bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
Listeria monocytogenes
Homolog of the
Escherichia coli era
Gene Is Involved in Adhesion to Inert Surfaces
Authors: Auvray Frédéric , Chassaing Danielle , Duprat Cécile , Carpentier Brigitte 
Published: October 2007

ABSTRACT

Two transposon-insertional mutants of
Listeria monocytogenes
showing smaller viable surface-attached cell populations after disinfection with
N
,
N
-didecyl-
N
,
N
-dimethylammonium chloride were identified. In both mutants, transposon Tn
917-lac
was found to be inserted into the same gene, lmo1462, which is homologous to the essential
Escherichia coli era
gene. Both
L. monocytogenes
lmo1462-disrupted mutants displayed lower growth rates, as was also shown for several
E. coli era
mutants, and the lmo1462 gene was able to complement the growth defect of an
E. coli era
mutant. We showed that the disruption of lmo1462 decreased the ability of
L. monocytogenes
cells to adhere to stainless steel. Our results suggest that this
era
-like gene is involved in adhesion and contributes to the presence of
L. monocytogenes
on surfaces.
Effect of CO
2
on Colony Development by
Bifidobacterium
Species
Authors: Kawasaki Shinji , Nagasaku Masahiro , Mimura Tsuyoshi , Katashima Hitomi , Ijyuin Susumu , Satoh Takumi , Niimura Youichi 
Published: October 2007

ABSTRACT

This report investigates the requirement for CO
2
for colony formation by
Bifidobacterium
species in both anoxic and oxic environments. All tested
Bifidobacterium
species exhibited difficulty in developing colonies in an atmosphere of 100% N
2
but developed well when 1% CO
2
was present. In the presence of CO
2
, the oxygen tolerance of the tested species was not improved. In the absence of CO
2
, only
B. boum
, a microaerophilic species, could develop colonies under an N
2
-based 5% O
2
atmosphere, indicating that while CO
2
is not an essential factor for colony development, both CO
2
and O
2
have stimulatory effects on
B. boum
colony development.
Detection of Bacteriophage-Infected Cells of
Lactococcus lactis
by Using Flow Cytometry
Authors: Michelsen Ole , Cuesta-Dominguez Álvaro , Albrechtsen Bjarne , Jensen Peter Ruhdal 
Published: October 2007

ABSTRACT

Bacteriophage infection in dairy fermentation constitutes a serious problem worldwide. We have studied bacteriophage infection in
Lactococcus lactis
by using the flow cytometer. The first effect of the infection of the bacterium is a change from cells in chains toward single cells. We interpret this change as a consequence of a cease in cell growth, while the ongoing cell divisions leave the cells as single cells. Late in the infection cycle, cells with low-density cell walls appear, and these cells can be detected on cytograms of light scatter versus, for instance, fluorescence of stained DNA. We describe a new method for detection of phage infection in
Lactococcus lactis
dairy cultures. The method is based on flow cytometric detection of cells with low-density cell walls. The method allows fast and early detection of phage-infected bacteria, independently of which phage has infected the culture. The method can be performed in real time and therefore increases the chance of successful intervention in the fermentation process.
Growth Characteristics of
Brevibacterium
,
Corynebacterium
,
Microbacterium
, and
Staphylococcus
spp. Isolated from Surface-Ripened Cheese
Authors: Mounier Jérôme , Rea Mary C. , O'Connor Paula M. , Fitzgerald Gerald F. , Cogan Timothy M. 
Published: October 2007

