Gnotobiotic Environments
Authors: Marques Antonio , Dinh Thi , Ioakeimidis Christos , Huys Geert , Swings Jean , Verstraete Willy , Dhont Jean , Sorgeloos Patrick , Bossier Peter 
Published: August 2005

ABSTRACT

The use of probiotics is receiving considerable attention as an alternative approach to control microbiota in aquaculture farms, especially in hatching facilities. However, application with consistent results is hampered by insufficient information on their modes of action. To investigate whether dead bacteria (allowing investigation of their nutritional effect) or live bacteria (allowing evaluation of their probiotic effect) have any beneficial effect towards
Artemia franciscana
and, subsequently, if live bacteria have probiotic effects beyond the effects observed with dead bacteria, a model system was employed using gnotobiotic
Artemia
as a test organism. Nauplii were cultured in the presence of 10 bacterial strains combined with four different major axenic live feeds (two strains of
Saccharomyces cerevisiae
and two strains of
Dunaliella tertiolecta
) differing in their nutritional values. In combination with poor- and medium-quality live feeds, dead bacteria exerted a strong effect on
Artemia
survival but a rather weak or no effect on individual length and constituted a maximum of only 5.9% of the total ash-free dry weight supplied. These effects were reduced or even disappeared when medium- to good-quality major feed sources were used, possibly due to improvements in the health status of
Artemia
. Some probiotic bacteria, such as GR 8 (
Cytophaga
spp.), improved (not always significantly) the performance of nauplii beyond the effect observed with dead bacteria, independently of the feed supplied. The present approach can be an excellent system to study the exact mode of action of bacteria, especially if combined with challenge tests or other types of analysis (e.g., transcriptome and proteonomic analysis).
Phylogenetic Characterization of a Polychlorinated-Dioxin- Dechlorinating Microbial Community by Use of Microcosm Studies
Authors: Yoshida Naoko , Takahashi Nobutaka , Hiraishi Akira 
Published: August 2005

ABSTRACTMicrocosms capable of reductive dechlorination of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were constructed in glass bottles by seeding them with a polluted river sediment and incubating them anaerobically with an organic medium. All of the PCDD/F congeners detected were equally reduced without the accumulation of significant amounts of less-chlorinated congeners as the intermediate or end products. Alternatively, large amounts of catechol and salicylic acid were produced in the upper aqueous phase. Thus, the dechlorination of PCDD/Fs and the oxidative degradation of the dechlorinated products seemed to take place simultaneously in the microcosm. Denaturing gel gradient electrophoresis and clone library analyses of PCR-amplified 16S rRNA genes from the microcosm showed that members of the phylaFirmicutes,Proteobacteria, andBacteroidetespredominated. A significant number ofChloroflexiclones were also detected. Quantitative real-time PCR with specific primer sets showed that the 16S rRNA genes of a putative dechlorinator, “Dehalococcoides,” and its relatives accounted for 0.1% of the total rRNA gene copies of the microcosm. Most of the clones thus obtained formed a cluster distinct from the typical “Dehalococcoides” group. Quinone profiling indicated that ubiquinones accounted for 18 to 25% of the total quinone content, suggesting the coexistence and activity of ubiquinone-containing aerobic bacteria. These results suggest that the apparent complete dechlorination of PCDD/Fs found in the microcosm was due to a combination of the dechlorinating activity of the “Dehalococcoides”-like organisms and the oxidative degradation of the dechlorinated products by aerobic bacteria with aromatic hydrocarbon dioxygenases.
Phosphate Starvation-Inducible Gene
ushA
Encodes a 5′ Nucleotidase Required for Growth of
Corynebacterium glutamicum
on Media with Nucleotides as the Phosphorus Source
Authors: Rittmann Doris , Sorger-Herrmann Ulrike , Wendisch Volker F. 
Published: August 2005

