Role of Bacterial Surface Structures on the Interaction of Klebsiella pneumoniae with Phagocytes, PLoS ONE, vol.154, issue.2, pp.56847-23457627, 2013. ,
DOI : 10.1371/journal.pone.0056847.s002
Upregulation of capsule enables Streptococcus pyogenes to evade immune recognition by antigen-specific antibodies directed to the G-related ??2-macroglobulin-binding protein GRAB located on the bacterial surface, Microbes and Infection, vol.9, issue.8, pp.922-953, 2007. ,
DOI : 10.1016/j.micinf.2007.03.011
The Streptococcus pneumoniae Capsule Inhibits Complement Activity and Neutrophil Phagocytosis by Multiple Mechanisms, Infection and Immunity, vol.78, issue.2, pp.704-719, 2010. ,
DOI : 10.1128/IAI.00881-09
URL : http://iai.asm.org/content/78/2/704.full.pdf
Pneumococcal Capsular Switching: A Historical Perspective, Journal of Infectious Diseases, vol.207, issue.3, pp.439-488, 2013. ,
DOI : 10.1093/infdis/jis703
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537446
Genetic, Biochemical, and Structural Analyses of Bacterial Surface Polysaccharides, Adv Exp Med Biol, vol.883, pp.295-315, 2015. ,
DOI : 10.1007/978-3-319-23603-2_16
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems, PLoS ONE, vol.22, issue.10, p.25330359, 2014. ,
DOI : 10.1371/journal.pone.0110726.s011
URL : https://hal.archives-ouvertes.fr/pasteur-01080418
Synthase-dependent exopolysaccharide secretion in Gram-negative bacteria. Trends Microbioly, pp.63-72, 2013. ,
DOI : 10.1016/j.tim.2012.10.001
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113494
Identification of protein secretion systems in bacterial genomes, Scientific Reports, vol.13, issue.1, pp.23080-26979785, 2016. ,
DOI : 10.1186/1471-2105-13-66
URL : https://hal.archives-ouvertes.fr/pasteur-01374967
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system, Nature Communications, vol.107, pp.13219-27774985, 2016. ,
DOI : 10.1021/cr050196r
DNA-DNA Hybridization of Methylotrophic Halophilic Methanogenic Bacteria and Transfer of Methanococcus halophilusvp to the Genus Methanohalophilus as Methanohalophilus halophilus comb. nov., International Journal of Systematic Bacteriology, vol.41, issue.4, pp.558-62, 1991. ,
DOI : 10.1099/00207713-41-4-558
Methanogenesis from Methanol at Low Temperatures by a Novel Psychrophilic Methanogen, "Methanolobus psychrophilus" sp. nov., Prevalent in Zoige Wetland of the Tibetan Plateau, Applied and Environmental Microbiology, vol.74, issue.19, pp.6114-6134, 2008. ,
DOI : 10.1128/AEM.01146-08
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2565969
The cell envelope of the hyperthermophilic archaebacterium Pyrobaculum organotrophum consists of two regularly arrayed protein layers: three-dimensional structure of the outer layer, Molecular Microbiology, vol.8, issue.2, pp.253-65, 1991. ,
DOI : 10.1016/S0723-2020(86)80077-7
Origin and fate of repeats in bacteria, Nucleic Acids Research, vol.30, issue.13, pp.2987-94, 2002. ,
DOI : 10.1093/nar/gkf391
phytools: an R package for phylogenetic comparative biology (and other things), Methods in Ecology and Evolution, vol.62, issue.2, pp.217-240, 2012. ,
DOI : 10.1111/j.1558-5646.2008.00519.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00169.x/pdf
Bayesian analysis of correlated evolution of discrete characters by reversiblejump Markov chain Monte Carlo, Am Nat, vol.167, issue.6, pp.808-833, 2006. ,
Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus, BMC Genomics, vol.15, issue.1, pp.830-25269819, 2014. ,
DOI : 10.1186/1471-2164-15-830
Genetic and life-history traits associated with the distribution of prophages in bacteria, The ISME Journal, vol.41, issue.11, pp.2744-54, 2016. ,
DOI : 10.1371/journal.pcbi.0030005
The systemic imprint of growth and its uses in ecological (meta)genomics):e1000808. https, PLoS Genet, vol.6, issue.1, 2010. ,
Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control, Trends in Microbiology, vol.20, issue.7, pp.336-378, 2012. ,
