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Manimozhiyan Arumugam,
Jeroen Raes,
Eric Pelletier,
Denis Le Paslier,
Takuji Yamada,
Daniel R Mende,
Gabriel R Fernandes,
Julien Tap,
Thomas Bruls,
Jean-Michel Batto, [......],
Shinichi Sunagawa,
Antonio Torrejon,
Keith Turner,
Gaetana Vandemeulebrouck,
Encarna Varela,
Yohanan Winogradsky,
Georg Zeller,
Jean Weissenbach,
S Dusko Ehrlich,
Peer Bork
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Manimozhiyan Arumugam,
Jeroen Raes,
Eric Pelletier,
Denis Le Paslier,
Takuji Yamada,
Daniel R Mende,
Gabriel R Fernandes,
Julien Tap,
Thomas Bruls,
Jean-Michel Batto, [......],
Shinichi Sunagawa,
Antonio Torrejon,
Keith Turner,
Gaetana Vandemeulebrouck,
Encarna Varela,
Yohanan Winogradsky,
Georg Zeller,
Jean Weissenbach,
S Dusko Ehrlich,
Peer Bork
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Manimozhiyan Arumugam,
Jeroen Raes,
Eric Pelletier,
Denis Le Paslier,
Takuji Yamada,
Daniel R Mende,
Gabriel R Fernandes,
Julien Tap,
Thomas Bruls,
Jean-Michel Batto, [......],
Shinichi Sunagawa,
Antonio Torrejon,
Keith Turner,
Gaetana Vandemeulebrouck,
Encarna Varela,
Yohanan Winogradsky,
Georg Zeller,
Jean Weissenbach,
S Dusko Ehrlich,
Peer Bork
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Manimozhiyan Arumugam,
Jeroen Raes,
Eric Pelletier,
Denis Le Paslier,
Takuji Yamada,
Daniel R Mende,
Gabriel R Fernandes,
Julien Tap,
Thomas Bruls,
Jean-Michel Batto, [......],
Shinichi Sunagawa,
Antonio Torrejon,
Keith Turner,
Gaetana Vandemeulebrouck,
Encarna Varela,
Yohanan Winogradsky,
Georg Zeller,
Jean Weissenbach,
S Dusko Ehrlich,
Peer Bork
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ABSTRACT: The random transposon mutagenesis system P(junc)-TpaseIS(1223) is composed of plasmids pVI129, expressing IS1223 transposase, and pVI110, a suicide transposon plasmid carrying the P(junc) sequence, the substrate of the IS1223 transposase. This system is particularly efficient in Lactobacillus casei, as more than 10,000 stable, random mutants were routinely obtained via electroporation.
Applied and environmental microbiology 05/2012; 78(15):5417-23. · 3.69 Impact Factor
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Clarissa Santos Rocha,
Omar Lakhdari,
Hervé M Blottière,
Sébastien Blugeon,
Harry Sokol,
Luis G Bermúdez-Humarán,
Vasco Azevedo,
Anderson Miyoshi,
Joël Doré,
Philippe Langella,
Emmanuelle Maguin, Maarten van de Guchte
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ABSTRACT: The intestinal microbiota plays an important role in human health through the modulation of innate immune responses. While selected commensal bacteria are marketed in specific probiotic products to control these responses, relatively little is known about the immune modulation potential of dairy bacteria that have principally been selected for their fermentation properties. The modulation of innate immune responses may reduce chronic inflammation in inflammatory bowel diseases like ulcerative colitis.
A collection of dairy Lactobacillus delbrueckii strains was screened for immune modulation effects in vitro through the quantification of nuclear factor kappa B (NF-κB) activation in a human intestinal epithelial cell line. Selected bacterial strains were then tested in vivo in a mouse dextran sodium sulfate (DSS) colitis model.
All L. delbrueckii strains tested showed anti-inflammatory effects in vitro, to an extent that varied between strains. These effects rely on bacterial surface exposed proteins and affect the central part of the NF-κB activation pathway. One of the selected strains significantly reduced the macroscopic and microscopic symptoms of DSS-induced colitis in the mouse intestinal tract, diminished body weight loss, and improved survival.
The results of this study show that dairy lactobacilli that often are part of a regular diet can modulate innate immune responses, and may thus affect health more than generally thought. One of the strains tested alleviated the symptoms of DSS-induced colitis in mice, a model of human ulcerative colitis.