ABSTRACT

Phosphorus is an essential component of macromolecules, like DNA, and central metabolic intermediates, such as sugar phosphates, and bacteria possess enzymes and control mechanisms that provide an optimal supply of phosphorus from the environment. UDP-sugar hydrolases and 5′ nucleotidases may play roles in signal transduction, as they do in mammals, in nucleotide salvage, as demonstrated for UshA of
Escherichia coli
, or in phosphorus metabolism. The
Corynebacterium glutamicum
gene
ushA
was found to encode a secreted enzyme which is active as a 5′ nucleotidase and a UDP-sugar hydrolase. This enzyme was synthesized and secreted into the medium when
C. glutamicum
was starved for inorganic phosphate. UshA was required for growth of
C. glutamicum
on AMP and UDP-glucose as sole sources of phosphorus. Thus, in contrast to UshA from
E. coli
,
C. glutamicum
UshA is an important component of the phosphate starvation response of this species and is necessary to access nucleotides and related compounds as sources of phosphorus.
Two Rhizobial Strains,Mesorhizobium lotiMAFF303099 andBradyrhizobium japonicumUSDA110, Encode Haloalkane Dehalogenases with Novel Structures and Substrate Specificities
Authors: Sato Yukari , Monincová Marta , Chaloupková Radka , Prokop Zbyňek , Ohtsubo Yoshiyuki , Minamisawa Kiwamu , Tsuda Masataka , Damborský Jiří , Nagata Yuji 
Published: August 2005

ABSTRACTHaloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. Two rhizobial strains,Mesorhizobium lotiMAFF303099 andBradyrhizobium japonicumUSDA110, have open reading frames (ORFs),mlr5434andblr1087, respectively, that encode putative haloalkane dehalogenase homologues. The crude extracts ofEscherichia colistrains expressingmlr5434andblr1087showed the ability to dehalogenate 18 halogenated compounds, indicating that these ORFs indeed encode haloalkane dehalogenases. Therefore, these ORFs were referred to asdmlA(dehalogenase fromMesorhizobium loti) anddbjA(dehalogenase fromBradyrhizobium japonicum), respectively. The principal component analysis of the substrate specificities of various haloalkane dehalogenases clearly showed that DbjA and DmlA constitute a novel substrate specificity class with extraordinarily high activity towards β-methylated compounds. Comparison of the circular dichroism spectra of DbjA and other dehalogenases strongly suggested that DbjA contains more α-helices than the other dehalogenases. The dehalogenase activity of resting cells and Northern blot analyses both revealed that thedmlAanddbjAgenes were expressed under normal culture conditions in MAFF303099 and USDA110 strain cells, respectively.
Correlation of Phenotype with the Genotype of Egg-Contaminating
Salmonella enterica
Serovar Enteritidis
Authors: Morales Cesar A. , Porwollik Steffen , Frye Jonathan G. , Kinde Hailu , McClelland Michael , Guard-Bouldin Jean 
Published: August 2005

ABSTRACT

The genotype of
Salmonella enterica
serovar Enteritidis was correlated with the phenotype using DNA-DNA microarray hybridization, ribotyping, and Phenotype MicroArray analysis to compare three strains that differed in colony morphology and phage type. No DNA hybridization differences were found between two phage type 13A (PT13A) strains that varied in biofilm formation; however, the ribotype patterns were different. Both PT13A strains had DNA sequences similar to that of bacteriophage Fels2, whereas the PT4 genome to which they were compared, as well as a PT4 field isolate, had a DNA sequence with some similarity to the bacteriophage ST64b sequence. Phenotype MicroArray analysis indicated that the two PT13A strains and the PT4 field isolate had similar respiratory activity profiles at 37°C. However, the wild-type
S. enterica
serovar Enteritidis PT13A strain grew significantly better in 20% more of the 1,920 conditions tested when it was assayed at 25°C than the biofilm-forming PT13A strain grew. Statistical analysis of the respiratory activity suggested that
S. enterica
serovar Enteritidis PT4 had a temperature-influenced dimorphic metabolism which at 25°C somewhat resembled the profile of the biofilm-forming PT13A strain and that at 37°C the metabolism was nearly identical to that of the wild-type PT13A strain. Although it is possible that lysogenic bacteriophage alter the balance of phage types on a farm either by lytic competition or by altering the metabolic processes of the host cell in subtle ways, the different physiologies of the
S. enterica
serovar Enteritidis strains correlated most closely with minor, rather than major, genomic changes. These results strongly suggest that the pandemic of egg-associated human salmonellosis that came into prominence in the 1980s is primarily an example of bacterial adaptive radiation that affects the safety of the food supply.
Expression of the
psl
Operon in
Pseudomonas aeruginosa
PAO1 Biofilms: PslA Performs an Essential Function in Biofilm Formation
Authors: Overhage Jörg , Schemionek Mirle , Webb Jeremy S. , Rehm Bernd H. A. 
Published: August 2005