DOI : 10.1016/j.tim.2012.04.005
Bacterial pathogens: from natural ecosystems to human hosts, Environmental Microbiology, vol.77, issue.2, pp.325-358, 2013. ,
DOI : 10.1128/IAI.01477-08
Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens, PLoS Pathogens, vol.152, issue.2, pp.1002503-22319444, 2012. ,
DOI : 10.1371/journal.ppat.1002503.s001
Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom, Dec, vol.12, issue.212, p.102, 2016. ,
DOI : 10.1099/mgen.0.000102
URL : http://mgen.microbiologyresearch.org/deliver/fulltext/mgen/2/12/mgen000102.pdf?itemId=/content/journal/mgen/10.1099/mgen.0.000102&mimeType=pdf&isFastTrackArticle=
Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution):e1004300. https, PLoS Genet, vol.10, issue.5, p.24786281, 2014. ,
Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258, Genome Biology and Evolution, vol.7, issue.5, pp.1267-79, 2015. ,
DOI : 10.1093/gbe/evv062
URL : http://doi.org/10.1093/gbe/evv062
Selfish operons: horizontal transfer may drive the evolution of gene clusters, Genetics, vol.143, issue.4, pp.1843-60, 1996. ,
Capsular polysaccharide inhibits adhesion of Bifidobacterium longum 105-A to enterocyte-like Caco-2 cells and phagocytosis by macrophages, Gut Pathogens, vol.74, issue.Suppl 1, pp.27-28469711, 2017. ,
DOI : 10.1128/AEM.00124-08
Capsules from Pathogenic and Non-Pathogenic Cryptococcus spp. Manifest Significant Differences in Structure and Ability to Protect against Phagocytic Cells, PLoS ONE, vol.75, issue.7???8, p.22253734, 2012. ,
DOI : 10.1371/journal.pone.0029561.t002
From grazing resistance to pathogenesis: the coincidental evolution of virulence factors):e11882. https, PloS one, vol.5, issue.8, p.20711443, 2010. ,
Surface polysaccharide involvement in establishing the rhizobium-legume symbiosis, European Journal of Biochemistry, vol.26, issue.7, pp.1365-80, 2003. ,
DOI : 10.1042/0264-6021:3420527
Abstract, Infection Control, vol.47, issue.02, pp.52-60, 1985. ,
DOI : 10.1007/BF02277362
Reservoirs of Acinetobacter baumannii outside the hospital and potential involvement in emerging human community-acquired infections, International Journal of Infectious Diseases, vol.17, issue.10, pp.802-807, 2013. ,
DOI : 10.1016/j.ijid.2013.03.021
Occurrence of an Environmental Acinetobacter baumannii Strain Similar to a Clinical Isolate in Paleosol from Croatia, Applied and Environmental Microbiology, vol.80, issue.9, pp.2860-2866, 2014. ,
DOI : 10.1128/AEM.00312-14
Enterococci in the Environment, Microbiology and Molecular Biology Reviews, vol.76, issue.4, pp.685-706, 2012. ,
DOI : 10.1128/MMBR.00023-12
The Proteobacteria, Bergey's manual of systematic bacteriology. 2 ed, 2005. ,
Transcriptional organization and regulation of the Escherichia coli K30 group 1 capsule biosynthesis (cps) gene cluster, Molecular Microbiology, vol.33, issue.4, pp.1045-60, 2003. ,
DOI : 10.1128/jb.178.6.1691-1698.1996
The Pathogenicity Island-Associated K15 Capsule Determinant Exhibits a Novel Genetic Structure and Correlates with Virulence in Uropathogenic Escherichia coli Strain 536, Infection and Immunity, vol.72, issue.10, pp.5993-6001, 2004. ,
DOI : 10.1128/IAI.72.10.5993-6001.2004
The genetic organisation of the capsule biosynthesis region of Actinobacillus pleuropneumoniae serotypes 1, 6, 7, and 12, Veterinary Microbiology, vol.129, issue.3-4, pp.3-4350, 2008. ,
DOI : 10.1016/j.vetmic.2007.12.003
Francisella tularensis Schu S4 O-Antigen and Capsule Biosynthesis Gene Mutants Induce Early Cell Death in Human Macrophages, Infection and Immunity, vol.79, issue.2, pp.581-94, 2011. ,
DOI : 10.1128/IAI.00863-10
URL : http://iai.asm.org/content/79/2/581.full.pdf
Characterization of Francisella tularensis Schu S4 mutants identified from a transposon library screened for O-antigen and capsule deficiencies, Frontiers in Microbiology, vol.6, pp.338-25999917, 2015. ,
