Diversity within Species: Interpreting Strains in Microbiomes
Open accessAbstract
Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
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There are no standards governing how many SNVs constitute a different strain or whether such SNVs must be fixed in the population or affect phenotypic.
“There are no standards governing how many SNVs constitute a different strain or whether such SNVs must be fixed in the population or affect phenotypic [57].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [57]
A generally applicable operational definition of strain with a strong biological basis has not yet been provided and may not exist.
“A generally applicable operational definition of strain with a strong biological basis has not yet been provided and may not exist [57].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [57]
Different individuals with similar diets, lifestyles, and health profiles can display an overall similar gut microbiome composition by convergence to a comparable set of species.
“Different individuals with similar diets, lifestyles, and health profiles can display an overall similar gut microbiome composition by convergence to a comparable set of species.”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [138]
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DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works
Tenover, F. C., Arbeit, R. D., Goering, R. V., Mickelsen, P. A., Murray, B. E., Persing, D. H., & Swaminathan, B. (1995) · Journal of Clinical Microbiology · doi:10.1128/jcm.33.9.2233-2239.1995 · Cited by 8,203 · see citing works
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics
Wayne, L. G., Moore, W. E., Stackebrandt, E. S., Kandler, O., Colwell, R. R., Krichevsky, M. I., Trüper, H. G., Murray, R. G. E., Grimont, P. A. D., Brenner, D. J., et al. (1987) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-37-4-463 · Cited by 7,338 · see citing works
Shifting the genomic gold standard for the prokaryotic species definition
Richter, M., & Rossello-Mora, R. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906412106 · Cited by 6,343 · see citing works
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018) · Nature Communications · doi:10.1038/s41467-018-07641-9 · Cited by 5,748 · see citing works
Kaper, J. B., Nataro, J. P., & Mobley, H. L. T. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro818 · Cited by 5,583 · see citing works
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P. A. R., & Tiedje, J. M. (2007) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.64483-0 · Cited by 4,733 · see citing works
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463 · see citing works
Mash: fast genome and metagenome distance estimation using MinHash
(2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373 · see citing works
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Chun, J., Oren, A., Ventosa, A., Christensen, H. K., Arahal, D. R., da Costa, M. S., Rooney, A. P., Yi, H., Xu, X.-W., Meyer, S. E. D., et al. (2018) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.002516 · Cited by 3,100 · see citing works
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624 · see citing works
Self-citationCommunity structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417 · see citing works
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Johnson, J. S., Spakowicz, D. J., Hong, B., Petersen, L., Demkowicz, P. C., Chen, L., Leopold, S. R., Hanson, B., Agresta, H. O., Gerstein, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13036-1 · Cited by 2,286 · see citing works
Bergey's Manual of Systematics of Archaea and Bacteria
(2015) · Wiley eBooks · doi:10.1002/9781118960608 · Cited by 2,219 · see citing works
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202 · see citing works
Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria
Thomas, C. M., & Nielsen, K. M. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1234 · Cited by 2,194 · see citing works
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185 · see citing works
Genomic insights that advance the species definition for prokaryotes
Konstantinidis, K. T., & Tiedje, J. M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409727102 · Cited by 2,124 · see citing works
Best practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030 · see citing works
Patterns and Processes of Microbial Community Assembly
Nemergut, D. R., Schmidt, S. K., Fukami, T., O’Neill, S., Bilinski, T. M., Stanish, L. F., Knelman, J. E., Darcy, J. L., Lynch, R. C., Wickey, P., et al. (2013) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00051-12 · Cited by 1,990 · see citing works
