bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salmonella enterica
Virulence Genes Are Required for Bacterial Attachment to Plant Tissue
Authors: Barak Jeri D. , Gorski Lisa , Naraghi-Arani Pejman , Charkowski Amy O. 
Published: October 2005

ABSTRACT

Numerous
Salmonella enterica
food-borne illness outbreaks have been associated with contaminated vegetables, in particular sprouted seeds, and the incidence of reported contamination has steadily risen. In order to understand the physiology of
S. enterica
serovar Newport on plants, a screen was developed to identify transposon mutants that were defective in attachment to alfalfa sprouts. Twenty independent mutants from a pool of 6,000 were selected for reduced adherence to alfalfa sprouts. Sixty-five percentage of these mutants had insertions in uncharacterized genes. Among the characterized genes were strains with insertions in the intergenic region between
agfB
, the surface-exposed aggregative fimbria (curli) nucleator, and
agfD
, a transcriptional regulator of the LuxR superfamily, and
rpoS
, the stationary-phase sigma factor. Both AgfD and RpoS have been reported to regulate curli and cellulose production and RpoS regulates other adhesins such as pili. The intergenic and
rpoS
mutants were reduced in initial attachment to alfalfa sprouts by 1 log unit compared to the wild type. Mutations of
agfA
, curli subunit, and
agfB
in
S. enterica
serovar Enteritidis differentially affected attachment to plant tissue. The
agfA
mutation was not reduced in ability to attach to or colonize alfalfa sprouts, whereas the
agfB
mutation was reduced. Thus,
agfB
alone can play a role in attachment of
S. enterica
to plant tissue. These results reveal that
S. enterica
genes important for virulence in animal systems are also required for colonization of plants, a secondary host that can serve as a vector of
S. enterica
from animal to animal.
Quantifying Transmission of
Campylobacter
spp. among Broilers
Authors: Van Gerwe T. J. W. M. , Bouma A. , Jacobs-Reitsma W. F. , van den Broek J. , Klinkenberg D. , Stegeman J. A. , Heesterbeek J. A. P. 
Published: October 2005

ABSTRACT

Campylobacter
species are frequently identified as a cause of human gastroenteritis, often from eating or mishandling contaminated poultry products. Quantitative knowledge of transmission of
Campylobacter
in broiler flocks is necessary, as this may help to determine the moment of introduction of
Campylobacter
in broiler flocks more precisely. The aim of this study was to determine the transmission rate parameter in broiler flocks. Four experiments were performed, each with four
Campylobacter-
inoculated chicks housed with 396 contact chicks per group. Colonization was monitored by regularly testing fecal samples for
Campylobacter
. A mathematical model was used to quantify the transmission rate, which was determined to be 1.04 new cases per colonized chick per day. This would imply that, for example, in a flock of 20,000 broilers, the prevalence of
Campylobacter
would increase from 5% to 95% within 6 days after
Campylobacter
introduction. The model and the estimated transmission rate parameter can be used to develop a suitable sampling scheme to determine transmission in commercial broiler flocks, to estimate whether control measures can reduce the transmission rate, or to estimate when
Campylobacter
was introduced into a colonized broiler flock on the basis of the time course of transmission in the flock.
Development of a Functional Genomics Platform for
Sinorhizobium meliloti
: Construction of an ORFeome
Authors: Schroeder Brenda K. , House Brent L. , Mortimer Michael W. , Yurgel Svetlana N. , Maloney Scott C. , Ward Kristel L. , Kahn Michael L. 
Published: October 2005

ABSTRACT

The nitrogen-fixing, symbiotic bacterium
Sinorhizobium meliloti
reduces molecular dinitrogen to ammonia in a specific symbiotic context, supporting the nitrogen requirements of various forage legumes, including alfalfa. Determining the DNA sequence of the
S. meliloti
genome was an important step in plant-microbe interaction research, adding to the considerable information already available about this bacterium by suggesting possible functions for many of the >6,200 annotated open reading frames (ORFs). However, the predictive power of bioinformatic analysis is limited, and putting the role of these genes into a biological context will require more definitive functional approaches. We present here a strategy for genetic analysis of
S. meliloti
on a genomic scale and report the successful implementation of the first step of this strategy by constructing a set of plasmids representing 100% of the 6,317 annotated ORFs cloned into a mobilizable plasmid by using efficient PCR and recombination protocols. By using integrase recombination to insert these ORFs into other plasmids in vitro or in vivo (B. L. House et al., Appl. Environ. Microbiol. 70:2806-2815, 2004), this ORFeome can be used to generate various specialized genetic materials for functional analysis of
S. meliloti
, such as operon fusions, mutants, and protein expression plasmids. The strategy can be generalized to many other genome projects, and the
S. meliloti
clones should be useful for investigators wanting an accessible source of cloned genes encoding specific enzymes.
Inducible Gene Expression in
Lactobacillus reuteri
LTH5531 during Type II Sourdough Fermentation
Authors: Dal Bello Fabio , Walter Jens , Roos Stefan , Jonsson Hans , Hertel Christian 
Published: October 2005