ABSTRACT

The growth characteristics of five bacteria,
Brevibacterium aurantiacum
1-16-58,
Corynebacterium casei
DPC 5298
T
,
Corynebacterium variabile
DPC 5310,
Microbacterium gubbeenense
DPC 5286
T
, and
Staphylococcus saprophyticus
4E61, all of which were isolated from the surface of smear cheese, were studied in complex and chemically defined media. All of the coryneforms, except
M. gubbeenense
, grew in 12% salt, while
B. aurantiacum
and
S. saprophyticus
grew in 15% salt. All five bacteria assimilated lactate in a semisynthetic medium, and none of the coryneform bacteria assimilated lactose. Glucose assimilation was poor, except by
S. saprophyticus
and
C. casei
. Five to seven amino acids were assimilated by the coryneforms and 12 by
S. saprophyticus
. Glutamate, phenylalanine, and proline were utilized by all five bacteria, whereas utilization of serine, threonine, aspartate, histidine, alanine, arginine, leucine, isoleucine, and glycine depended on the organism. Growth of
C. casei
restarted after addition of glutamate, proline, serine, and lactate at the end of the exponential phase, indicating that these amino acids and lactate can be used as energy sources. Pantothenic acid was essential for the growth of
C. casei
and
M. gubbeenense
. Omission of biotin reduced the growth of
B. aurantiacum
,
C. casei
, and
M. gubbeenense
. All of the bacteria contained lactate dehydrogenase activity (with both pyruvate and lactate as substrates) and glutamate pyruvate transaminase activity but not urease activity.
Molecular Analysis of the Diversity of Sulfate-Reducing and Sulfur-Oxidizing Prokaryotes in the Environment, Using
aprA
as Functional Marker Gene
Authors: Meyer Birte , Kuever Jan 
Published: October 2007

ABSTRACT

The dissimilatory adenosine-5′-phosposulfate reductase is a key enzyme of the microbial sulfate reduction and sulfur oxidation processes. Because the alpha- and beta-subunit-encoding genes,
aprBA
, are highly conserved among sulfate-reducing and sulfur-oxidizing prokaryotes, they are most suitable for molecular profiling of the microbial community structure of the sulfur cycle in environment. In this study, a new
aprA
gene-targeting assay using a combination of PCR and denaturing gradient gel electrophoresis is presented. The screening of sulfate-reducing and sulfur-oxidizing reference strains as well as the analyses of environmental DNA from diverse habitats (e.g., microbial mats, invertebrate tissue, marine and estuarine sediments, and filtered hydrothermal water) by the new primer pair revealed an improved microbial diversity coverage and less-pronounced template-to-PCR product bias in direct comparison to those of the previously published primer set (B. Deplancke, K. R. Hristova, H. A. Oakley, V. J. McCracken, R. Aminov, R. I. Mackie, and H. R. Gaskins, Appl. Environ. Microbiol. 66:2166-2174, 2000). The concomitant molecular detection of sulfate-reducing and sulfur-oxidizing prokaryotes was confirmed. The new assay was applied in comparison with the 16S rRNA gene-based analysis to investigate the microbial diversity of the sulfur cycle in sediment, seawater, and manganese crust samples from four study sites in the area of the Lesser Antilles volcanic arc, Caribbean Sea (Caribflux project). The
aprA
gene-based approach revealed putative sulfur-oxidizing
Alphaproteobacteria
of chemolithoheterotrophic lifestyle to have been abundant in the nonhydrothermal sediment and water column. In contrast, the sulfur-based microbial community that inhabited the surface of the volcanic manganese crust was more complex, consisting predominantly of putative chemolithoautotrophic sulfur oxidizers of the
Betaproteobacteria
and
Gammaproteobacteria
.
DNA Fingerprinting of Lactic Acid Bacteria in Sauerkraut Fermentations
Authors: Plengvidhya Vethachai , Breidt Fredrick , Lu Zhongjing , Fleming Henry P. 
Published: October 2007