Inflammatory Bowel Diseases 08/2011; 18(4):657-66. · 4.86 Impact Factor
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Eric Guédon,
Christine Delorme,
Nicolas Pons,
Corinne Cruaud,
Valentin Loux,
Arnaud Couloux,
Céline Gautier,
Nicolas Sanchez,
Séverine Layec,
Nathalie Galleron,
Mathieu Almeida, Maarten van de Guchte,
Sean P Kennedy,
S Dusko Ehrlich,
Jean-François Gibrat,
Patrick Wincker,
Pierre Renault
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ABSTRACT: The commensal bacterium Streptococcus salivarius is a prevalent species of the human oropharyngeal tract with an important role in oral ecology. Here, we report the complete 2.2-Mb genome sequence and annotation of strain JIM8777, which was recently isolated from the oral cavity of a healthy, dentate infant.
Journal of bacteriology 07/2011; 193(18):5024-5. · 3.94 Impact Factor
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Manimozhiyan Arumugam,
Jeroen Raes,
Eric Pelletier,
Denis Le Paslier,
Takuji Yamada,
Daniel R Mende,
Gabriel R Fernandes,
Julien Tap,
Thomas Bruls,
Jean-Michel Batto, [......],
Shinichi Sunagawa,
Antonio Torrejon,
Keith Turner,
Gaetana Vandemeulebrouck,
Encarna Varela,
Yohanan Winogradsky,
Georg Zeller,
Jean Weissenbach,
S Dusko Ehrlich,
Peer Bork
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ABSTRACT: Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
Nature 05/2011; 473(7346):174-80. · 36.28 Impact Factor
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Caroline Le Maréchal,
Nubia Seyffert,
Julien Jardin,
David Hernandez,
Gwenaël Jan,
Lucie Rault,
Vasco Azevedo,
Patrice François,
Jacques Schrenzel, Maarten van de Guchte,
Sergine Even,
Nadia Berkova,
Richard Thiéry,
J Ross Fitzgerald,
Eric Vautor,
Yves Le Loir
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ABSTRACT: S. aureus is one of the main pathogens involved in ruminant mastitis worldwide. The severity of staphylococcal infection is highly variable, ranging from subclinical to gangrenous mastitis. This work represents an in-depth characterization of S. aureus mastitis isolates to identify bacterial factors involved in severity of mastitis infection.
We employed genomic, transcriptomic and proteomic approaches to comprehensively compare two clonally related S. aureus strains that reproducibly induce severe (strain O11) and milder (strain O46) mastitis in ewes. Variation in the content of mobile genetic elements, iron acquisition and metabolism, transcriptional regulation and exoprotein production was observed. In particular, O11 produced relatively high levels of exoproteins, including toxins and proteases known to be important in virulence. A characteristic we observed in other S. aureus strains isolated from clinical mastitis cases.
Our data are consistent with a dose-dependant role of some staphylococcal factors in the hypervirulence of strains isolated from severe mastitis. Mobile genetic elements, transcriptional regulators, exoproteins and iron acquisition pathways constitute good targets for further research to define the underlying mechanisms of mastitis severity.
PLoS ONE 01/2011; 6(11):e27354. · 4.09 Impact Factor
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ABSTRACT: Lactic acid bacteria (LAB) represent a heterogeneous group of microorganisms that are naturally present in many foods and possess a wide range of therapeutic properties. The aim of this paper is to present an overview of the current expanding knowledge of one of the mechanisms by which LAB and other probiotic microorganisms participate in the prevention and treatment of gastrointestinal inflammatory disease through their immune-modulating properties. A special emphasis will be placed on the critical role of the anti-inflammatory cytokine IL-10, and a brief overview of the uses of genetically engineered LAB that produce this important immune response mediator will also be discussed. Thus, this paper will demonstrate the critical role that IL-10 plays in gastrointestinal inflammatory diseases and how probiotics could be used in their treatment.
ISRN gastroenterology. 01/2011; 2011:892971.
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Proteomics 03/2009; 9(5):1416. · 4.43 Impact Factor
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ABSTRACT: Lactic acid bacteria (LAB) gradually acidify their environment through the conversion of pyruvate to lactate, an essential process to regenerate NAD(+) used during glycolysis. A clear demonstration of acidification can be found in yogurt, the product of milk fermentation by the LAB Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) and Streptococcus thermophilus, where the pH falls to 4.2. Acid adaptation therefore plays an important role in the physiology of LAB. Here we present the results of a proteomic approach to reveal cellular changes associated with acid adaptation in L. bulgaricus. These results were complemented with transcription data for selected genes to show three major effects: (i) induction of the chaperones GroES, GroEL, HrcA, GrpE, DnaK, DnaJ, ClpE, ClpP, and ClpL, and the repression of ClpC; (ii) induction of genes involved in the biosynthesis of fatty acids (fabH, accC, fabI); (iii) repression of genes involved in the mevalonate pathway of isoprenoid synthesis (mvaC, mvaS). Together with changes in the expression of other genes from the local metabolic network, these results for the first time show a coherent picture of changes in gene expression expected to result in a rerouting of pyruvate metabolism to favor fatty acid biosynthesis, and thereby affect membrane fluidity.