ABSTRACT

Lactobacillus reuteri
LTH5531 is a dominant member of the microbiota of type II sourdough fermentations. To investigate the genetic background of the ecological performance of LTH5531, in vivo expression technology was used to identify promoters that show elevated levels of expression during growth of this organism in a type II sourdough fermentation. Thirty-eight sourdough-induced fusions were detected, and 29 genes could be identified on the basis of the available sequence information. Four genes encoded stress-related functions (e.g., acid and general stress response), reflecting the harsh conditions prevailing during sourdough fermentation. Further, eight genes were involved in acquisition and synthesis of amino acids and nucleotides, indicating their limited availability in sourdough. The remaining genes were either part of functionally unrelated pathways or encoded hypothetical proteins. The identification of a putative proteinase and a component of the arginine deiminase pathway is of technological interest, as they are potentially involved in the formation of aroma precursors. Our study allowed insight into the transcriptional response of
Lactobacillus reuteri
to the dough environment, which establishes the molecular basis to investigate bacterial properties that are likely to contribute to the ecological performance of the organism and influence the final outcome of the fermentation.
Genetic Diversity of
Listeria monocytogenes
Strains from a High-Prevalence Dairy Farm
Authors: Borucki Monica K. , Gay Clive C. , Reynolds James , McElwain Katherine L. , Kim So Hyun , Call Douglas R. , Knowles Donald P. 
Published: October 2005

ABSTRACT

Listeria monocytogenes
is a significant food-borne human and veterinary pathogen. Contaminated silage commonly leads to disease in livestock, but the pervasive nature of the bacterium can make it difficult to identify the source of infection. An investigation of bovine listeriosis that occurred on a Pacific Northwest dairy farm (“farm A”) revealed that the clinical strain was closely related to fecal strains from asymptomatic cows, and that farm environment was heavily contaminated with a diversity of
L. monocytogenes
strains. In addition, the farm A clinical strain was closely related to clinical and environmental strains obtained 1 year prior from a second Northwest dairy farm (“farm B”). To investigate the source(s) of contamination on farm A, environmental samples were collected from farm A at two time points. Pulsed-field gel electrophoresis characterization of 538 isolates obtained from that farm identified 57 different AscI pulsovars. Fecal isolates obtained from individual cows were the most genetically diverse, with up to 94% of fecal samples containing more than one pulsovar. The maximum numbers of pulsovars and serotypes isolated from a fecal sample of one cow were 6 and 4, respectively. Serotype 1/2a was isolated most frequently at both time points. Microarray genotyping of bovine listeriosis, fecal, and silage strains from both farms identified four probes that differentiated listeriosis strains from environmental strains; however, no probe was common to both bovine listeriosis strains.
Ecological Differentiation within a Cosmopolitan Group of Planktonic Freshwater Bacteria (SOL Cluster,
Saprospiraceae
,
Bacteroidetes
)
Authors: Schauer Michael , Kamenik Christian , Hahn Martin W. 
Published: October 2005