ABSTRACT

The
psl
gene cluster, comprising 15 cotranscribed genes from
Pseudomonas aeruginosa
, was recently identified as being involved in exopolysaccharide biosynthesis and biofilm formation. In this study, we investigated the regulation of the
psl
gene cluster and the function of the first gene in this cluster, the
pslA
gene. PslA shows strong similarities to UDP-glucose lipid carriers. An isogenic marker-free
pslA
deletion mutant of
P. aeruginosa
PAO1 deficient in attachment and biofilm formation was used for complementation studies. The expression of only the
pslA
gene, comprising a coding region of 1,437 bp, restored the biofilm-forming phenotype of the wild type, indicating that PslA is required for biofilm formation by nonmucoid
P. aeruginosa
. The promoter region of the
psl
gene cluster, which encodes PslA-PslO, was identified by rapid amplification of cDNA 5′ ends. Promoter assays using transcriptional fusions to
lacZ
and
gfp
indicated a constitutive expression of the
psl
cluster in planktonic cells and a highly regulated and localized expression in biofilms, respectively. Expression of the
psl
cluster in biofilms was almost exclusively found in the centers of microcolonies, as revealed by confocal laser scanning microscopy. These data suggest that constitutive expression of the
psl
operon enables efficient attachment to surfaces and that regulated localized
psl
operon expression is required for biofilm differentiation.
Allophanate Hydrolase, Not Urease, Functions in Bacterial Cyanuric Acid Metabolism
Authors: Cheng Gang , Shapir Nir , Sadowsky Michael J. , Wackett Lawrence P. 
Published: August 2005

ABSTRACT

Growth substrates containing an
s
-triazine ring are typically metabolized by bacteria to liberate 3 mol of ammonia via the intermediate cyanuric acid. Over a 25-year period, a number of original research papers and reviews have stated that cyanuric acid is metabolized in two steps to the 2-nitrogen intermediate urea. In the present study, allophanate, not urea, was shown to be the 2-nitrogen intermediate in cyanuric acid metabolism in all the bacteria examined. Six different experimental results supported this conclusion: (i) synthetic allophanate was shown to readily decarboxylate to form urea under acidic extraction and chromatography conditions used in previous studies; (ii) alkaline extraction methods were used to stabilize and detect allophanate in bacteria actively metabolizing cyanuric acid; (iii) the kinetic course of allophanate formation and disappearance was consistent with its being an intermediate in cyanuric acid metabolism, and no urea was observed in those experiments; (iv) protein extracts from cells grown on cyanuric acid contained allophanate hydrolase activity; (v) genes encoding the enzymes AtzE and AtzF, which produce and hydrolyze allophanate, respectively, were found in several cyanuric acid-metabolizing bacteria; and (vi) TrzF, an AtzF homolog found in
Enterobacter cloacae
strain 99, was cloned, expressed in
Escherichia coli
, and shown to have allophanate hydrolase activity. In addition, we have observed that there are a large number of genes homologous to
atzF
and
trzF
distributed in phylogenetically distinct bacteria. In total, the data indicate that
s
-triazine metabolism in a broad class of bacteria proceeds through allophanate via allophanate hydrolase, rather than through urea using urease.
Use of
Saccharomyces cerevisiae
BLYES Expressing Bacterial Bioluminescence for Rapid, Sensitive Detection of Estrogenic Compounds
Authors: Sanseverino John , Gupta Rakesh K. , Layton Alice C. , Patterson Stacey S. , Ripp Steven A. , Saidak Leslie , Simpson Michael L. , Schultz T. Wayne , Sayler Gary S. 
Published: August 2005

