bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental Transmission of Infectious Pancreatic Necrosis Virus from the Blue Mussel, Mytilus edulis, to Cohabitating Atlantic Salmon (Salmo salar) Smolts
Authors: Molloy Sally D. , Pietrak Michael R. , Bricknell Ian , Bouchard Deborah A. 
Published: July 2013

ABSTRACT

Integrated multitrophic aquaculture (IMTA) reduces the environmental impacts of commercial aquaculture systems by combining the cultivation of fed species with extractive species. Shellfish play a critical role in IMTA systems by filter-feeding particulate-bound organic nutrients. As bioaccumulating organisms, shellfish may also increase disease risk on farms by serving as reservoirs for important finfish pathogens such as infectious pancreatic necrosis virus (IPNV). The ability of the blue mussel (
Mytilus edulis
) to bioaccumulate and transmit IPNV to naive Atlantic salmon (
Salmo salar
) smolts was investigated. To determine the ability of mussels to filter and accumulate viable IPNV, mussels were held in water containing log 4.6 50% tissue culture infective dose(s) (TCID
50
) of the West Buxton strain of IPNV ml
−1
. Viable IPNV was detected in the digestive glands (DGs) of IPNV-exposed mussels as early as 2 h postexposure. The viral load in mussel DG tissue significantly increased with time and reached log 5.35 ± 0.25 TCID
50
g of DG tissue
−1
after 120 h of exposure. IPNV titers never reached levels that were significantly greater than that in the water. Viable IPNV was detected in mussel feces out to 7 days postdepuration, and the virus persisted in DG tissues for at least 18 days of depuration. To determine whether IPNV can be transmitted from mussels to Atlantic salmon, IPNV-exposed mussels were cohabitated with naive Atlantic salmon smolts. Transmission of IPNV did occur from mussels to smolts at a low frequency. The results demonstrate that a nonenveloped virus, such as IPNV, can accumulate in mussels and be transferred to naive fish.
Diet Complexity and Estrogen Receptor β Status Affect the Composition of the Murine Intestinal Microbiota
Authors: Menon Rani , Watson Sara E. , Thomas Laura N. , Allred Clinton D. , Dabney Alan , Azcarate-Peril M. Andrea , Sturino Joseph M. 
Published: July 2013

ABSTRACTIntestinal microbial dysbiosis contributes to the dysmetabolism of luminal factors, including steroid hormones (sterones) that affect the development of chronic gastrointestinal inflammation and the incidence of sterone-responsive cancers of the breast, prostate, and colon. Little is known, however, about the role of specific host sterone nucleoreceptors, including estrogen receptor β (ERβ), in microbiota maintenance. Herein, we test the hypothesis that ERβ status affects microbiota composition and determine if such compositionally distinct microbiota respond differently to changes in diet complexity that favorProteobacteriaenrichment. To this end, conventionally raised female ERβ+/+and ERβ−/−C57BL/6J mice (mean age of 27 weeks) were initially reared on 8604, a complex diet containing estrogenic isoflavones, and then fed AIN-76, an isoflavone-free semisynthetic diet, for 2 weeks. 16S rRNA gene surveys revealed that the fecal microbiota of 8604-fed mice and AIN-76-fed mice differed, as expected. The relative diversity ofProteobacteria, especially theAlphaproteobacteriaandGammaproteobacteria, increased significantly following the transition to AIN-76. Distinct patterns for beneficialLactobacillaleswere exclusive to and highly abundant among 8604-fed mice, whereas severalProteobacteriawere exclusive to AIN-76-fed mice. Interestingly, representative orders of the phylaProteobacteria,Bacteroidetes, andFirmicutes, including theLactobacillales, also differed as a function of murine ERβ status. Overall, these interactions suggest that sterone nucleoreceptor status and diet complexity may play important roles in microbiota maintenance. Furthermore, we envision that this model for gastrointestinal dysbiosis may be used to identify novel probiotics, prebiotics, nutritional strategies, and pharmaceuticals for the prevention and resolution ofProteobacteria-rich dysbiosis.
Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity
Authors: Sun Dong-Lei , Jiang Xuan , Wu Qinglong L. , Zhou Ning-Yi 
Published: July 2013