ABSTRACT

Previous studies using traditional biochemical identification methods to study the ecology of commercial sauerkraut fermentations revealed that four species of lactic acid bacteria,
Leuconostoc mesenteroides, Lactobacillus plantarum, Pediococcus pentosaceus
, and
Lactobacillus brevis
, were the primary microorganisms in these fermentations. In this study, 686 isolates were collected from four commercial fermentations and analyzed by DNA fingerprinting. The results indicate that the species of lactic acid bacteria present in sauerkraut fermentations are more diverse than previously reported and include
Leuconostoc citreum, Leuconostoc argentinum, Lactobacillus paraplantarum, Lactobacillus coryniformis
, and
Weissella
sp. The newly identified species
Leuconostoc fallax
was also found. Unexpectedly, only two isolates of
P. pentosaceus
and 15 isolates of
L. brevis
were recovered during this study. A better understanding of the microbiota may aid in the development of low-salt fermentations, which may have altered microflora and altered sensory characteristics.
N
-(3-Hydroxyhexanoyl)-
l
-Homoserine Lactone Is the Biologically Relevant Quormone That Regulates the
phz
Operon of
Pseudomonas chlororaphis
Strain 30-84
Authors: Khan Sharik R. , Herman Jake , Krank Jessica , Serkova Natalie J. , Churchill Mair E. A. , Suga Hiroaki , Farrand Stephen K. 
Published: October 2007

ABSTRACT

Phenazine production by
Pseudomonas fluorescens
2-79 and
P. chlororaphis
isolates 30-84 and PCL1391 is regulated by quorum sensing through the activator PhzR and acyl-homoserine lactones (acyl-HSLs) synthesized by PhzI. PhzI from
P. fluorescens
2-79 produces five acyl-HSLs that include four 3-hydroxy species. Of these,
N
-(3-hydroxyhexanoyl)-HSL is the biologically relevant ligand for PhzR. The quorum-sensing systems of
P. chlororaphis
strains 30-84 and PCL1391 have been reported to produce and respond to
N
-(hexanoyl)-HSL. These differences were of interest since PhzI and PhzR of strain 2-79 share almost 90% sequence identity with orthologs from strains 30-84 and PCL1391. In this study, as assessed by thin-layer chromatography, the three strains produce almost identical complements of acyl-HSLs. The major species produced by
P. chlororaphis
30-84 were identified by mass spectrometry as 3-OH-acyl-HSLs with chain lengths of 6, 8, and 10 carbons. Heterologous bacteria expressing cloned
phzI
from strain 30-84 produced the four 3-OH acyl-HSLs in amounts similar to those seen for the wild type. Strain 30-84, but not strain 2-79, also produced
N
-(butanoyl)-HSL. A second acyl-HSL synthase of strain 30-84, CsaI, is responsible for the synthesis of this short-chain signal. Strain 30-84 accumulated
N
-(3-OH-hexanoyl)-HSL to the highest levels, more than 100-fold greater than that of
N
-(hexanoyl)-HSL. In titration assays, PhzR
30-84
responded to both
N
-(3-OH-hexanoyl)- and
N
-(hexanoyl)-HSL with equal sensitivities. However, only the 3-OH-hexanoyl signal is produced by strain 30-84 at levels high enough to activate PhzR. We conclude that strains 2-79, 30-84, and PCL1391 use
N
-(3-OH-hexanoyl)-HSL to activate PhzR.
Comparison of Cyanopeptolin Genes in
Planktothrix
,
Microcystis
, and
Anabaena
Strains: Evidence for Independent Evolution within Each Genus
Authors: Rounge Trine B. , Rohrlack Thomas , Tooming-Klunderud Ave , Kristensen Tom , Jakobsen Kjetill S. 
Published: October 2007

ABSTRACT

The major cyclic peptide cyanopeptolin 1138, produced by
Planktothrix
strain NIVA CYA 116, was characterized and shown to be structurally very close to the earlier-characterized oscillapeptin E. A cyanopeptolin gene cluster likely to encode the corresponding peptide synthetase was sequenced from the same strain. The 30-kb
oci
gene cluster contains two novel domains previously not detected in nonribosomal peptide synthetase gene clusters (a putative glyceric acid-activating domain and a sulfotransferase domain), in addition to seven nonribosomal peptide synthetase modules. Unlike in two previously described cyanopeptolin gene clusters from
Anabaena
and
Microcystis
, a halogenase gene is not present. The three cyanopeptolin gene clusters show similar gene and domain arrangements, while the binding pocket signatures deduced from the adenylation domain sequences and the additional tailoring domains vary. This suggests loss and gain of tailoring domains within each genus, after the diversification of the three clades, as major events leading to the present diversity. The ABC transporter genes associated with the cyanopeptolin gene clusters form a monophyletic clade and accordingly are likely to have evolved as part of the functional unit. Phylogenetic analyses of adenylation and condensation domains, including domains from cyanopeptolins and microcystins, show a closer similarity between the
Planktothrix
and
Microcystis
cyanopeptolin domains than between these and the
Anabaena
domain. No clear evidence of recombination between cyanopeptolins and microcystins could be detected. There were no strong indications of horizontal gene transfer of cyanopeptolin gene sequences across the three genera, supporting independent evolution within each genus.
Genome-Wide Screen ofSalmonellaGenes Expressed during Infection in Pigs, Using In Vivo Expression Technology
Authors: Huang Yanyan , Leming Christopher L. , Suyemoto Mitsu , Altier Craig 
Published: October 2007

