Diversity within species: interpreting strains in microbiomes

[1]  F. Tarazona-Santabalbina,et al.  Enfermedad por coronavirus 2019 (COVID-19) y edadismo: revisión narrativa de la literatura , 2020, Revista Española de Geriatría y Gerontología.

[2]  P. Bork,et al.  Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity , 2020, The ISME Journal.

[3]  T. Peto,et al.  Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines , 2020, GigaScience.

[4]  J. Banfield,et al.  Consistent metagenome-derived metrics verify and define bacterial species boundaries , 2019, bioRxiv.

[5]  M. Gerstein,et al.  Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis , 2019, Nature Communications.

[6]  Tom O. Delmont,et al.  Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade , 2019, eLife.

[7]  N. Dubilier,et al.  Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels , 2019, Nature Microbiology.

[8]  G. Douglas,et al.  Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes , 2019, Genome biology and evolution.

[9]  Jeff Gore,et al.  A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations , 2019, Cell.

[10]  Mick Watson,et al.  Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery , 2019, Nature Biotechnology.

[11]  Kasie Raymann,et al.  Population Genetics of Host-Associated Microbiomes , 2019, Current Molecular Biology Reports.

[12]  Enrico Seiler,et al.  Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation , 2019, PLoS Comput. Biol..

[13]  C. Ahrens,et al.  Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system , 2018, BMC Microbiology.

[14]  A. Murat Eren,et al.  Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories , 2019, mBio.

[15]  Jun Yu,et al.  Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics , 2019, mSystems.

[16]  E. Segal,et al.  The pros, cons, and many unknowns of probiotics , 2019, Nature Medicine.

[17]  Eric J Alm,et al.  Adaptive Evolution within Gut Microbiomes of Healthy People. , 2019, Cell host & microbe.

[18]  G. Cochrane,et al.  Marine DNA Viral Macro- and Microdiversity from Pole to Pole , 2019, Cell.

[19]  Jingyuan Fu,et al.  Structural variation in the gut microbiome associates with host health , 2019, Nature.

[20]  Katherine S. Pollard,et al.  New insights from uncultivated genomes of the global human gut microbiome , 2019, Nature.

[21]  Edoardo Pasolli,et al.  Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets. , 2019, Cell host & microbe.

[22]  Luis Pedro Coelho,et al.  Microbial abundance, activity and population genomic profiling with mOTUs2 , 2019, Nature Communications.

[23]  T. Thomas,et al.  MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches , 2019, Microbiome.

[24]  Peer Bork,et al.  Extensive transmission of microbes along the gastrointestinal tract , 2019, eLife.

[25]  Robert D. Finn,et al.  A new genomic blueprint of the human gut microbiota , 2019, Nature.

[26]  Yuzhen Ye,et al.  CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis , 2019, The CRISPR journal.

[27]  J. Antón,et al.  Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes , 2019, mBio.

[28]  Mark B. Schultz,et al.  Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing , 2019, mSphere.

[29]  Christian H. Ahrens,et al.  Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system , 2018, BMC Microbiology.

[30]  F. Raymond,et al.  Clostridium difficile: Investigating Transmission Patterns Between Infected and Colonized Patients Using Whole Genome Sequencing , 2018, Clinical Infectious Diseases.

[31]  George M Garrity,et al.  International Code of Nomenclature of Prokaryotes. , 2015, International journal of systematic and evolutionary microbiology.

[32]  M. Polz,et al.  Population Genomics: Microorganisms , 2019, Population Genomics.

[33]  A. Phillippy,et al.  High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries , 2018, Nature Communications.

[34]  H. Ochman,et al.  Factors driving effective population size and pan-genome evolution in bacteria , 2018, BMC Evolutionary Biology.

[35]  S. Bertilsson,et al.  Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes , 2018, Microbiome.

[36]  Itai Sharon,et al.  Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features , 2018, Cell.

[37]  A. Bhatt,et al.  Precision Identification of Diverse Bloodstream Pathogens in the Gut Microbiome , 2018, Nature Medicine.

[38]  J. Graf,et al.  Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing , 2018, bioRxiv.

[39]  S. Sheppard,et al.  Population genomics of bacterial host adaptation , 2018, Nature Reviews Genetics.

[40]  Duy Tin Truong,et al.  Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome , 2018, Cell host & microbe.

[41]  M. Savitski,et al.  Thermal proteome profiling in bacteria: probing protein state in vivo , 2018, Molecular systems biology.

[42]  Luke R. Thompson,et al.  Best practices for analysing microbiomes , 2018, Nature Reviews Microbiology.