Extensive impact of non-antibiotic drugs on human gut bacteria
Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E. E., Brochado, A. R., Fernandez, K. C., Dose, H., Mori, H., et al. (2018) · Nature · doi:10.1038/nature25979 · Cited by 1,905 · see citing works
Self-citationDeblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
Amir, A., McDonald, D., Navas-Molina, J. A., Kopylova, E., Morton, J. T., Zech Xu, Z., Kightley, E. P., Thompson, L. R., Hyde, E. R., Gonzalez, A., et al. (2017) · mSystems · doi:10.1128/msystems.00191-16 · Cited by 1,881 · see citing works
The Niche Exploitation Pattern of the Blue‐Gray Gnatcatcher
Root, R. B. (1967) · Ecological Monographs · doi:10.2307/1942327 · Cited by 1,817 · see citing works
Effective population size and patterns of molecular evolution and variation
Charlesworth, B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2526 · Cited by 1,698 · see citing works
Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., Kotler, E., Zur, M., Regev-Lehavi, D., Brik, R. B.-Z., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.041 · Cited by 1,695 · see citing works
Genome structural variation discovery and genotyping
Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630 · see citing works
Recent Advances in Understanding Enteric Pathogenic Escherichia coli
Croxen, M. A., Law, R. J., Scholz, R., Keeney, K. M., Wlodarska, M., & Finlay, B. B. (2013) · Clinical Microbiology Reviews · doi:10.1128/cmr.00022-13 · Cited by 1,578 · see citing works
The population genetics of commensal Escherichia coli
Tenaillon, O., Skurnik, D., Picard, B., & Denamur, É. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2298 · Cited by 1,536 · see citing works
The pros, cons, and many unknowns of probiotics
Suez, J., Zmora, N., Segal, E., & Elinav, E. (2019) · Nature Medicine · doi:10.1038/s41591-019-0439-x · Cited by 1,398 · see citing works
Single-cell genome sequencing: current state of the science
Gawad, C., Koh, W., & Quake, S. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.16 · Cited by 1,334 · see citing works
A new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works
Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292 · see citing works
Self-citationStrains, functions and dynamics in the expanded Human Microbiome Project
Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267 · see citing works
MetaHIT Consortium, Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2939 · Cited by 1,184 · see citing works
Self-citationHorizontal gene transfer among genomes: The complexity hypothesis
Jain, R., Rivera, M. C., & Lake, J. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.7.3801 · Cited by 1,170 · see citing works
Hermisson (2005) · doi:10.1534/genetics.104.036947 · Cited by 1,009 · see citing works
Microbial community profiling for human microbiome projects: Tools, techniques, and challengesPreprint
Hamady, M., & Knight, R. D. (2009) · Genome Research · doi:10.1101/gr.085464.108 · Cited by 1,002 · see citing works
An African origin for the intimate association between humans and Helicobacter pylori
Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., der Merwe, V., et al. (2007) · Nature · doi:10.1038/nature05562 · Cited by 977 · see citing works
A functional perspective on phenotypic heterogeneity in microorganisms
Ackermann, M. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3491 · Cited by 922 · see citing works
Towards standards for human fecal sample processing in metagenomic studies
Costea, P. I., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F.-E., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3960 · Cited by 893 · see citing works
Self-citationCulturing the human microbiota and culturomics
Lagier, J., Dubourg, G., Million, M., Cadoret, F., Bilen, M., Fenollar, F., Levasseur, A., Rolain, J., Fournier, P., & Raoult, D. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0041-0 · Cited by 882 · see citing works
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4458 · Cited by 873 · see citing works
Deletional bias and the evolution of bacterial genomes.
Mira, A., Ochman, H., & Moran, N. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02447-7 · Cited by 850 · see citing works
The Human Gut Microbiome: From Association to Modulation
Schmidt, T. S. B., Raes, J., & Bork, P. (2018) · Cell · doi:10.1016/j.cell.2018.02.044 · Cited by 845 · see citing works
Microbial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839 · see citing works
Biogeography: An Ecological and Evolutionary Approach.
Cox, C. B., Healey, I. N., & Moore, P. D. (1977) · Systematic Botany · doi:10.2307/2418264 · Cited by 806 · see citing works
