Journal ArticleDOI
The population genetics of commensal Escherichia coli.
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TLDR
The population structure of commensal E. coli is described, the factors involved in the spread of different strains, how the bacteria can adapt to different niches and how a Commensal lifestyle can evolve into a pathogenic one are described.Abstract:
The primary habitat of Escherichia coli is the vertebrate gut, where it is the predominant aerobic organism, living in symbiosis with its host. Despite the occurrence of recombination events, the population structure is predominantly clonal, allowing the delineation of major phylogenetic groups. The genetic structure of commensal E. coli is shaped by multiple host and environmental factors, and the determinants involved in the virulence of the bacteria may in fact reflect adaptation to commensal habitats. A better characterization of the commensal niche is necessary to understand how a useful commensal can become a harmful pathogen. In this Review we describe the population structure of commensal E. coli, the factors involved in the spread of different strains, how the bacteria can adapt to different niches and how a commensal lifestyle can evolve into a pathogenic one.read more
Citations
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The Clermont Escherichia coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups
Olivier Clermont,Olivier Clermont,Julia K. Christenson,Erick Denamur,Erick Denamur,David M. Gordon +5 more
TL;DR: A new PCR-based method is developed that enables an E. coli isolate to be assigned to one of the eight phylo-groups and which allows isolates that are members of the other cryptic clades (II to V) of Escherichia to be identified.
Journal ArticleDOI
Recent Advances in Understanding Enteric Pathogenic Escherichia coli
Matthew A. Croxen,Robyn J. Law,Roland Scholz,Kristie M. Keeney,Marta Wlodarska,B. Brett Finlay +5 more
TL;DR: A comprehensive review highlights recent advances in understanding of the intestinal pathotypes of E. coli, which carry an enormous potential to cause disease and continue to present challenges to human health.
Journal ArticleDOI
Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution
Michael R. Gillings,William H. Gaze,Amy Pruden,Kornelia Smalla,James M. Tiedje,Yong-Guan Zhu +5 more
TL;DR: It is suggested that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because it is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals.
Journal ArticleDOI
Genomic variation landscape of the human gut microbiome
Siegfried Schloissnig,Manimozhiyan Arumugam,Shinichi Sunagawa,Makedonka Mitreva,Julien Tap,Ana Zhu,Alison S. Waller,Daniel R. Mende,Jens Roat Kultima,John Martin,Karthik Kota,Shamil R. Sunyaev,George M. Weinstock,Peer Bork +13 more
TL;DR: Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota, indicating that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.
Journal ArticleDOI
The Human Gut Microbiome: Ecology and Recent Evolutionary Changes
Jens Walter,Ruth E. Ley +1 more
TL;DR: The human gastrointestinal tract is divided into sections, allowing digestion and nutrient absorption in the proximal region to be separate from the vast microbial populations in the large intestine, thereby reducing conflict between host and microbes.
References
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Journal ArticleDOI
Prokaryotes: The unseen majority
TL;DR: The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4-6 x 10(30) cells and 350-550 Pg of C (1 Pg = 10(15) g), respectively, which is 60-100% of the estimated total carbon in plants.
Journal ArticleDOI
Lateral gene transfer and the nature of bacterial innovation
TL;DR: Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms.
Journal ArticleDOI
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
TL;DR: Parsimony or minimum evolution methods were first introduced into phylogenetic inference by Camin and Sokal (1965), and a number of other parsimony methods have since appeared in the systematic literature and found widespread use in studies of molecular evolution.
Journal ArticleDOI
Evolution of mammals and their gut microbes
Ruth E. Ley,Micah Hamady,Catherine A. Lozupone,Catherine A. Lozupone,Peter J. Turnbaugh,Rob Roy Ramey,J. Stephen Bircher,Michael L. Schlegel,Tammy A. Tucker,Mark D. Schrenzel,Rob Knight,Jeffrey I. Gordon +11 more
TL;DR: It is indicated that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
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