[43]  Daniel M. Cornforth,et al.  Pseudomonas aeruginosa transcriptome during human infection , 2018, Proceedings of the National Academy of Sciences.

[44]  D. Raoult,et al.  Culturing the human microbiota and culturomics , 2018, Nature Reviews Microbiology.

[45]  Peer Bork,et al.  Extensive impact of non-antibiotic drugs on human gut bacteria , 2018, Nature.

[46]  Nicola Segata,et al.  On the Road to Strain-Resolved Comparative Metagenomics , 2018, mSystems.

[47]  M. Gelfand,et al.  Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. , 2018, Front. Microbiol..

[48]  P. Bork,et al.  The Human Gut Microbiome: From Association to Modulation , 2018, Cell.

[49]  H. Smidt,et al.  The multi-omics promise in context: from sequence to microbial isolate , 2018, Critical reviews in microbiology.

[50]  N. Young,et al.  Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments , 2018, Proceedings of the National Academy of Sciences.

[51]  D. Gevers,et al.  Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. , 2018, Cell host & microbe.

[52]  J. Pernthaler,et al.  Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria , 2017, The ISME Journal.

[53]  B. Shapiro,et al.  What Microbial Population Genomics Has Taught Us About Speciation , 2018 .

[54]  Henrik Christensen,et al.  Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. , 2018, International journal of systematic and evolutionary microbiology.

[55]  Davide Albanese,et al.  Strain profiling and epidemiology of bacterial species from metagenomic sequencing , 2017, Nature Communications.

[56]  Luis Pedro Coelho,et al.  Subspecies in the global human gut microbiome , 2017, Molecular systems biology.

[57]  J. Banfield,et al.  Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome , 2017, Nature Communications.

[58]  A. Lerner,et al.  Potential Effects of Horizontal Gene Exchange in the Human Gut , 2017, Front. Immunol..

[59]  Johannes Alneberg,et al.  Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes , 2017, Microbiome.

[60]  J. Dillner,et al.  Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides , 2017, Front. Microbiol..

[61]  Nina Luhmann,et al.  Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes , 2017, bioRxiv.

[62]  F. Cohan.  Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla , 2017, Microbiology spectrum.

[63]  Luis Pedro Coelho,et al.  Towards standards for human fecal sample processing in metagenomic studies , 2017, Nature Biotechnology.

[64]  Johannes Alneberg,et al.  DESMAN: a new tool for de novo extraction of strains from metagenomes , 2017, Genome Biology.

[65]  Arthur Brady,et al.  Strains, functions and dynamics in the expanded Human Microbiome Project , 2017, Nature.

[66]  N. Segata,et al.  Shotgun metagenomics, from sampling to analysis , 2017, Nature Biotechnology.

[67]  M. Lynch,et al.  Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen Vibrio shilonii AK1 , 2017, mBio.

[68]  George C. diCenzo,et al.  The Divided Bacterial Genome: Structure, Function, and Evolution , 2017, Microbiology and Molecular Biology Reviews.

[69]  Natalia N. Ivanova,et al.  Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea , 2017, Nature Biotechnology.

[70]  Luis Pedro Coelho,et al.  metaSNV: A tool for metagenomic strain level analysis , 2017, PloS one.

[71]  J. Shin,et al.  Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level , 2017, Current Microbiology.

[72]  Philip D. Blood,et al.  Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software , 2017, Nature Methods.

[73]  S. Lee,et al.  Dissemination of antibiotic resistance genes from antibiotic producers to pathogens , 2017, Nature Communications.

[74]  E. Hesse,et al.  Prokaryote genome fluidity is dependent on effective population size , 2017, The ISME Journal.

[75]  J. Hermisson,et al.  Soft sweeps and beyond: Understanding the patterns and probabilities of selection footprints under rapid adaptation , 2017, bioRxiv.

[76]  Jose A Navas-Molina,et al.  Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns , 2017, mSystems.

[77]  S. Quake,et al.  Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples , 2017, bioRxiv.

[78]  H. Ochman,et al.  Biological Species Are Universal across Life’s Domains , 2017, Genome biology and evolution.

[79]  Duy Tin Truong,et al.  Microbial strain-level population structure and genetic diversity from metagenomes , 2017, Genome research.

[80]  Brian C. Thomas,et al.  Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. , 2017, Genome Research.

[81]  Duy Tin Truong,et al.  Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling , 2016, mSystems.

[82]  Sarah L. R. Stevens,et al.  Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations , 2016, The ISME Journal.

[83]  Claudio Donati,et al.  MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples , 2016, Nucleic acids research.

[84]  Robert G. Beiko,et al.  SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology , 2016, bioRxiv.