ABSTRACT
Members of the monophyletic SOL cluster are large filamentous bacteria inhabiting the pelagic zone of many freshwater habitats. The abundances of SOL bacteria and compositions of SOL communities in samples from 115 freshwater ecosystems around the globe were determined by fluorescence in situ hybridization with cluster- and subcluster-specific oligonucleotide probes. The vast majority (73%) of sampled ecosystems harbored SOL bacteria, and all three previously described SOL subclusters (LD2, HAL, and GKS2-217) were detected. The morphometric and chemicophysical parameters and trophic statuses of ecosystems were related to the occurrence and subcluster-specific composition of SOL bacteria by multivariate statistical methods. SOL bacteria did not occur in acidic lakes (pH < 6), and their abundance was negatively related to high trophy and pH. The subcluster-specific variation in the compositions of SOL communities could be related to the pH, electrical conductivity, altitude, and trophic status of ecosystems. All three known SOL subclusters differed in respect to their tolerated ranges of pH and conductivity. Complete niche separation was observed between the vicarious subclusters GKS2-217 and LD2; the former occurred in soft-water lakes, whereas the latter was found in a broad range of hard-water habitats. The third subgroup (HAL) showed a wide environmental tolerance and was usually found sympatrically with the LD2 or GKS2-217 subcluster. Ecological differentiation of SOL bacteria at the subcluster level was most probably driven by differential adaptation to water chemistry. The distribution of the two vicarious taxa seems to be predominantly controlled by the geological backgrounds of the catchment areas of the habitats.
Characterization of a
Corynebacterium glutamicum
Lactate Utilization Operon Induced during Temperature-Triggered Glutamate Production
Authors: Stansen Corinna , Uy Davin , Delaunay Stephane , Eggeling Lothar , Goergen Jean-Louis , Wendisch Volker F. 
Published: October 2005

ABSTRACT

Gene expression changes of glutamate-producing
Corynebacterium glutamicum
were identified in transcriptome comparisons by DNA microarray analysis. During glutamate production induced by a temperature shift,
C. glutamicum
strain 2262 showed significantly higher mRNA levels of the NCgl2816 and NCgl2817 genes than its non-glutamate-producing derivative 2262NP. Reverse transcription-PCR analysis showed that the two genes together constitute an operon. NCgl2816 putatively codes for a lactate permease, while NCgl2817 was demonstrated to encode quinone-dependent
l
-lactate dehydrogenase, which was named LldD.
C. glutamicum
LldD displayed Michaelis-Menten kinetics for the substrate
l
-lactate with a

K
m

of about 0.51 mM. The specific activity of LldD was about 10-fold higher during growth on
l
-lactate or on an
l
-lactate-glucose mixture than during growth on glucose,
d
-lactate, or pyruvate, while the specific activity of quinone-dependent
d
-lactate dehydrogenase differed little with the carbon source. RNA levels of NCgl2816 and
lldD
were about 18-fold higher during growth on
l
-lactate than on pyruvate. Disruption of the NCgl2816-
lldD
operon resulted in loss of the ability to utilize
l
-lactate as the sole carbon source. Expression of
lldD
restored
l
-lactate utilization, indicating that the function of the permease gene NCgl2816 is dispensable, while LldD is essential, for growth of
C. glutamicum
on
l
-lactate.
Metabolism of Carbaryl via 1,2-Dihydroxynaphthalene by Soil Isolates
Pseudomonas
sp. Strains C4, C5, and C6
Authors: Swetha Vandana P. , Phale Prashant S. 
Published: October 2005

ABSTRACT

Pseudomonas
sp. strains C4, C5, and C6 utilize carbaryl as the sole source of carbon and energy. Identification of 1-naphthol, salicylate, and gentisate in the spent media; whole-cell O
2
uptake on 1-naphthol, 1,2-dihydroxynaphthalene, salicylaldehyde, salicylate, and gentisate; and detection of key enzymes, viz, carbaryl hydrolase, 1-naphthol hydroxylase, 1,2-dihydroxynaphthalene dioxygenase, and gentisate dioxygenase, in the cell extract suggest that carbaryl is metabolized via 1-naphthol, 1,2-dihydroxynaphthalene, and gentisate. Here, we demonstrate 1-naphthol hydroxylase and 1,2-dihydroxynaphthalene dioxygenase activities in the cell extracts of carbaryl-grown cells. 1-Naphthol hydroxylase is present in the membrane-free cytosolic fraction, requires NAD(P)H and flavin adenine dinucleotide, and has optimum activity in the pH range 7.5 to 8.0. Carbaryl-degrading enzymes are inducible, and maximum induction was observed with carbaryl. Based on these results, the proposed metabolic pathway is carbaryl → 1-naphthol → 1,2-dihydroxynaphthalene → salicylaldehyde → salicylate → gentisate → maleylpyruvate.
Role of the Regulatory GenerirAin the Transcriptional Response ofSinorhizobium melilotito Iron Limitation
Authors: Chao Tzu-Chiao , Buhrmester Jens , Hansmeier Nicole , Pühler Alfred , Weidner Stefan 
Published: October 2005