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
Gregory, A., Zayed, A. A., Conceição‐Neto, N., Temperton, B., Bolduc, B., Alberti, A., Ardyna, M., Arkhipova, K., Carmichael, M., Cruaud, C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.040 · Cited by 793 · see citing works
New insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works
International Code of Nomenclature of Prokaryotes
Parker, C. T., Tindall, B. J., & Garrity, G. M. (2015) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.000778 · Cited by 727 · see citing works
Insights from 20 years of bacterial genome sequencing
Land, M., Hauser, L., Jun, S., Nookaew, I., Leuze, M. R., Ahn, T.-H., Karpinets, T. V., Lund, O., Kora, G., Wassenaar, T. M., et al. (2015) · Functional & Integrative Genomics · doi:10.1007/s10142-015-0433-4 · Cited by 717 · see citing works
Genetic drift at expanding frontiers promotes gene segregation
Hallatschek, O., Hersen, P., Ramanathan, S., & Nelson, D. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0710150104 · Cited by 712 · see citing works
Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak
Gardy, J. L., Johnston, J. C., Sui, S. J. H., Cook, V. J., Shah, L., Brodkin, E., Rempel, S., Moore, R. L., Zhao, Y., Holt, R. A., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1003176 · Cited by 710 · see citing works
Genome phylogeny based on gene content
Snel, ., Peer Bork, B., & Huynen, M. A. (1999) · Nature Genetics · doi:10.1038/5052 · Cited by 708 · see citing works
Meier‐Kolthoff, J. P., Hahnke, R. L., Petersen, J., Scheuner, C., Michael, V., Fiebig, A., Rohde, C., Rohde, M., Fartmann, B., Goodwin, L., et al. (2014) · Standards in Genomic Sciences · doi:10.1186/1944-3277-9-2 · Cited by 617 · see citing works
Microbial diversity and the genetic nature of microbial species
Achtman, M., & Wagner, M. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1872 · Cited by 611 · see citing works
The bacterial species definition in the genomic era
Konstantinidis, K. T., Ramette, A., & Tiedje, J. M. (2006) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2006.1920 · Cited by 604 · see citing works
Extensive transmission of microbes along the gastrointestinal tract
Schmidt, T. S., Hayward, M. R., Coelho, L. P., Li, S. S., Costea, P. I., Voigt, A. Y., Wirbel, J., Maistrenko, O. M., Alves, R. J., Bergsten, E., et al. (2019) · eLife · doi:10.7554/elife.42693 · Cited by 596 · see citing works
Self-citationEren, A. M., Morrison, H. G., Lescault, P. J., Réveillaud, J., Vineis, J. H., & Sogin, M. L. (2014) · The ISME Journal · doi:10.1038/ismej.2014.195 · Cited by 594 · see citing works
Stewart, R. D., Auffret, M. D., Warr, A., Walker, A. W., Roehe, R., & Watson, M. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0202-3 · Cited by 593 · see citing works
Recombination and the Nature of Bacterial Speciation
Fraser, C., Hanage, W. P., & Spratt, B. G. (2007) · Science · doi:10.1126/science.1127573 · Cited by 562 · see citing works
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
Shapiro, B., Friedman, J., Cordero, O., Preheim, S., Timberlake, S. C., Szabó, G., Polz, M., & Alm, E. J. (2012) · Science · doi:10.1126/science.1218198 · Cited by 515 · see citing works
Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470 · see citing works
Within-host evolution of bacterial pathogens
Didelot, X., Walker, A. S., Peto, T., Crook, D. W., & Wilson, D. J. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2015.13 · Cited by 462 · see citing works
Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems
Struelens, M. J. (1996) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.1996.tb00193.x · Cited by 458 · see citing works
Microbial abundance, activity and population genomic profiling with mOTUs2
Milanese, A., Mende, D. R., Paoli, L., Salazar, G., Ruscheweyh, H.-J., Cuenca, M., Hingamp, P., Alves, R., Costea, P. I., Coelho, L. P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08844-4 · Cited by 446 · see citing works
Species : the units of biodiversity
CLARIDGE, M. F., Dawah, H. A., & Wilson, M. R. (1997) · Chapman & Hall eBooks · Cited by 445 · see citing works
Asnicar, F., Manara, S., Zolfo, M., Truong, D. T., Scholz, M., Armanini, F., Ferretti, P., Gorfer, V., Pedrotti, A., Tett, A., et al. (2017) · mSystems · doi:10.1128/msystems.00164-16 · Cited by 445 · see citing works
Self-citationAdaptive Evolution within Gut Microbiomes of Healthy People
Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434 · see citing works
Metagenome-wide association studies: fine-mining the microbiome
Wang, J., & Jia, H. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.83 · Cited by 429 · see citing works