Proteomics 08/2008; 8(15):3154-63. · 4.43 Impact Factor
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ABSTRACT: While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii) and yogurt (Lactobacillus delbrueckii ssp. bulgaricus), is ambiguous due to contradictory phenotypical and 16S rRNA based classifications.
Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract.
This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive horizontal gene transfer. The data give a first indication of the large extent of gene transfer that may take place in the gastrointestinal tract and its accumulated effect. For future studies, our results should encourage a careful weighing of data on phylogenetic tree topology, confidence and distribution to conclude on the absence or presence and extent of horizontal gene transfer.
BMC Evolutionary Biology 02/2007; 7:141. · 3.52 Impact Factor
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ABSTRACT: Lactic acid bacteria (LAB) are generally sensitive to H2O2, a compound that they can paradoxically produce themselves, as is the case for Lactobacillus bulgaricus. Lactobacillus plantarum ATCC 14431 is one of the very few LAB strains able to degrade H2O2 through the action of a nonheme, manganese-dependent catalase (hereafter called MnKat). The MnKat gene was expressed in three catalase-deficient LAB species: L. bulgaricus ATCC 11842, Lactobacillus casei BL23, and Lactococcus lactis MG1363. While the protein could be detected in all heterologous hosts, enzyme activity was observed only in L. casei. This is probably due to the differences in the Mn contents of the cells, which are reportedly similar in L. plantarum and L. casei but at least 10- and 100-fold lower in Lactococcus lactis and L. bulgaricus, respectively. The expression of the MnKat gene in L. casei conferred enhanced oxidative stress resistance, as measured by an increase in the survival rate after exposure to H2O2, and improved long-term survival in aerated cultures. In mixtures of L. casei producing MnKat and L. bulgaricus, L. casei can eliminate H2O2 from the culture medium, thereby protecting both L. casei and L. bulgaricus from its deleterious effects.
Applied and Environmental Microbiology 09/2006; 72(8):5143-9. · 3.83 Impact Factor
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ABSTRACT: The genome of bacteriophage Tuc2009 consists of 38347 base pairs on which 57 open reading frames (ORFs) were identified, divided in two oppositely transcribed regions. The leftward-transcribed region harbors three ORFs, two of which are involved in the establishment of lysogeny. The rightward-transcribed region contains 54 ORFs, which are assumed to be required for the lytic life cycle. An exception to the above organization is ORF 10, of unknown function, located within the rightward-transcribed region that has an orientation opposite to the ORFs surrounding it. Transcriptional analysis of the Tuc2009 genome following infection of a sensitive host revealed that most ORFs are transcribed in a sequential manner. ORFs that are presumed to form (part of) the genetic switch along with the superinfection exclusion-encoding gene are transcribed immediately after infection, followed by transcription of the presumed replication region. Subsequent to this, several small transcripts could be identified followed by a single 24-kb transcript. This latter transcript was shown to specify most of the identified structural proteins as well as two proteins required for host lysis. Interestingly, the 24-kb mRNA was shown to undergo splicing through the activity of a type I intron whose removal from the mRNA resulted in the formation of an ORF specifying a major structural protein. Primer extension analysis was employed to identify the 5' ends of mRNA transcripts and the genome and transcriptional data are discussed in relation to other lactococcal bacteriophages.