ABSTRACT
Ever since Carl Woese introduced the use of 16S rRNA genes for determining the phylogenetic relationships of prokaryotes, this method has been regarded as the “gold standard” in both microbial phylogeny and ecology studies. However, intragenomic heterogeneity within 16S rRNA genes has been reported in many investigations and is believed to bias the estimation of prokaryotic diversity. In the current study, 2,013 completely sequenced genomes of bacteria and archaea were analyzed and intragenomic heterogeneity was found in 952 genomes (585 species), with 87.5% of the divergence detected being below the 1% level. In particular, some extremophiles (thermophiles and halophiles) were found to harbor highly divergent 16S rRNA genes. Overestimation caused by 16S rRNA gene intragenomic heterogeneity was evaluated at different levels using the full-length and partial 16S rRNA genes usually chosen as targets for pyrosequencing. The result indicates that, at the unique level, full-length 16S rRNA genes can produce an overestimation of as much as 123.7%, while at the 3% level, an overestimation of 12.9% for the V6 region may be introduced. Further analysis showed that intragenomic heterogeneity tends to concentrate in specific positions, with the V1 and V6 regions suffering the most intragenomic heterogeneity and the V4 and V5 regions suffering the least intragenomic heterogeneity in bacteria. This is the most up-to-date overview of the diversity of 16S rRNA genes within prokaryotic genomes. It not only provides general guidance on how much overestimation can be introduced when applying 16S rRNA gene-based methods, due to its intragenomic heterogeneity, but also recommends that, for bacteria, this overestimation be minimized using primers targeting the V4 and V5 regions.
Combining Individual-Based Modeling and Food Microenvironment Descriptions To Predict the Growth of Listeria monocytogenes on Smear Soft Cheese
Authors: Ferrier Rachel , Hezard Bernard , Lintz Adrienne , Stahl Valérie , Augustin Jean-Christophe 
Published: July 2013

ABSTRACT

An individual-based modeling (IBM) approach was developed to describe the behavior of a few
Listeria monocytogenes
cells contaminating smear soft cheese surface. The IBM approach consisted of assessing the stochastic individual behaviors of cells on cheese surfaces and knowing the characteristics of their surrounding microenvironments. We used a microelectrode for pH measurements and micro-osmolality to assess the water activity of cheese microsamples. These measurements revealed a high variability of microscale pH compared to that of macroscale pH. A model describing the increase in pH from approximately 5.0 to more than 7.0 during ripening was developed. The spatial variability of the cheese surface characterized by an increasing pH with radius and higher pH on crests compared to that of hollows on cheese rind was also modeled. The microscale water activity ranged from approximately 0.96 to 0.98 and was stable during ripening. The spatial variability on cheese surfaces was low compared to between-cheese variability. Models describing the microscale variability of cheese characteristics were combined with the IBM approach to simulate the stochastic growth of
L. monocytogenes
on cheese, and these simulations were compared to bacterial counts obtained from irradiated cheeses artificially contaminated at different ripening stages. The simulated variability of
L. monocytogenes
counts with the IBM/microenvironmental approach was consistent with the observed one. Contrasting situations corresponding to no growth or highly contaminated foods could be deduced from these models. Moreover, the IBM approach was more effective than the traditional population/macroenvironmental approach to describe the actual bacterial behavior variability.
Adhesion of Human and Animal Escherichia coli Strains in Association with Their Virulence-Associated Genes and Phylogenetic Origins
Authors: Frömmel Ulrike , Lehmann Werner , Rödiger Stefan , Böhm Alexander , Nitschke Jörg , Weinreich Jörg , Groß Julia , Roggenbuck Dirk , Zinke Olaf , Ansorge Hermann , Vogel Steffen , Klemm Per , Wex Thomas , Schröder Christian , Wieler Lothar H. , Schierack Peter 
Published: July 2013

ABSTRACT

Intestinal colonization is influenced by the ability of the bacterium to inhabit a niche, which is based on the expression of colonization factors.
Escherichia coli
carries a broad range of virulence-associated genes (VAGs) which contribute to intestinal (inVAGs) and extraintestinal (exVAGs) infection. Moreover, initial evidence indicates that inVAGs and exVAGs support intestinal colonization. We developed new screening tools to genotypically and phenotypically characterize
E. coli
isolates originating in humans, domestic pigs, and 17 wild mammal and avian species. We analyzed 317 isolates for the occurrence of 44 VAGs using a novel multiplex PCR microbead assay (MPMA) and for adhesion to four epithelial cell lines using a new adhesion assay. We correlated data for the definition of new adhesion genes. inVAGs were identified only sporadically, particularly in roe deer (
Capreolus capreolus
) and the European hedgehog (
Erinaceus europaeus
). The prevalence of exVAGs depended on isolation from a specific host. Human uropathogenic
E. coli
isolates carried exVAGs with the highest prevalence, followed by badger (
Meles meles
) and roe deer isolates. Adhesion was found to be very diverse. Adhesion was specific to cells, host, and tissue, though it was also unspecific. Occurrence of the following VAGs was associated with a higher rate of adhesion to one or more cell lines:
afa-dra
,
daaD
,
tsh
,
vat
,
ibeA
,
fyuA
,
mat
,
sfa-foc
,
malX
,
pic
,
irp2
, and
papC
. In summary, we established new screening methods which enabled us to characterize large numbers of
E. coli
isolates. We defined reservoirs for potential pathogenic
E. coli
. We also identified a very broad range of colonization strategies and defined potential new adhesion genes.
Unique Contribution of the Cell Wall-Binding Endoglucanase G to the Cellulolytic Complex in Clostridium cellulovorans
Authors: Jeon Sang Duck , Lee Ji Eun , Kim Su Jung , Park Sung Hyun , Choi Gi-Wook , Han Sung Ok 
Published: July 2013