Dissemination of antibiotic resistance genes from antibiotic producers to pathogens
Jiang, X., Ellabaan, M. M. H., Charusanti, P., Munck, C., Blin, K., Tong, Y., Weber, T., Sommer, M. O. A., & Lee, S. Y. (2017) · Nature Communications · doi:10.1038/ncomms15784 · Cited by 417 · see citing works
Smillie, C. S., Sauk, J. S., Gevers, D., Friedman, J., Sung, J., Youngster, I., Hohmann, E. L., Staley, C. M., Khoruts, A., Sadowsky, M. J., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.01.003 · Cited by 417 · see citing works
Genotypic Microbial Community Profiling: A Critical Technical Review
Nocker, A., Burr, M. D., & Camper, A. K. (2007) · Microbial Ecology · doi:10.1007/s00248-006-9199-5 · Cited by 411 · see citing works
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
Koren, S., & Phillippy, A. M. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.11.014 · Cited by 406 · see citing works
Evolution of mutation rates in bacteria
Denamur, É., & Matić, I. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05150.x · Cited by 402 · see citing works
Filippis, F. D., Pasolli, E., Tett, A., Tarallo, S., Naccarati, A., Angelis, M. D., Neviani, E., Cocolin, L., Gobbetti, M., Segata, N., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.004 · Cited by 399 · see citing works
Bacterial Species and Speciation
Cohan, F. M. (2001) · Systematic Biology · doi:10.1080/10635150118398 · Cited by 398 · see citing works
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Scholz, M., Ward, D. V., Pasolli, E., Tolio, T., Zolfo, M., Asnicar, F., Truong, D. T., Tett, A., Morrow, A. L., & Segata, N. (2016) · Nature Methods · doi:10.1038/nmeth.3802 · Cited by 374 · see citing works
E. coli as an All-Rounder: The Thin Line Between Commensalism and Pathogenicity
Leimbach, A., Hacker, J. H., & Dobrindt, U. (2013) · Current topics in microbiology and immunology · doi:10.1007/82_2012_303 · Cited by 366 · see citing works
Structural variation in the gut microbiome associates with host health
Zeevi, D., Korem, T., Godneva, A., Bar, N., Kurilshikov, A., Lotan-Pompan, M., Weinberger, A., Fu, J., Wijmenga, C., Zhernakova, A., et al. (2019) · Nature · doi:10.1038/s41586-019-1065-y · Cited by 351 · see citing works
Oligotyping analysis of the human oral microbiome
Eren, A. M., Borisy, G. G., Huse, S. M., & Mark Welch, J. L. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1409644111 · Cited by 347 · see citing works
Comparative and Evolutionary Analysis of the Bacterial Homologous Recombination Systems
Rocha, E. P. C., Cornet, E., & Michel, B. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010015 · Cited by 341 · see citing works
The mind of the species problem
Hey, J. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(01)02145-0 · Cited by 333 · see citing works
Accurate and universal delineation of prokaryotic species
Mende, D. R., Sunagawa, S., Zeller, G., & Peer Bork, B. (2013) · Nature Methods · doi:10.1038/nmeth.2575 · Cited by 328 · see citing works
Jackson, R. W., Athanassopoulos, E., Tsiamis, G., Mansfıeld, J. W., Sesma, A., Arnold, D. L., Gibbon, M. J., Murillo, J., Taylor, J. D., & Vivian, A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.19.10875 · Cited by 306 · see citing works
The effect of hitch-hiking on neutral genealogies
Barton, N. H. (1998) · Genetics Research · doi:10.1017/s0016672398003462 · Cited by 292 · see citing works
The Divided Bacterial Genome: Structure, Function, and Evolution
diCenzo, G. C., & Finan, T. M. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00019-17 · Cited by 281 · see citing works
Pseudomonas aeruginosa transcriptome during human infection
Cornforth, D. M., Dees, J. L., Ibberson, C. B., Huse, H., Mathiesen, I. H. M., Kirketerp‐Møller, K., Wolcott, R. D., Rumbaugh, K. P., Bjarnsholt, T., & Whiteley, M. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717525115 · Cited by 270 · see citing works
ConStrains identifies microbial strains in metagenomic datasets
Luo, C., Knight, R. D., Siljander, H., Knip, M., Xavier, R. J., & Gevers, D. (2015) · Nature Biotechnology · doi:10.1038/nbt.3319 · Cited by 267 · see citing works
GENETICS OF COMPETITION FOR NODULATION OF LEGUMES
Triplett, E. W., & Sadowsky, M. J. (1992) · Annual Review of Microbiology · doi:10.1146/annurev.mi.46.100192.002151 · Cited by 267 · see citing works
Hong, C., Manimaran, S., Shen, Y., Perez-Rogers, J. F., Byrd, A. L., Castro‐Nallar, E., Crandall, K. A., & Johnson, W. E. (2014) · Microbiome · doi:10.1186/2049-2618-2-33 · Cited by 257 · see citing works
Hermisson, J., & Pennings, P. S. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12808 · Cited by 256 · see citing works
Population genomics of bacterial host adaptation