ABSTRACTA regulatory network ofSinorhizobium melilotigenes involved in adaptation to iron-limiting conditions and the involvement of the rhizobial iron regulator gene (rirA) were analyzed by mutation and microarray analyses. A constructedS. meliloti rirAmutant exhibited growth defects and enhanced H2O2sensitivity in the presence of iron, but symbiotic nitrogen fixation was not affected. To identify iron-responsive and RirA-regulatedS. melilotigenes, a transcriptome approach using whole-genome microarrays was used. Altogether, 45 genes were found to be jointly derepressed by mutation ofrirAand under different iron-limited conditions. As expected, a number of genes involved in iron transport (e.g.,hmuPSTU,shmR,rhbABCDEF,rhtX, andrhtA) and also genes with predicted functions in energy metabolism (e.g.,fixN3,fixP3, andqxtAB) and exopolysaccharide production (e.g.,exoYandexoN) were found in this group of genes. In addition, the iron deficiency response ofS. melilotialso involvedrirA-independent expression changes, including repression of theS. melilotiflagellar regulon. Finally, the RirA modulon also includes genes that are not iron responsive, including a gene cluster putatively involved in Fe-S cluster formation (sufA,sufS,sufD,sufC, andsufB).
Comparison of
Bacteroides-Prevotella
16S rRNA Genetic Markers for Fecal Samples from Different Animal Species
Authors: Fogarty Lisa R. , Voytek Mary A. 
Published: October 2005

ABSTRACT

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group
Bacteroides-Prevotella
as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of
Bacteroides-Prevotella
community T-RFLP profiles indicates that
Bacteroides-Prevotella
populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying
Bacteroides-Prevotella
molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.
Restoration of Gibberellin Production in
Fusarium proliferatum
by Functional Complementation of Enzymatic Blocks
Authors: Malonek S. , Rojas M. C. , Hedden P. , Hopkins P. , Tudzynski B. 
Published: October 2005

ABSTRACT

Nine biological species, or mating populations (MPs), denoted by letters A to I, and at least 29 anamorphic
Fusarium
species have been identified within the
Gibberella fujikuroi
species complex. Members of this species complex are the only species of the genus
Fusarium
that contain the gibberellin (GA) biosynthetic gene cluster or at least parts of it. However, the ability of fusaria to produce GAs is so far restricted to
Fusarium fujikuroi
, although at least six other MPs contain all the genes of the GA biosynthetic gene cluster. Members of
Fusarium proliferatum
, the closest related species, have lost the ability to produce GAs as a result of the accumulation of several mutations in the coding and 5′ noncoding regions of genes
P450
-
4
and
P450
-
1
, both encoding cytochrome P450 monooxygenases, resulting in metabolic blocks at the early stages of GA biosynthesis. In this study, we have determined additional enzymatic blocks at the first specific steps in the GA biosynthesis pathway of
F. proliferatum
: the synthesis of geranylgeranyl diphosphate and the synthesis of
ent
-kaurene. Complementation of these enzymatic blocks by transferring the corresponding genes from GA-producing
F. fujikuroi
to
F. proliferatum
resulted in the restoration of GA production. We discuss the reasons for
Fusarium
species outside the
G. fujikuroi
species complex having no GA biosynthetic genes, whereas species distantly related to
Fusarium
, e.g.,
Sphaceloma
spp. and
Phaeosphaeria
spp., produce GAs.
Investigation of Specific Substitutions in Virulence Genes Characterizing Phenotypic Groups of Low-Virulence Field Strains of
Listeria monocytogenes
Authors: Roche S. M. , Gracieux P. , Milohanic E. , Albert I. , Virlogeux-Payant I. , Témoin S. , Grépinet O. , Kerouanton A. , Jacquet C. , Cossart P. , Velge P. 
Published: October 2005