DOI : 10.3389/fmicb.2015.00338
Characterization of the cassette containing genes for type 3 capsular polysaccharide biosynthesis in Streptococcus pneumoniae, Journal of Experimental Medicine, vol.181, issue.3, pp.973-83, 1995. ,
DOI : 10.1084/jem.181.3.973
Transcription of the Streptococcus pyogenes Hyaluronic Acid Capsule Biosynthesis Operon Is Regulated by Previously Unknown Upstream Elements, Infection and Immunity, vol.82, issue.12, pp.5293-307, 2014. ,
DOI : 10.1128/IAI.02035-14
Molecular characterization and protein analysis of the cap region, which is essential for encapsulation in Bacillus anthracis., Journal of Bacteriology, vol.171, issue.2, pp.722-752, 1989. ,
DOI : 10.1128/jb.171.2.722-730.1989
Characterization of the Bacillus subtilis ywsC Gene, Involved in ??-Polyglutamic Acid Production, Journal of Bacteriology, vol.184, issue.2, pp.337-380, 2002. ,
DOI : 10.1128/JB.184.2.337-343.2002
CapE, a 47-Amino-Acid Peptide, Is Necessary for Bacillus anthracis Polyglutamate Capsule Synthesis, Journal of Bacteriology, vol.187, issue.22, pp.7765-72, 2005. ,
DOI : 10.1128/JB.187.22.7765-7772.2005
URL : https://hal.archives-ouvertes.fr/hal-00082806
Type 37 Capsular Polysaccharide, The Journal of Experimental Medicine, vol.41, issue.2, pp.241-51, 1999. ,
DOI : 10.1099/00221287-144-11-3069
Identification and Characterization of the Capsular Polysaccharide (K-Antigen) Locus of Porphyromonas gingivalis, Infection and Immunity, vol.74, issue.1, pp.449-60, 2006. ,
DOI : 10.1128/IAI.74.1.449-460.2006
HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.39, issue.suppl, pp.29-37, 2011. ,
DOI : 10.1093/nar/gkr367
URL : http://doi.org/10.1093/nar/gkr367
Pfam: A comprehensive database of protein domain families based on seed alignments, Proteins: Structure, Function, and Genetics, vol.183, issue.3, pp.405-425, 1997. ,
DOI : 10.1016/0076-6879(90)83031-4
BLAST: at the core of a powerful and diverse set of sequence analysis tools, Nucleic Acids Research, vol.32, issue.Web Server, pp.20-25, 2004. ,
DOI : 10.1093/nar/gkh435
Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, issue.1, pp.116-21513511, 2011. ,
DOI : 10.1186/1471-2105-8-396
URL : https://hal.archives-ouvertes.fr/hal-00698365
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-80, 2013. ,
DOI : 10.1093/molbev/mst010
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603318
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-551, 1996. ,
DOI : 10.1093/bioinformatics/12.6.543
URL : https://hal.archives-ouvertes.fr/hal-00435028
The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences, Genome Biology and Evolution, vol.6, issue.10, pp.2866-82, 2014. ,
DOI : 10.1093/gbe/evu225
URL : https://hal.archives-ouvertes.fr/pasteur-01132634
Inference and Analysis of the Relative Stability of Bacterial Chromosomes, Molecular Biology and Evolution, vol.23, issue.3, pp.513-535, 2006. ,
DOI : 10.1093/molbev/msj052
Structural RNA homology search and alignment using covariance models, 2009. ,
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1975, 2009. ,
DOI : 10.1093/bioinformatics/btp348
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies, Molecular Biology and Evolution, vol.32, issue.1, pp.268-74, 2015. ,
DOI : 10.1093/molbev/msu300
URL : https://academic.oup.com/mbe/article-pdf/32/1/268/13171186/msu300.pdf
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.210, 2010. ,
DOI : 10.1186/1471-2148-10-210
APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-90, 2004. ,
DOI : 10.1093/bioinformatics/btg412
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Research, vol.44, issue.W1, pp.242-247, 2016. ,
DOI : 10.1093/nar/gkw290
The Pairwise Multiple Comparison of Mean Ranks Package (PMCMR). R package, 2014. ,
NCStats: Helper Functions for Statistics at Northland College. R package Capsule abundance and co-occurrence among prokaryotes ,