Sheppard, S. K., Guttman, D. S., & Fitzgerald, J. R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0032-z · Cited by 251 · see citing works
Encyclopedia and Dictionary of Medicine, Nursing and Allied Health
Miller, B. F., & Keane, C. B. (1978) · Medical Entomology and Zoology · Cited by 249 · see citing works
Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species
Greenblum, S. I., Carr, R., & Borenstein, E. (2015) · Cell · doi:10.1016/j.cell.2014.12.038 · Cited by 244 · see citing works
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
Bendall, M. L., Stevens, S. L. R., Chan, L., Malfatti, S., Schwientek, P., Tremblay, J., Schackwitz, W., Martin, J., Pati, A., Bushnell, B., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2015.241 · Cited by 238 · see citing works
Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria
Neuenschwander, S. M., Ghai, R., Pernthaler, J., & Salcher, M. M. (2017) · The ISME Journal · doi:10.1038/ismej.2017.156 · Cited by 232 · see citing works
Prokaryotic evolution and the tree of life are two different things
Bapteste, E. P., O’Malley, M. A., Beiko, R. G., Ereshefsky, M., Gogarten, J. P., Franklin-Hall, L. R., Lapointe, F., Dupré, J., Dagan, T., Boucher, Y., et al. (2009) · Biology Direct · doi:10.1186/1745-6150-4-34 · Cited by 226 · see citing works
Brooks, B., Olm, M. R., Firek, B. A., Baker, R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F. (2017) · Nature Communications · doi:10.1038/s41467-017-02018-w · Cited by 226 · see citing works
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
Lo, I., Denef, V. J., VerBerkmoes, N. C., Shah, M. B., Goltsman, D. S. A., DiBartolo, G., Tyson, G. W., Allen, E. E., Ram, R. J., Detter, J. C., et al. (2007) · Nature · doi:10.1038/nature05624 · Cited by 222 · see citing works
The multi-omics promise in context: from sequence to microbial isolate
Gutleben, J., Mares, M. C. D., van Elsas, J. D., Smidt, H., Overmann, J., & Sipkema, D. (2017) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2017.1332003 · Cited by 216 · see citing works
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
Tikhonov, M., Leach, R. W., & Wingreen, N. S. (2014) · The ISME Journal · doi:10.1038/ismej.2014.117 · Cited by 203 · see citing works
Inter-individual differences in the gene content of human gut bacterial species
Zhu, A., Sunagawa, S., Mende, D. R., & Peer Bork, B. (2015) · Genome biology · doi:10.1186/s13059-015-0646-9 · Cited by 202 · see citing works
A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations
Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J., & Polz, M. F. (2019) · Cell · doi:10.1016/j.cell.2019.06.033 · Cited by 201 · see citing works
Potential Effects of Horizontal Gene Exchange in the Human Gut
Lerner, A., Matthias, T., & Aminov, R. I. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01630 · Cited by 200 · see citing works
Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
Olm, M., Crits-Christoph, A., Diamond, S., Lavy, A., Carnevali, P. B. M., & Banfield, J. (2020) · mSystems · doi:10.1128/msystems.00731-19 · Cited by 195 · see citing works
Precision identification of diverse bloodstream pathogens in the gut microbiome
Tamburini, F. B., Andermann, T. M., Tkachenko, E., Senchyna, F., Banaei, N., & Bhatt, A. S. (2018) · Nature Medicine · doi:10.1038/s41591-018-0202-8 · Cited by 192 · see citing works
Thermal proteome profiling in bacteria: probing protein state in vivo
Mateus, A., Bobonis, J., Kurzawa, N., Stein, F., Helm, D., Hevler, J. F., Typas, A., & Savitski, M. M. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188242 · Cited by 190 · see citing works
Bacterial species may exist, metagenomics reveal
Caro‐Quintero, A., & Konstantinidis, K. T. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02668.x · Cited by 188 · see citing works
Denef, V. J., Kalnejais, L. H., Mueller, R., Wilmes, P., Baker, B. J., Thomas, B. C., VerBerkmoes, N. C., Hettich, R. L., & Banfield, J. F. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907041107 · Cited by 186 · see citing works
Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers
Brouwer, M. S. M., Roberts, A. P., Hussain, H. A., Williams, R. J., Allan, E., & Mullany, P. P. (2013) · Nature Communications · doi:10.1038/ncomms3601 · Cited by 184 · see citing works
DESMAN: a new tool for de novo extraction of strains from metagenomes
Quince, C., Delmont, T., Raguideau, S., Alneberg, J., Darling, A., Collins, G., & Eren, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1309-9 · Cited by 175 · see citing works
Biological Species Are Universal across Life’s Domains
Bobay, L., & Ochman, H. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx026 · Cited by 167 · see citing works