ABSTRACT

An estrogen-inducible bacterial
lux
-based bioluminescent reporter was developed in
Saccharomyces cerevisiae
for applications in chemical sensing and environmental assessment of estrogen disruptor activity. The strain, designated
S. cerevisiae
BLYES, was constructed by inserting tandem estrogen response elements between divergent yeast promoters GPD and ADH1 on pUTK401 (formerly pUA12B7) that constitutively express
luxA
and
luxB
to create pUTK407. Cotransformation of this plasmid with a second plasmid (pUTK404) containing the genes required for aldehyde synthesis (
luxCDE
) and FMN reduction (
frp
) yielded a bioluminescent bioreporter responsive to estrogen-disrupting compounds. For validation purposes, results with strain BLYES were compared to the colorimetric-based estrogenic assay that uses the yeast
lac
Z reporter strain (YES). Strains BLYES and YES were exposed to 17β-estradiol over the concentration range of 1.2 × 10
−8
through 5.6 × 10
−12
M. Calculated 50% effective concentration values from the colorimetric and bioluminescence assays (
n
= 7) were similar at (4.4 ± 1.1) × 10
−10
and (2.4 ± 1.0) × 10
−10
M, respectively. The lower and upper limits of detection for each assay were also similar and were approximately 4.5 × 10
−11
to 2.8 × 10
−9
M. Bioluminescence was observed in as little as 1 h and reached its maximum in 6 h. In comparison, the YES assay required a minimum of 3 days for results. Strain BLYES fills the niche for rapid, high-throughput screening of estrogenic compounds and has the ability to be used for remote, near-real-time monitoring of estrogen-disrupting chemicals in the environment.
Characterization of Botulinum Progenitor Toxins by Mass Spectrometry
Authors: Hines Harry B. , Lebeda Frank , Hale Martha , Brueggemann Ernst E. 
Published: August 2005

ABSTRACT

Botulinum toxin analysis has renewed importance. This study included the use of nanochromatography-nanoelectrospray-mass spectrometry/mass spectrometry to characterize the protein composition of botulinum progenitor toxins and to assign botulinum progenitor toxins to their proper serotype and strain by using currently available sequence information.
Clostridium botulinum
progenitor toxins from strains Hall, Okra, Stockholm, MDPH, Alaska, and Langeland and 89 representing serotypes A through G, respectively, were reduced, alkylated, digested with trypsin, and identified by matching the processed product ion spectra of the tryptic peptides to proteins in accessible databases. All proteins known to be present in progenitor toxins from each serotype were identified. Additional proteins, including flagellins, ORF-X1, and neurotoxin binding protein, not previously reported to be associated with progenitor toxins, were present also in samples from several serotypes. Protein identification was used to assign toxins to a serotype and strain. Serotype assignments were accurate, and strain assignments were best when either sufficient nucleotide or amino acid sequence data were available. Minor difficulties were encountered using neurotoxin-associated protein identification for assigning serotype and strain. This study found that combined nanoscale chromatographic and mass spectrometric techniques can characterize
C. botulinum
progenitor toxin protein composition and that serotype/strain assignments based upon these proteins can provide accurate serotype and, in most instances, strain assignments using currently available information. Assignment accuracy will continue to improve as more nucleotide/amino acid sequence information becomes available for different botulinum strains.
Isolation and Characterization of a Genetically Tractable Photoautotrophic Fe(II)-Oxidizing Bacterium,
Rhodopseudomonas palustris
Strain TIE-1
Authors: Jiao Yongqin , Kappler Andreas , Croal Laura R. , Newman Dianne K. 
Published: August 2005

ABSTRACT

We report the isolation and characterization of a phototrophic ferrous iron [Fe(II)]-oxidizing bacterium named TIE-1 that differs from other Fe(II)-oxidizing phototrophs in that it is genetically tractable. Under anaerobic conditions, TIE-1 grows photoautotrophically with Fe(II), H
2
, or thiosulfate as the electron donor and photoheterotrophically with a variety of organic carbon sources. TIE-1 also grows chemoheterotrophically in the dark. This isolate appears to be a new strain of the purple nonsulfur bacterial species
Rhodopseudomonas palustris
, based on physiological and phylogenetic analysis. Fe(II) oxidation is optimal at pH 6.5 to 6.9. The mineral products of Fe(II) oxidation are pH dependent: below pH 7.0 goethite (α-FeOOH) forms, and above pH 7.2 magnetite (Fe
3
O
4
) forms. TIE-1 forms colonies on agar plates and is sensitive to a variety of antibiotics. A hyperactive mariner transposon is capable of random insertion into the chromosome with a transposition frequency of ∼10
−5
. To identify components involved in phototrophic Fe(II) oxidation, mutants of TIE-1 were generated by transposon mutagenesis and screened for defects in Fe(II) oxidation in a cell suspension assay. Among approximately 12,000 mutants screened, 6 were identified that are specifically impaired in Fe(II) oxidation. Five of these mutants have independent disruptions in a gene that is predicted to encode an integral membrane protein that appears to be part of an ABC transport system; the sixth mutant has an insertion in a gene that is a homolog of CobS, an enzyme involved in cobalamin (vitamin B
12
) biosynthesis.