ABSTRACTPigs are a food-producing species that readily carrySalmonellabut, in the great majority of cases, do not show clinical signs of disease. Little is known about the functions required bySalmonellato be maintained in pigs. We have devised a recombinase-based promoter-trapping strategy to identify genes with elevated expression during pig infection withSalmonella entericaserovar Typhimurium. A total of 55 clones with in vivo-induced promoters were selected from a genomic library of ∼10,000 randomSalmonellaDNA fragments fused to the recombinasecre, and the cloned DNA fragments were analyzed by sequencing. Thirty-one genes encoding proteins involved in bacterial adhesion and colonization (includingbcfA, hscA, rffG, andyciR), virulence (metL), heat shock (hscA), and a sensor of a two-component regulator (hydH) were identified. Among the 55 clones, 19 were isolated from both the tonsils and the intestine, while 23 were identified only in the intestine and 13 only in tonsils. High temperature and increased osmolarity were identified as environmental signals that induced in vivo-expressed genes, suggesting possible signals for expression.
Distribution and Replication of the Pathogenicity Plasmid pPATH in Diverse Populations of the Gall-Forming Bacterium
Pantoea agglomerans
Authors: Weinthal Dan M. , Barash Isaac , Panijel Mary , Valinsky Lea , Gaba Victor , Manulis-Sasson Shulamit 
Published: October 2007

ABSTRACT

Pantoea agglomerans
has been transformed from a commensal bacterium into two related gall-forming pathovars by acquisition of pPATH plasmids containing a pathogenicity island (PAI). This PAI harbors an
hrp/hrc
gene cluster, type III effectors, and phytohormone biosynthetic genes. DNA typing by pulsed-field gel electrophoresis revealed two major groups of
P. agglomerans
pv. gypsophilae and one group of
P. agglomerans
pv. betae. The pPATH plasmids of the different groups had nearly identical replicons (98% identity), and the RepA protein showed the highest level of similarity with IncN plasmid proteins. A series of plasmids, designated pRAs, in which the whole replicon region (2,170 bp) or deleted derivatives of it were ligated with
nptI
were generated for replicon analysis. A basic 929-bp replicon (pRA6) was sufficient for replication in
Escherichia coli
and in nonpathogenic
P. agglomerans
. However, the whole replicon region (pRA1) was necessary for expulsion of the pPATH plasmid, which resulted in the loss of pathogenicity. The presence of direct repeats in the replicon region suggests that the pPATH plasmid is an iteron plasmid and that the repeats may regulate its replication. The pPATH plasmids are nonconjugative but exhibit a broad host range, as shown by replication of pRA1 in
Erwinia, Pseudomonas
, and
Xanthomonas
. Restriction fragment length polymorphism analyses indicated that the PAIs in the two groups of
P. agglomerans
pv. gypsophilae are similar but different from those in
P. agglomerans
pv. betae. The results could indicate that the pPATH plasmids evolved from a common ancestral mobilizable plasmid that was transferred into different strains of
P. agglomerans
.
The Cyclic AMP Receptor Protein Modulates Colonial Morphology in
Vibrio cholerae
Authors: Liang Weili , Silva Anisia J. , Benitez Jorge A. 
Published: October 2007