Advances in Molecular Serotyping and Subtyping of Escherichia coli
Fratamico, P., Debroy, C., Liu, Y.-H., Needleman, D., Baranzoni, G., & Feng, P. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00644 · Cited by 166 · see citing works
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
Petkau, A., Mabon, P., Sieffert, C., Knox, N., Cabral, J., Iskander, M., Iskander, M., Weedmark, K. A., Zaheer, R., Katz, L. S., et al. (2017) · Microbial Genomics · doi:10.1099/mgen.0.000116 · Cited by 166 · see citing works
DNA replication fidelity in Escherichia coli : a multi-DNA polymerase affair
Fijałkowska, I. J., Schaaper, R. M., & Jonczyk, P. (2012) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2012.00338.x · Cited by 165 · see citing works
Nowrouzian, F. L., Adlerberth, I., & Wold, A. E. (2006) · Microbes and Infection · doi:10.1016/j.micinf.2005.10.011 · Cited by 164 · see citing works
Pseudogenes, Junk DNA, and the Dynamics of Rickettsia Genomes
Andersson, J. O., & Andersson, S. G. E. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003864 · Cited by 163 · see citing works
Ecology and evolution of bacterial microdiversity: Table 1
Schloter, M., Lebuhn, M., Heulin, T., & Hartmann, A. (2000) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2000.tb00564.x · Cited by 161 · see citing works
Song, W.-Z., Wemheuer, B., Zhang, S., Steensen, K., & Thomas, T. (2019) · Microbiome · doi:10.1186/s40168-019-0649-y · Cited by 160 · see citing works
Goldstein, S., Beka, L., Graf, J., & Klassen, J. L. (2019) · BMC Genomics · doi:10.1186/s12864-018-5381-7 · Cited by 154 · see citing works
Factors driving effective population size and pan-genome evolution in bacteria
Bobay, L., & Ochman, H. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1272-4 · Cited by 150 · see citing works
Subspecies and the philosophy of science
Patten, M. A. (2015) · The Auk · doi:10.1642/auk-15-1.1 · Cited by 141 · see citing works
Subspecies in the global human gut microbiome
Costea, P. I., Coelho, L. P., Sunagawa, S., Munch, R., Huerta‐Cepas, J., Forslund, S. K., Hildebrand, F., Kushugulova, A. R., Zeller, G., & Bork, P. (2017) · Molecular Systems Biology · doi:10.15252/msb.20177589 · Cited by 141 · see citing works
Self-citationDelmont, T. O., Kiefl, E., Kilinc, O., Esen, Ö. C., Uysal, I., Rappé, M. S., Giovannoni, S. J., & Eren, A. M. (2019) · eLife · doi:10.7554/elife.46497 · Cited by 137 · see citing works
Beitel, C. W., Froenicke, L., Lang, J., Korf, I. F., Michelmore, R. W., Eisen, J. A., & Darling, A. E. (2014) · PeerJ · doi:10.7717/peerj.415 · Cited by 134 · see citing works
Genome dynamics in a natural archaeal population
Allen, E. E., Tyson, G. W., Whitaker, R. J., Detter, J. C., Richardson, P. M., & Banfield, J. F. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604851104 · Cited by 133 · see citing works
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines
Bush, S. J., Foster, D., Eyre, D. W., Clark, E. L., Maio, N. D., Shaw, L. P., Stoesser, N. E., Peto, T., Crook, D. W., & Walker, A. S. (2020) · GigaScience · doi:10.1093/gigascience/giaa007 · Cited by 133 · see citing works
Maistrenko, O. M., Mende, D. R., Lütge, M., Hildebrand, F., Schmidt, T., Li, S. S., Rodrigues, J. F. M., von Mering, C., Coelho, L. P., Huerta‐Cepas, J., et al. (2020) · The ISME Journal · doi:10.1038/s41396-020-0600-z · Cited by 133 · see citing works
Self-citationSomerville, V., Lutz, S., Schmid, M., Frei, D., Moser, A. I., Irmler, S., Frey, J. E., & Ahrens, C. H. (2019) · BMC Microbiology · doi:10.1186/s12866-019-1500-0 · Cited by 132 · see citing works
Strain profiling and epidemiology of bacterial species from metagenomic sequencing
Albanese, D., & Donati, C. (2017) · Nature Communications · doi:10.1038/s41467-017-02209-5 · Cited by 129 · see citing works
On the road to strain-resolved comparative metagenomics
Segata, N. (2018) · mSystems · doi:10.1128/msystems.00190-17 · Cited by 127 · see citing works
Strain, clone and species: comments on three basic concepts of bacteriology
Dijkshoorn, L., Ursing, B. M., & Ursing, J. (2000) · Journal of Medical Microbiology · doi:10.1099/0022-1317-49-5-397 · Cited by 123 · see citing works
Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels
Ansorge, R., Romano, S., Sayavedra, L., Porras, M. Á. G., Kupczok, A., Tegetmeyer, H. E., Dubilier, N., & Petersen, J. M. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0572-9 · Cited by 123 · see citing works
Olm, M. R., Brown, C. T., Brooks, B., Firek, B., Baker, R. W., Burstein, D. E., Soenjoyo, K. R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F. (2017) · Genome Research · doi:10.1101/gr.213256.116 · Cited by 122 · see citing works