ABSTRACT

The cellulosomes produced by
Clostridium cellulovorans
are organized by the specific interactions between the cohesins in the scaffolding proteins and the dockerins of the catalytic components. Using a cohesin biomarker, we identified a cellulosomal enzyme which belongs to the glycosyl hydrolase family 5 and has a domain of unknown function 291 (DUF291) with functions similar to those of the surface layer homology domain in
C. cellulovorans
. The purified endoglucanase G (EngG) had the highest synergistic degree with exoglucanase (ExgS) in the hydrolysis of crystalline cellulose (EngG/ExgS ratio = 3:1; 1.71-fold). To measure the binding affinity of the dockerins in EngG for the cohesins of the main scaffolding protein, a competitive enzyme-linked interaction assay was performed. Competitors, such as ExgS, reduced the percentage of EngG that were bound to the cohesins to less than 20%; the results demonstrated that the cohesins prefer to bind to the common cellulosomal enzymes rather than to EngG. Additionally, in surface plasmon resonance analysis, the dockerin in EngG had a relatively weak affinity (30- to 123-fold) for cohesins compared with the other cellulosomal enzymes. In the cell wall affinity assay, EngG anchored to the cell surfaces of
C. cellulovorans
using its DUF291 domain. Immunofluorescence microscopy confirmed the cell surface display of the EngG complex. These results indicated that in
C. cellulovorans
, EngG assemble into both the cellulolytic complex and the cell wall complex to aid in the hydrolysis of cellulose substrates.
The Carbohydrate Metabolism Signature of Lactococcus lactis Strain A12 Reveals Its Sourdough Ecosystem Origin
Authors: Passerini Delphine , Coddeville Michèle , Le Bourgeois Pascal , Loubière Pascal , Ritzenthaler Paul , Fontagné-Faucher Catherine , Daveran-Mingot Marie-Line , Cocaign-Bousquet Muriel 
Published: July 2013

ABSTRACT

Lactococcus lactis
subsp.
lactis
strain A12 was isolated from sourdough. Combined genomic, transcriptomic, and phenotypic analyses were performed to understand its survival capacity in the complex sourdough ecosystem and its role in the microbial community. The genome sequence comparison of strain A12 with strain IL1403 (a derivative of an industrial dairy strain) revealed 78 strain-specific regions representing 23% of the total genome size. Most of the strain-specific genes were involved in carbohydrate metabolism and are potentially required for its persistence in sourdough. Phenotype microarray, growth tests, and analysis of glycoside hydrolase content showed that strain A12 fermented plant-derived carbohydrates, such as arabinose and α-galactosides. Strain A12 exhibited specific growth rates on raffinose that were as high as they were on glucose and was able to release sucrose and galactose outside the cell, providing soluble carbohydrates for sourdough microflora. Transcriptomic analysis identified genes specifically induced during growth on raffinose and arabinose and reveals an alternative pathway for raffinose assimilation to that used by other lactococci.
Utilization of Heme as an Iron Source by Marine Alphaproteobacteria in the Roseobacter Clade
Authors: Roe Kelly L. , Hogle Shane L. , Barbeau Katherine A. 
Published: July 2013