[85]  K. Pollard,et al.  An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography , 2016, Genome research.

[86]  C. Saak,et al.  The Self-Identity Protein IdsD Is Communicated between Cells in Swarming Proteus mirabilis Colonies , 2016, Journal of bacteriology.

[87]  D. Falush,et al.  Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas , 2016, bioRxiv.

[88]  E. Lang,et al.  Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessarius , 2016, International journal of systematic and evolutionary microbiology.

[89]  M. Lynch,et al.  Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri , 2016, bioRxiv.

[90]  Jun Wang,et al.  Metagenome-wide association studies: fine-mining the microbiome , 2016, Nature Reviews Microbiology.

[91]  H. Bernstein,et al.  Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis , 2016, PloS one.

[92]  P. Fratamico,et al.  Advances in Molecular Serotyping and Subtyping of Escherichia coli , 2016, Front. Microbiol..

[93]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[94]  Duy Tin Truong,et al.  Strain-level microbial epidemiology and population genomics from shotgun metagenomics , 2016, Nature Methods.

[95]  F. Cohan,et al.  Bacterial Speciation: Genetic Sweeps in Bacterial Species , 2019 .

[96]  W. Koh,et al.  Single-cell genome sequencing: current state of the science , 2016, Nature Reviews Genetics.

[97]  Daniel J. Wilson,et al.  Within-host evolution of bacterial pathogens , 2016, Nature Reviews Microbiology.

[98]  Dongwan D. Kang,et al.  Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations , 2016, The ISME Journal.

[99]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[100]  W. Whitman.  Bergey's Manual of Systematics of Archaea and Bacteria , 2016 .

[101]  Leszek P. Pryszcz,et al.  Interactions between Closely Related Bacterial Strains Are Revealed by Deep Transcriptome Sequencing , 2015, Applied and Environmental Microbiology.

[102]  Duy Tin Truong,et al.  MetaPhlAn2 for enhanced metagenomic taxonomic profiling , 2015, Nature Methods.

[103]  J. T. Staley,et al.  Classification of Procaryotic Organisms and the Concept of Bacterial Speciation , 2015 .

[104]  Rob Knight,et al.  ConStrains identifies microbial strains in metagenomic datasets , 2015, Nature Biotechnology.

[105]  H. Ochman,et al.  Impermanence of bacterial clones , 2015, Proceedings of the National Academy of Sciences.

[106]  Martin Ackermann,et al.  A functional perspective on phenotypic heterogeneity in microorganisms , 2015, Nature Reviews Microbiology.

[107]  H. S. Bhaduria,et al.  HgsDb: Haplogroups Database to understand migration and molecular risk assessment , 2015, Bioinformation.

[108]  P. Bork,et al.  Inter-individual differences in the gene content of human gut bacterial species , 2015, Genome Biology.

[109]  M. Patten.  Subspecies and the philosophy of science , 2015 .

[110]  I. Nookaew,et al.  Insights from 20 years of bacterial genome sequencing , 2015, Functional & Integrative Genomics.

[111]  Elhanan Borenstein,et al.  Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species , 2015, Cell.

[112]  S. Koren,et al.  One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. , 2015, Current opinion in microbiology.

[113]  M. Sogin,et al.  Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences , 2014, The ISME Journal.

[114]  Chongle Pan,et al.  Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance , 2014, Bioinform..

[115]  Mikhail Tikhonov,et al.  Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution , 2013, The ISME Journal.

[116]  Victor Markowitz,et al.  Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy , 2014, Standards in genomic sciences.

[117]  J. Kaper,et al.  Overview and Historical Perspectives , 2014, Microbiology spectrum.

[118]  Paul Turner,et al.  Reagent and laboratory contamination can critically impact sequence-based microbiome analyses , 2014, BMC Biology.

[119]  Changjin Hong,et al.  PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples , 2014, Microbiome.

[120]  Jens Roat Kultima,et al.  Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes , 2014, Nature Biotechnology.

[121]  Susan M. Huse,et al.  Oligotyping analysis of the human oral microbiome , 2014, Proceedings of the National Academy of Sciences.

[122]  Martin Wu,et al.  Genomic Heterogeneity and Ecological Speciation within One Subspecies of Bacillus subtilis , 2014, Applied and Environmental Microbiology.

[123]  Jenna M. Lang,et al.  Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products , 2014, PeerJ.

[124]  Luis Pedro Coelho,et al.  Metagenomic insights into the human gut resistome and the forces that shape it. , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

[125]  Zamin Iqbal,et al.  A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data , 2013, Genetics.