Temporal Fragmentation of Speciation in Bacteria
Retchless, A. C., & Lawrence, J. G. (2007) · Science · doi:10.1126/science.1144876 · Cited by 119 · see citing works
Molecular mechanisms of CRISPR-mediated microbial immunity
Gasiūnas, G., Šinkūnas, T., & Šikšnys, V. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1438-6 · Cited by 117 · see citing works
Why Genes Evolve Faster on Secondary Chromosomes in Bacteria
Cooper, V. S., Vohr, S. H., Wrocklage, S. C., & Hatcher, P. J. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000732 · Cited by 116 · see citing works
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Ahn, T.-H., Chai, J., & Pan, C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu641 · Cited by 115 · see citing works
Genomic patterns of recombination, clonal divergence and environment in marine microbial populations
Konstantinidis, K. T., & DeLong, E. F. (2008) · The ISME Journal · doi:10.1038/ismej.2008.62 · Cited by 113 · see citing works
Alneberg, J., Karlsson, C. M. G., Divne, A., Bergin, C., Homa, F., Lindh, M. V., Hugerth, L. W., Ettema, T. J. G., Bertilsson, S., Andersson, A. F., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0550-0 · Cited by 113 · see citing works
Overview and Historical Perspectives
Kaper, J. B., & O’Brien, A. D. (2014) · Microbiology Spectrum · doi:10.1128/microbiolspec.ehec-0028-2014 · Cited by 111 · see citing works
Dzink, J. L., SHEENAN, M. T., & SOCRANSKY, S. S. (1990) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-40-1-74 · Cited by 111 · see citing works
Unification of Bifidobacterium infantis and Bifidobacterium suis as Bifidobacterium longum.
Sakata, S., Kitahara, M., Sakamoto, M., Hayashi, H., Fukuyama, M., & Benno, Y. (2002) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-52-6-1945 · Cited by 111 · see citing works
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples
Zolfo, M., Tett, A., Jousson, O., Donati, C., & Segata, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw837 · Cited by 105 · see citing works
Prokaryote genome fluidity is dependent on effective population size
Andreani, N. A., Hesse, E., & Vos, M. (2017) · The ISME Journal · doi:10.1038/ismej.2017.36 · Cited by 103 · see citing works
metaSNV: A tool for metagenomic strain level analysis
Costea, P. I., Munch, R., Coelho, L. P., Paoli, L., Sunagawa, S., & Bork, P. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182392 · Cited by 103 · see citing works
Self-citationYu, F. B., Blainey, P. C., Schulz, F., Woyke, T., Horowitz, M., & Quake, S. R. (2017) · eLife · doi:10.7554/elife.26580 · Cited by 102 · see citing works
Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments
Burghardt, L. T., Epstein, B., Guhlin, J. G., Nelson, M. S., Taylor, M. R., Young, N. D., Sadowsky, M. J., & Tiffin, P. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1714246115 · Cited by 101 · see citing works
Metagenomic insights into the human gut resistome and the forces that shape it
Forslund, S. K., Sunagawa, S., Coelho, L. P., & Bork, P. (2014) · BioEssays · doi:10.1002/bies.201300143 · Cited by 100 · see citing works
Self-citationGenome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level
Kook, J., Park, S., Lim, Y. K., Cho, E., Jo, E., Roh, H., Shin, Y., Paek, J., Kim, H.-S., Kim, H., et al. (2017) · Current Microbiology · doi:10.1007/s00284-017-1296-9 · Cited by 100 · see citing works
Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas
Thorell, K., Yahara, K., Berthenet, E., Lawson, D. J., Mikhail, J. M., Kato, I., Méndez-Tenorio, A., Rizzato, C., Bravo, M. M., Suzuki, R., et al. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006546 · Cited by 99 · see citing works
Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories
Shaiber, A., & Eren, A. M. (2019) · mBio · doi:10.1128/mbio.00725-19 · Cited by 85 · see citing works
Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes
González‐Torres, P., Rodríguez, F., Antón, J., & Gabaldón, T. (2019) · mBio · doi:10.1128/mbio.02494-18 · Cited by 81 · see citing works
Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes
Douglas, G. M., & Langille, M. G. I. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz184 · Cited by 79 · see citing works
Classification of Procaryotic Organisms and the Concept of Bacterial Speciation
Brenner, D. J., Staley, J. T., & Krieg, N. R. (2015) · Bergey's Manual of Systematics of Archaea and Bacteria · doi:10.1002/9781118960608.bm00006 · Cited by 76 · see citing works
Reverse Ecology: From Systems to Environments and Back
Levy, R., & Borenstein, E. (2012) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-3567-9_15 · Cited by 74 · see citing works