ABSTRACT

The bioavailability and utilization of porphyrin-bound iron, specifically heme, by marine microorganisms have rarely been examined. This study used
Ruegeria
sp. strain TrichCH4B as a model organism to study heme acquisition by a member of the
Roseobacter
clade. Analogs of known heme transporter proteins were found within the
Ruegeria
sp. TrichCH4B genome. The identified heme uptake and utilization system appears to be functional, as the heme genes were upregulated under iron stress, the bacterium could grow on ferric-porphyrin complexes as the sole iron source, and internalization of
55
Fe from ferric protoporphyrin IX was observed. The potential ability to utilize heme in the
Roseobacter
clade appears to be common, as half of the isolates in the RoseoBase database were found to have a complete heme uptake system. A degenerate primer set was designed and successfully used to identify the putative heme oxygenase gene (
hmus
) in the roseobacter heme uptake system from diverse nonenriched marine environments. This study found that members of the
Roseobacter
clade are capable of utilizing heme as an iron source and that this capability may be present in all types of marine environments. The results of this study add a new perspective to the current picture of iron cycling in marine systems, whereby relatively refractory intracellular pools of heme-bound iron may be taken up quickly and directly reincorporated into living bacteria without previous degradation or the necessity of a siderophore intermediate.
Detoxification of Mercury by Methanobactin from Methylosinus trichosporium OB3b
Authors: Vorobev Alexey , Jagadevan Sheeja , Baral Bipin S. , DiSpirito Alan A. , Freemeier Brittani C. , Bergman Brandt H. , Bandow Nathan L. , Semrau Jeremy D. 
Published: July 2013

ABSTRACT

Many methanotrophs have been shown to synthesize methanobactin, a novel biogenic copper-chelating agent or chalkophore. Methanobactin binds copper via two heterocyclic rings with associated enethiol groups. The structure of methanobactin suggests that it can bind other metals, including mercury. Here we report that methanobactin from
Methylosinus trichosporium
OB3b does indeed bind mercury when added as HgCl
2
and, in doing so, reduced toxicity associated with Hg(II) for both
Alphaproteobacteria
methanotrophs, including
M. trichosporium
OB3b,
M. trichosporium
OB3b Δ
mbnA
(a mutant defective in methanobactin production), and
Methylocystis
sp. strain SB2, and a
Gammaproteobacteria
methanotroph,
Methylomicrobium album
BG8. Mercury binding by methanobactin was evident in both the presence and absence of copper, despite the fact that methanobactin had a much higher affinity for copper due to the rapid and irreversible binding of mercury by methanobactin. The formation of a gray precipitate suggested that Hg(II), after being bound by methanobactin, was reduced to Hg(0) but was not volatilized. Rather, mercury remained associated with methanobactin and was also found associated with methanotrophic biomass. It thus appears that although the mercury-methanobactin complex was cell associated, mercury was not removed from methanobactin. The amount of biomass-associated mercury in the presence of methanobactin from
M. trichosporium
OB3b was greatest for
M. trichosporium
wild-type strain OB3b and the Δ
mbnA
mutant and least for
M. album
BG8, suggesting that methanotrophs may have selective methanobactin uptake systems that may be based on TonB-dependent transporters but that such uptake systems exhibit a degree of infidelity.
Abundant DNase I-Sensitive Bacterial DNA in Healthy Porcine Lungs and Its Implications for the Lung Microbiome
Authors: Pezzulo Alejandro A. , Kelly Patrick H. , Nassar Boulos S. , Rutland Cedric J. , Gansemer Nicholas D. , Dohrn Cassie L. , Costello Andrew J. , Stoltz David A. , Zabner Joseph 
Published: July 2013

ABSTRACTHuman lungs are constantly exposed to bacteria in the environment, yet the prevailing dogma is that healthy lungs are sterile. DNA sequencing-based studies of pulmonary bacterial diversity challenge this notion. However, DNA-based microbial analysis currently fails to distinguish between DNA from live bacteria and that from bacteria that have been killed by lung immune mechanisms, potentially causing overestimation of bacterial abundance and diversity. We investigated whether bacterial DNA recovered from lungs represents live or dead bacteria in bronchoalveolar lavage (BAL) fluid and lung samples in young healthy pigs. Live bacterial DNA was DNase I resistant and became DNase I sensitive upon human antimicrobial-mediated killingin vitro. We determined live and total bacterial DNA loads in porcine BAL fluid and lung tissue by comparing DNase I-treated versus untreated samples. In contrast to the case for BAL fluid, we were unable to culture bacteria from most lung homogenates. Surprisingly, total bacterial DNA was abundant in both BAL fluid and lung homogenates. In BAL fluid, 63% was DNase I sensitive. In 6 out of 11 lung homogenates, all bacterial DNA was DNase I sensitive, suggesting a predominance of dead bacteria; in the remaining homogenates, 94% was DNase I sensitive, and bacterial diversity determined by 16S rRNA gene sequencing was similar in DNase I-treated and untreated samples. Healthy pig lungs are mostly sterile yet contain abundant DNase I-sensitive DNA from inhaled and aspirated bacteria killed by pulmonary host defense mechanisms. This approach and conceptual framework will improve analysis of the lung microbiome in disease.
Enantioselective Dehydrochlorination of δ-Hexachlorocyclohexane and δ-Pentachlorocyclohexene by LinA1 and LinA2 from Sphingobium indicum B90A
Authors: Geueke Birgit , Miska Milena E. , Poiger Thomas , Rentsch Daniel , Lal Rup , Holliger Christof , Kohler Hans-Peter E. 
Published: July 2013