ABSTRACT

Inactivation of the quorum-sensing regulator HapR causes
Vibrio cholerae
El Tor biotype strain C7258 to adopt a rugose colonial morphology that correlates with enhanced biofilm formation.
V. cholerae
mutants lacking the cyclic AMP (cAMP) receptor protein (CRP) produce very little HapR, which results in elevated expression of
Vibrio
exopolysaccharide (
vps
) genes and biofilm compared to the wild type. However, Δ
crp
mutants still exhibited smooth colonial morphology and expressed reduced levels of
vps
genes compared to isogenic
hapR
mutants. In this study we demonstrate that deletion of
crp
and
cya
(adenylate cyclase) converts a rugose Δ
hapR
mutant to a smooth one. The smooth Δ
hapR
Δ
crp
and Δ
hapR
Δ
cya
double mutants could be converted back to rugose by complementation with
crp
and
cya
, respectively. CRP was found to enhance the expression of VpsR, a strong activator of
vps
expression, but to diminish transcription of VpsT. Ectopic expression of VpsR in smooth Δ
hapR
Δ
crp
and Δ
hapR
Δ
cya
double mutants restored rugose colonial morphology. Lowering intracellular cAMP levels in a Δ
hapR
mutant by the addition of glucose diminished VpsR expression and colonial rugosity. On the basis of our results, we propose a model for the regulatory input of CRP on exopolysaccharide biosynthesis.
Epidemiology, Relative Invasive Ability, Molecular Characterization, and Competitive Performance of
Campylobacter jejuni
Strains in the Chicken Gut
Authors: Pope Christopher , Wilson Janet , Taboada Eduardo N. , MacKinnon Joanne , Felipe Alves Cristiano A. , Nash John H. E. , Rahn Kris , Tannock Gerald W. 
Published: October 2007

ABSTRACT

One hundred forty-one
Campylobacter jejuni
isolates from humans with diarrhea and 100 isolates from retailed poultry meat were differentiated by
flaA
typing. The bacteria were isolated in a specific geographical area (Dunedin) in New Zealand over a common time period. Twenty nine
flaA
types were detected, one of which (
flaA
restriction fragment length polymorphism type 15 [
flaA
-15]) predominated among isolates from humans (∼30% of isolates). This strain was of low prevalence (5% of isolates) among poultry isolates.
flaA
-15 strains were five to six times more invasive of HEp2 cells in an in vitro assay than a
flaA
type (
flaA
-3) that was commonly encountered on poultry meat (23% of isolates) but was seldom associated with human illness (5%). Competitive-exclusion experiments with chickens, utilizing real-time quantitative PCR to measure the population sizes of specific strains representing
flaA
-15 (T1016) and
flaA
-3 (Pstau) in digesta, were carried out. These experiments showed that T1016 always outcompeted Pstau in the chicken intestine. Genomic comparisons of T1016 and Pstau were made using DNA microarrays representing the genome of
C. jejuni
NCTC 11168. These comparisons revealed differences between the strains in the gene content of the Cj1417c-to-Cj1442c region of the genome, which is associated with the formation of capsular polysaccharide. The strains differed in Penner type (T1016, O42; Pstau, O53). It was concluded that poultry meat was at least one source of human infection with
C. jejuni
, that some
Campylobacter
strains detected in poultry meat are of higher virulence for humans than others, and that bacterial attributes affecting strain virulence and commensal colonization ability may be linked.
Variability of Total and PathogenicVibrio parahaemolyticusDensities in Northern Gulf of Mexico Water and Oysters
Authors: Zimmerman A. M. , DePaola A. , Bowers J. C. , Krantz J. A. , Nordstrom J. L. , Johnson C. N. , Grimes D. J. 
Published: October 2007