[126]  Peter Mullany,et al.  Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers , 2013, Nature Communications.

[127]  B. Finlay,et al.  Recent Advances in Understanding Enteric Pathogenic Escherichia coli , 2013, Clinical Microbiology Reviews.

[128]  P. Bork,et al.  Accurate and universal delineation of prokaryotic species , 2013, Nature Methods.

[129]  Diana R. Nemergut,et al.  Patterns and Processes of Microbial Community Assembly , 2013, Microbiology and Molecular Reviews.

[130]  G. Gasiunas,et al.  Molecular mechanisms of CRISPR-mediated microbial immunity , 2013, Cellular and Molecular Life Sciences.

[131]  Ulrich Dobrindt,et al.  E. coli as an all-rounder: the thin line between commensalism and pathogenicity. , 2013, Current topics in microbiology and immunology.

[132]  R. Schaaper,et al.  DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair. , 2012, FEMS microbiology reviews.

[133]  W. Doolittle,et al.  Population Genomics: How Bacterial Species Form and Why They Don't Exist , 2012, Current Biology.

[134]  Otto X. Cordero,et al.  Population Genomics of Early Events in the Ecological Differentiation of Bacteria , 2012, Science.

[135]  K. Konstantinidis,et al.  Bacterial species may exist, metagenomics reveal. , 2012, Environmental microbiology.

[136]  Elhanan Borenstein,et al.  Reverse Ecology: from systems to environments and back. , 2012, Advances in experimental medicine and biology.

[137]  T. Ferenci,et al.  The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example , 2011, BMC Microbiology.

[138]  Bradley P. Coe,et al.  Genome structural variation discovery and genotyping , 2011, Nature Reviews Genetics.

[139]  Steven J. M. Jones,et al.  Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. , 2011, The New England journal of medicine.

[140]  Philip J. Hatcher,et al.  Why Genes Evolve Faster on Secondary Chromosomes in Bacteria , 2010, PLoS Comput. Biol..

[141]  Olivier Tenaillon,et al.  The population genetics of commensal Escherichia coli , 2010, Nature Reviews Microbiology.

[142]  Vincent J. Denef,et al.  Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities , 2010, Proceedings of the National Academy of Sciences.

[143]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[144]  Maureen A. O’Malley,et al.  Prokaryotic evolution and the tree of life are two different things , 2009, Biology Direct.

[145]  R. Knight,et al.  Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. , 2009, Genome research.

[146]  B. Charlesworth.  Effective population size and patterns of molecular evolution and variation , 2009, Nature Reviews Genetics.

[147]  J. Lawrence,et al.  The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. , 2009, Methods in molecular biology.

[148]  E. Delong,et al.  Genomic patterns of recombination, clonal divergence and environment in marine microbial populations , 2008, The ISME Journal.

[149]  M. Wagner,et al.  Microbial diversity and the genetic nature of microbial species , 2008, Nature Reviews Microbiology.

[150]  J. Dzink,et al.  Proposal of Three Subspecies of Fusobacterium nucleaturn Knorr 1922 : Fusobacterium nucleatum subsp . nucleatum subsp . nov . , 2008 .

[151]  D. Schluter,et al.  Adaptation from standing genetic variation. , 2008, Trends in ecology & evolution.

[152]  D. Nelson,et al.  Genetic drift at expanding frontiers promotes gene segregation , 2007, Proceedings of the National Academy of Sciences.

[153]  Wayne M. Getz,et al.  Strainer: software for analysis of population variation in community genomic datasets , 2007, BMC Bioinformatics.

[154]  Wayne M. Getz,et al.  Genetic Exchange Across a Species Boundary in the Archaeal Genus Ferroplasma , 2007, Genetics.

[155]  S. Ferriera,et al.  Supporting Online Material Materials and Methods Figs. S1 and S2 Tables S1 and S2 References Temporal Fragmentation of Speciation in Bacteria , 2022 .

[156]  Vincent J. Denef,et al.  Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria , 2007, Nature.

[157]  Daniel Falush,et al.  An African origin for the intimate association between humans and Helicobacter pylori , 2007, Nature.

[158]  Jillian F. Banfield,et al.  Genome dynamics in a natural archaeal population , 2007, Proceedings of the National Academy of Sciences.

[159]  C. Fraser,et al.  Recombination and the Nature of Bacterial Speciation , 2007, Science.

[160]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[161]  A. Nocker,et al.  Genotypic Microbial Community Profiling: A Critical Technical Review , 2007, Microbial Ecology.