Virology 12/2004; 329(1):40-52. · 3.35 Impact Factor
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ABSTRACT: Lactic acid bacteria (LAB) constitute a heterogeneous group of bacteria that are traditionally used to produce fermented foods. The industrialization of food bio-transformations increased the economical importance of LAB, as they play a crucial role in the development of the organoleptique and hygienic quality of fermented products. Therefore, the reliability of starter strains in terms of quality and functional properties (important for the development of aroma and texture), but also in terms of growth performance and robustness has become essential. These strains should resist to adverse conditions encountered in industrial processes, for example during starter handling and storage (freeze-drying, freezing or spray-drying). The development of new applications such as life vaccines and probiotic foods reinforces the need for robust LAB since they may have to survive in the digestive tract, resist the intestinal flora, maybe colonize the digestive or uro-genital mucosa and express specific functions under conditions that are unfavorable to growth (for example, during stationary phase or storage). Also in nature, the ability to quickly respond to stress is essential for survival and it is now well established that LAB, like other bacteria, evolved defense mechanisms against stress that allow them to withstand harsh conditions and sudden environmental changes. While genes implicated in stress responses are numerous, in LAB the levels of characterization of their actual role and regulation differ widely between species. The functional conservation of several stress proteins (for example, HS proteins, Csp, etc) and of some of their regulators (for example, HrcA, CtsR) renders even more striking the differences that exist between LAB and the classical model micro-organisms. Among the differences observed between LAB species and B. subtilis, one of the most striking is the absence of a sigma B orthologue in L. lactis ssp. lactis as well as in at least two streptococci and probably E. faecalis. The overview of LAB stress responses also reveals common aspects of stress responses. As in other bacteria, adaptive responses appear to be a usual mode of stress protection in LAB. However, the cross-protection to other stress often induced by the expression of a given adaptive response, appears to vary between species. This observation suggests that the molecular bases of adaptive responses are, at least in part, species (or even subspecies) specific. A better understanding of the mechanisms of stress resistance should allow to understand the bases of the adaptive responses and cross protection, and to rationalize their exploitation to prepare LAB to industrial processes. Moreover, the identification of crucial stress related genes will reveal targets i) for specific manipulation (to promote or limit growth), ii) to develop tools to screen for tolerant or sensitive strains and iii) to evaluate the fitness and level of adaptation of a culture. In this context, future genome and transcriptome analyses will undoubtedly complement the proteome and genetic information available today, and shed a new light on the perception of, and the response to, stress by lactic acid bacteria.
Antonie van Leeuwenhoek 09/2002; 82(1-4):187-216. · 2.09 Impact Factor
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Todd Klaenhammer,
Eric Altermann,
Fabrizio Arigoni,
Alexander Bolotin,
Fred Breidt,
Jeffrey Broadbent,
Raul Cano,
Stephane Chaillou,
Josef Deutscher,
Mike Gasson, [......],
David Pridmore,
Milton Saier,
Douwe van Sinderen,
Alexei Sorokin,
James Steele,
Daniel O'Sullivan,
Willem de Vos,
Bart Weimer,
Monique Zagorec,
Roland Siezen
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ABSTRACT: This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics.
Antonie van Leeuwenhoek 09/2002; 82(1-4):29-58. · 2.09 Impact Factor
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ABSTRACT: The putative repressor-encoding gene cI of the temperate lactococcal bacteriophage Tuc2009 was cloned and sequenced. In the inferred amino-acid sequence, two domains can be recognized, one of which shows homology to DNA-binding domains of various regulatory proteins, while the other is thought to be involved in oligomerisation.
Gene 07/1994; · 2.34 Impact Factor
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ABSTRACT: Tolerance and adaptative acid stress response of Lactobacillus delbrueckii ssp. bulgaricus. Using several approaches, we studied the acid stress response of different strains of Lactobacillus bulgaricus. We showed that after an acid shock, the cell survival varied considerably between strains and that all the studied strains were able to develop an acid adaptive response. For one of these strains, we characterized, using two-dimensional electrophoresis, the modifications in the protein pattern induced by acid adaptation. Out of the 50 proteins up-regulated under the adaptive conditions, 21 were identified after N-terminal sequencing. They belong to different functional categories including stress response and general metabolism. To allow a larger genetic exploration of L. bulgaricus, the genome of the type strain ATCC 11842 was sequenced in collaboration with the Genoscope. All together, these genomic and post-genomic data should lead to a better understanding of L. bulgaricus physiology and its environmental adaptability. En utilisant plusieurs approches, nous avons étudié le comportement de différentes souches de Lactobacillus bulgaricus face à un stress acide. Nous avons observé que la survie des cellules à un choc acide variait considérablement entre les souches et que toutes les souches étudiées étaient capables d'initier une réponse adaptative à l'acidité. Pour l'une des souches, nous avons caractérisé, par électrophorèse bidimensionnelle, les changements protéiques intervenant dans la réponse adaptative à l'acidité. Parmi les 50 protéines induites pendant l'adaptation, 21 ont pu être identifiées après séquençage N-terminal. Elles appartiennent à différentes catégories fonctionnelles dont celles des réponses aux stress et du métabolisme général. Afin de permettre une exploration génétique plus large de L. bulgaricus, le génome complet de la souche type ATCC 11842 a été séquencé en collaboration avec le Génoscope. Toutes ces données de génomique et de post-génomique nous conduiront à une meilleure compréhension de la physiologie de L. bulgaricus et notamment de son adaptabilité environnementale.
http://dx.doi.org/10.1051/lait:2003044.