ABSTRACT

Several models have shown that virulence varies from one strain of
Listeria monocytogenes
to another, but little is known about the cause of low virulence. Twenty-six field
L. monocytogenes
strains were shown to be of low virulence in a plaque-forming assay and in a subcutaneous inoculation test in mice. Using the results of cell infection assays and phospholipase activities, the low-virulence strains were assigned to one of four groups by cluster analysis and then virulence-related genes were sequenced. Group I included 11 strains that did not enter cells and had no phospholipase activity. These strains exhibited a mutated PrfA; eight strains had a single amino acid substitution, PrfAK220T, and the other three had a truncated PrfA, PrfAΔ174-237. These genetic modifications could explain the low virulence of group I strains, since mutated PrfA proteins were inactive. Group II and III strains entered cells but did not form plaques. Group II strains had low phosphatidylcholine phospholipase C activity, whereas group III strains had low phosphatidylinositol phospholipase C activity. Several substitutions were observed for five out of six group III strains in the
plcA
gene and for one out of three group II strains in the
plcB
gene. Group IV strains poorly colonized spleens of mice and were practically indistinguishable from fully virulent strains on the basis of the above-mentioned in vitro criteria. These results demonstrate a relationship between the phenotypic classification and the genotypic modifications for at least group I and III strains and suggest a common evolution of these strains within a group.
Intestinal Bacterial Communities That Produce Active Estrogen-Like Compounds Enterodiol and Enterolactone in Humans
Authors: Clavel Thomas , Henderson Gemma , Alpert Carl-Alfred , Philippe Catherine , Rigottier-Gois Lionel , Doré Joël , Blaut Michael 
Published: October 2005

ABSTRACT

Lignans are dietary diphenolic compounds which require activation by intestinal bacteria to exert possible beneficial health effects. The intestinal ecosystem plays a crucial role in lignan metabolism, but the organisms involved are poorly described. To characterize the bacterial communities responsible for secoisolariciresinol (SECO) activation, i.e., the communities that produce the enterolignans enterodiol (ED) and enterolactone (EL), a study with 24 human subjects was undertaken. SECO activation was detected in all tested fecal samples. The intestinal bacteria involved in ED production were part of the dominant microbiota (6 × 10
8
CFU g
−1
), as revealed by most-probable-number enumerations. Conversely, organisms that catalyzed the formation of EL occurred at a mean concentration of approximately 3 × 10
5
CFU g
−1
. Women tended to have higher concentrations of both ED- and EL-producing organisms than men. Significantly larger amounts of EL were produced by fecal dilutions from individuals with moderate to high concentrations of EL-producing bacteria. Two organisms able to demethylate and dehydroxylate SECO were isolated from human feces. Based on 16S rRNA gene sequence analyses, they were named
Peptostreptococcus productus
SECO-Mt75m3 and
Eggerthella lenta
SECO-Mt75m2. A new 16S rRNA-targeted oligonucleotide probe specific for
P. productus
and related species was designed and further used in fluorescent in situ hybridization experiments, along with five additional group-specific probes. Significantly higher proportions of
P. productus
and related species (
P
= 0.012), as well as bacteria belonging to the
Atopobium
group (
P
= 0.035), were typical of individuals with moderate to high concentrations of EL-producing communities.
A
Lactobacillus acidophilus
Strain of Human Gastrointestinal Microbiota Origin Elicits Killing of Enterovirulent
Salmonella enterica
Serovar Typhimurium by Triggering Lethal Bacterial Membrane Damage
Authors: Coconnier-Polter Marie-Hélène , Liévin-Le Moal Vanessa , Servin Alain L. 
Published: October 2005

ABSTRACT

The human gastrointestinal microbiota produces antagonistic activities against gastrointestinal bacterial pathogens. We undertook a study to investigate the mechanism(s) by which a
Lactobacillus acidophilus
strain of human microbiota origin antagonizes the gram-negative enteroinvasive pathogen
Salmonella enterica
serovar Typhimurium. We showed that the cell-free culture supernatant of
L. acidophilus
strain LB (LB-CFCS) induced the following effects in
S. enterica
SL1344: (i) a decrease in intracellular ATP that paralleled bacterial death, (ii) the release of lipopolysaccharide, (iii) permeabilization of the bacterial membrane, and (iv) an increase in the sensitivity of
Salmonella
to the lytic action of sodium dodecyl sulfate. Finally, we showed using two mutant strains of
Salmonella
, PhoP MS7953s and PmrA JKS1170, that the two-component regulatory systems PhoP-PhoQ and PmrA-PmrB that regulate the mechanisms of resistance to antibacterial agents in
Salmonella
did not influence the anti-
Salmonella
effect of LB-CFCS.