ABSTRACTVibrio parahaemolyticusis indigenous to coastal environments and a frequent cause of seafood-borne gastroenteritis in the United States, primarily due to raw-oyster consumption. Previous seasonal-cycle studies ofV. parahaemolyticushave identified water temperature as the strongest environmental predictor. Salinity has also been identified, although it is evident that its effect on annual variation is not as pronounced. The effects of other environmental factors, both with respect to the seasonal cycle and intraseasonal variation, are uncertain. This study investigated intraseasonal variations of densities of total and pathogenicV. parahaemolyticusorganisms in oysters and overlying waters during the summer of 2004 at two sites in the northern Gulf of Mexico. Regression analyses indicated significant associations (P< 0.001) between totalV. parahaemolyticusdensities and salinity, as well as turbidity in water and in oysters at the Mississippi site but not at the Alabama site. PathogenicV. parahaemolyticusorganisms in Mississippi oyster and water samples were detected in 56% (9 out of 16) and 78% (43 out of 55) of samples, respectively. In contrast, 44% (7 out of 16) of oyster samples and 30% (14 out of 47) of water samples from Alabama were positive. At both sites, there was greater sample-to-sample variability in pathogenicV. parahaemolyticusdensities than in totalV. parahaemolyticusdensities. These data suggest that, although totalV. parahaemolyticusdensities may be very informative, there is greater uncertainty when totalV. parahaemolyticusdensities are used to predict the risk of infection by pathogenicV. parahaemolyticusthan previously recognized.
Improvement of NADPH-Dependent Bioconversion by Transcriptome-Based Molecular Breeding
Authors: Hibi Makoto , Yukitomo Hiromi , Ito Mikito , Mori Hideo 
Published: October 2007

ABSTRACT

Transcriptome data for a xylitol-producing recombinant
Escherichia coli
were obtained and used to tune up its productivity. Structural genes of NADPH-dependent
d
-xylose reductase and
d
-xylose permease were inserted into an
Escherichia coli
chromosome to construct a recombinant strain producing xylitol from
d
-xylose for use as a model system for NADPH-dependent bioconversion. Transcriptome analysis of xylitol-producing and nonproducing conditions for the recombinant revealed that xylitol production down-regulated 56 genes. These genes were then selected as candidate factors for suppression of the NADPH supply and were disrupted to validate their functions. Of the gene disruptants, that resulting from the deletion of
yhbC
showed the best bioconversion rate. Also, the deletion accelerated cell growth during log phase. The features of the mutant could be maintained in jar fermenter-scale production of xylitol. Thus, our novel molecular host strain breeding method using transcriptome analysis was fully effective and could be applied to improving various industrial strains.
Genomic and Biochemical Studies Demonstrating the Absence of an Alkane-Producing Phenotype in
Vibrio furnissii
M1
Authors: Wackett Lawrence P. , Frias Janice A. , Seffernick Jennifer L. , Sukovich David J. , Cameron Stephan M. 
Published: October 2007

ABSTRACT

Vibrio furnissii
M1 was recently reported to biosynthesize
n
-alkanes when grown on biopolymers, sugars, or organic acids (M. O. Park, J. Bacteriol.
187:
1426-1429, 2005). In the present study,
V. furnissii
M1 was subjected to genomic analysis and studied biochemically. The sequence of the 16S rRNA gene and repetitive PCR showed that
V. furnissii
M1 was not identical to other
V. furnissii
strains tested, but the level of relatedness was consistent with its assignment as a
V. furnissii
strain. Pulsed-field gel electrophoresis showed chromosomal bands at approximately 3.2 and 1.8 Mb, similar to other
Vibrio
strains. Complete genomic DNA from
V. furnissii
M1 was sequenced with 21-fold coverage. Alkane biosynthetic and degradation genes could not be identified. Moreover,
V. furnissii
M1 did not produce demonstrable levels of
n
-alkanes in vivo or in vitro. In vivo experiments were conducted by growing
V. furnissii
M1 under different conditions, extracting with solvent, and analyzing extracts by gas chromatography-mass spectrometry. A highly sensitive assay was used for in vitro experiments with cell extracts and [
14
C]hexadecanol. The data are consistent with the present strain being a
V. furnissii
with properties similar to those previously described but lacking the alkane-producing phenotype.
V. furnissii
ATCC 35016, also reported to biosynthesize alkanes, was found in the present study not to produce alkanes.