ABSTRACT

δ-Hexachlorocyclohexane (δ-HCH), one of the prevalent isomers of technical HCH, was enantioselectively dehydrochlorinated by the dehydrochlorinases LinA1 and LinA2 from
Sphingobium indicum
B90A to the very same δ-pentachlorocyclohexene enantiomer. Racemic δ-pentachlorocyclohexene, however, was transformed with opposite enantioselectivities by the two enzymes. A transformation pathway based on an
anti
-1,2-elimination, followed by a
syn
-1,4-elimination and a subsequent
syn
-1,2-elimination is postulated.
Genetic Characterization of Atypical Enteropathogenic Escherichia coli Isolates from Ewes' Milk, Sheep Farm Environments, and Humans by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis
Authors: Otero Verónica , Rodríguez-Calleja José-María , Otero Andrés , García-López María-Luisa , Santos Jesús A. 
Published: July 2013

ABSTRACT

A collection of 81 isolates of enteropathogenic
Escherichia coli
(EPEC) was obtained from samples of bulk tank sheep milk (62 isolates), ovine feces (4 isolates), sheep farm environment (water, 4 isolates; air, 1 isolate), and human stool samples (9 isolates). The strains were considered atypical EPEC organisms, carrying the
eae
gene without harboring the pEAF plasmid. Multilocus sequence typing (MLST) was carried out with seven housekeeping genes and 19 sequence types (ST) were detected, with none of them having been previously reported for atypical EPEC. The most frequent ST included 41 strains isolated from milk and human stool samples. Genetic typing by pulsed-field gel electrophoresis (PFGE) resulted in 57 patterns which grouped in 24 clusters. Comparison of strains isolated from the different samples showed phylogenetic relationships between milk and human isolates and also between milk and water isolates. The results obtained show a possible risk for humans due to the presence of atypical EPEC in ewes' milk and suggest a transmission route for this emerging pathogen through contaminated water.
Alternative Sigma Factor σ
E
Has an Important Role in Stress Tolerance of Yersinia pseudotuberculosis IP32953
Authors: Palonen Eveliina , Lindström Miia , Somervuo Panu , Korkeala Hannu 
Published: July 2013

ABSTRACT

Yersinia pseudotuberculosis
is an important pathogen that probably survives well in the modern food chain. However, little is known about the mechanisms that allow the growth of this pathogen in foods under stress conditions. The expression of
rpoE
encoding σ
E
was defined by quantitative real-time reverse transcription-PCR. Expression of
rpoE
was induced at 3°C, 37°C, and 42°C, under exposure to 3% NaCl, 3% ethanol, or high and low pH, in relation to its expression at the optimum growth temperature of 28°C of
Y. pseudotuberculosis
. Mutation of
rpoE
either impaired or abolished growth under stresses caused by low or high temperature, low pH, and ethanol. In addition, the growth temperature range of the mutant was significantly diminished compared to that of the wild-type strain IP32953. The results were confirmed with complementation of the mutant. Thus, σ
E
plays a significant role in the stress tolerance of
Y. pseudotuberculosis
IP32953 and probably contributes to the survival of this pathogen in the food chain.
Extending the Cellulosome Paradigm: the Modular Clostridium thermocellum Cellulosomal Serpin PinA Is a Broad-Spectrum Inhibitor of Subtilisin-Like Proteases
Authors: Ó Cuív Páraic , Gupta Rajesh , Goswami Hareshwar P. , Morrison Mark 
Published: July 2013

ABSTRACT

Clostridium thermocellum
encodes a cellulosomal, modular, and thermostable serine protease inhibitor (serpin), PinA. PinA stability but not inhibitory activity is affected by the Fn(III) and Doc(I) domains, and PinA is a broad inhibitor of subtilisin-like proteases and may play a key role in protecting the cellulosome from protease attack.
Clostridium acidurici Electron-Bifurcating Formate Dehydrogenase
Authors: Wang Shuning , Huang Haiyan , Kahnt Jörg , Thauer Rudolf K. 
Published: July 2013

ABSTRACT

Cell extracts of uric acid-grown
Clostridium acidurici
catalyzed the coupled reduction of NAD
+
and ferredoxin with formate at a specific activity of 1.3 U/mg. The enzyme complex catalyzing the electron-bifurcating reaction was purified 130-fold and found to be composed of four subunits encoded by the gene cluster
hylCBA-fdhF2
.