[162]  K. Konstantinidis,et al.  The bacterial species definition in the genomic era , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[163]  J. Hinds,et al.  Genomic Diversity between Strains of the Same Serotype and Multilocus Sequence Type among Pneumococcal Clinical Isolates , 2006, Infection and Immunity.

[164]  I. Matic,et al.  Evolution of mutation rates in bacteria , 2006, Molecular microbiology.

[165]  F. Nowrouzian,et al.  Enhanced persistence in the colonic microbiota of Escherichia coli strains belonging to phylogenetic group B2: role of virulence factors and adherence to colonic cells. , 2006, Microbes and infection.

[166]  Christopher M Thomas,et al.  Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria , 2005, Nature Reviews Microbiology.

[167]  E. Rocha,et al.  Comparative and Evolutionary Analysis of the Bacterial Homologous Recombination Systems , 2005, PLoS genetics.

[168]  J. Hermisson,et al.  Soft Sweeps , 2005, Genetics.

[169]  K. Konstantinidis,et al.  Genomic insights that advance the species definition for prokaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[170]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[171]  Harry L. T. Mobley,et al.  Pathogenic Escherichia coli , 2004, Nature Reviews Microbiology.

[172]  J. Wilkins.  How to be a chaste species pluralist-realist: the origins of species modes and the synapomorphic species concept , 2003 .

[173]  H. Hayashi,et al.  Unification of Bifidobacterium infantis and Bifidobacterium suis as Bifidobacterium longum. , 2002, International journal of systematic and evolutionary microbiology.

[174]  L. Fisher,et al.  Quinolone Resistance Mutations in Streptococcus pneumoniae GyrA and ParC Proteins: Mechanistic Insights into Quinolone Action from Enzymatic Analysis, Intracellular Levels, and Phenotypes of Wild-Type and Mutant Proteins , 2001, Antimicrobial Agents and Chemotherapy.

[175]  N. Moran,et al.  Deletional bias and the evolution of bacterial genomes. , 2001, Trends in genetics : TIG.

[176]  F. Cohan.  Bacterial species and speciation. , 2001, Systematic biology.

[177]  J. Hey,et al.  The mind of the species problem. , 2001, Trends in ecology & evolution.

[178]  J. Andersson,et al.  Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. , 2001, Molecular biology and evolution.

[179]  M. Schloter,et al.  Ecology and evolution of bacterial microdiversity. , 2000, FEMS microbiology reviews.

[180]  L. Dijkshoorn,et al.  Strain, clone and species: comments on three basic concepts of bacteriology. , 2000, Journal of medical microbiology.

[181]  G. Tsiamis,et al.  Identification of a pathogenicity island, which contains genes for virulence and avirulence, on a large native plasmid in the bean pathogen Pseudomonas syringae pathovar phaseolicola. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[182]  J. Lake,et al.  Horizontal gene transfer among genomes: the complexity hypothesis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[183]  B. Snel,et al.  Genome phylogeny based on gene content , 1999, Nature Genetics.

[184]  Nicholas H. Barton,et al.  The effect of hitch-hiking on neutral genealogies , 1998 .

[185]  H. Dawah,et al.  Species :the units of biodiversity , 1997 .

[186]  M. Struelens.  Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. , 1996, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[187]  D H Persing,et al.  Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing , 1995, Journal of clinical microbiology.

[188]  J. Jakobek,et al.  Restriction fragment length polymorphism evidence for genetic homology within a pathovar of Pseudomonas syringae , 1994, Applied and environmental microbiology.

[189]  J. Sherris,et al.  Medical Microbiology: An Introduction to Infectious Diseases , 1992 .

[190]  E. Triplett,et al.  Genetics of competition for nodulation of legumes. , 1992, Annual review of microbiology.

[191]  S. Socransky,et al.  Proposal of three subspecies of Fusobacterium nucleatum Knorr 1922: Fusobacterium nucleatum subsp. nucleatum subsp. nov., comb. nov.; Fusobacterium nucleatum subsp. polymorphum subsp. nov., nom. rev., comb. nov.; and Fusobacterium nucleatum subsp. vincentii subsp. nov., nom. rev., comb. nov. , 1990, International journal of systematic bacteriology.

[192]  C. Pedrós-Alió.  Toward an Autecology of Bacterioplankton , 1989 .

[193]  O. Kandler,et al.  International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1987, Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology.

[194]  Benjamin F. Miller,et al.  Encyclopedia and dictionary of medicine, nursing, and allied health , 1978 .

[195]  Peter D. Moore,et al.  Biogeography: An Ecological and Evolutionary Approach , 1974 .

[196]  R. B. Root.  The Niche Exploitation Pattern of the Blue‐Gray Gnatcatcher , 1967 .