The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation
Lawrence, J. G., & Retchless, A. C. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-853-9_3 · Cited by 74 · see citing works
Dillon, M. M., Sung, W., Sebra, R., Lynch, M., & Cooper, V. S. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw224 · Cited by 74 · see citing works
Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
Garcia, S. L., Stevens, S. L. R., Crary, B. C., et al. (2017) · The ISME Journal · doi:10.1038/s41396-017-0001-0 · Cited by 74 · see citing works
Wilkins, J. (2003) · Biology & Philosophy · doi:10.1023/a:1026390327482 · Cited by 73 · see citing works
Genetic Exchange Across a Species Boundary in the Archaeal Genus Ferroplasma
Eppley, J. M., Tyson, G. W., Getz, W. M., & Banfield, J. F. (2007) · Genetics · doi:10.1534/genetics.107.072892 · Cited by 69 · see citing works
Pan, X.-S., Yagüe, G., & Fisher, L. M. (2001) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.45.11.3140-3147.2001 · Cited by 68 · see citing works
Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis
Pierce, J. V., & Bernstein, H. D. (2016) · PLoS ONE · doi:10.1371/journal.pone.0158171 · Cited by 67 · see citing works
Kong, L. Y., Eyre, D. W., Corbeil, J., Raymond, F., Walker, A. S., Wilcox, M. H., Crook, D. W., Michaud, S., Toye, B., Frost, E., et al. (2019) · Clinical Infectious Diseases · doi:10.1093/cid/ciy457 · Cited by 63 · see citing works
Genomic Heterogeneity and Ecological Speciation within One Subspecies of Bacillus subtilis
Kopac, S., Wang, Z., Wiedenbeck, J., Sherry, J., Wu, M., & Cohan, F. M. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00576-14 · Cited by 61 · see citing works
Silva, N. A., McCluskey, J., Jefferies, J. M., et al. (2006) · Infection and Immunity · doi:10.1128/iai.00079-06 · Cited by 61 · see citing works
Impermanence of bacterial clones
Bobay, L., Traverse, C. C., & Ochman, H. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1501724112 · Cited by 54 · see citing works
Spira, B., Toledo, R. D. A., Maharjan, R. P., et al. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-248 · Cited by 51 · see citing works
Bacterial Speciation: Genetic Sweeps in Bacterial Species
Cohan, F. M. (2016) · Current Biology · doi:10.1016/j.cub.2015.10.022 · Cited by 46 · see citing works
Population Genomics: How Bacterial Species Form and Why They Don't Exist
Doolittle, W. F. (2012) · Current Biology · doi:10.1016/j.cub.2012.04.034 · Cited by 45 · see citing works
Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.
Moldovan, M. A., & Gelfand, M. S. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00428 · Cited by 45 · see citing works
The Self-Identity Protein IdsD Is Communicated between Cells in Swarming Proteus mirabilis Colonies
Saak, C. C., & Gibbs, K. A. (2016) · Journal of Bacteriology · doi:10.1128/jb.00402-16 · Cited by 40 · see citing works
Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla
Cohan, F. M. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.mtbp-0014-2016 · Cited by 39 · see citing works
Hahn, M. W., Schmidt, J., Pitt, A., et al. (2016) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.001073 · Cited by 35 · see citing works
Strainer: software for analysis of population variation in community genomic datasets
Eppley, J. M., Tyson, G. W., Getz, W. M., et al. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-398 · Cited by 32 · see citing works
Smelov, V., Vrbanac, A. F., van Ess, E. F., Noz, M. P., Wan, R., Eklund, C., Morgan, T., Shrier, L. A., Sanders, B., Dillner, J., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02195 · Cited by 28 · see citing works
Population Genomics: Microorganisms
(2019) · Population genomics · doi:10.1007/978-3-030-04756-6 · Cited by 28 · see citing works
A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data
O’Brien, J., Didelot, X., Iqbal, Z., Amenga-Etego, L. N.-K., Ahiska, B., & Falush, D. (2014) · Genetics · doi:10.1534/genetics.114.161299 · Cited by 26 · see citing works
Toward an Autecology of Bacterioplankton
Pedrós‐Alió, C. (1989) · Brock/Springer series in contemporary bioscience · doi:10.1007/978-3-642-74890-5_8 · Cited by 24 · see citing works
Interactions between Closely Related Bacterial Strains Are Revealed by Deep Transcriptome Sequencing
González‐Torres, P., Pryszcz, L. P., Santos, F., et al. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.02690-15 · Cited by 24 · see citing works
A Modern Concept of the Subspecies
Monroe, B. L. (1982) · Digital Commons - University of South Florida (University of South Florida) · doi:10.1093/auk/99.3.608 · Cited by 24 · see citing works
Correction: Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas
Thorell, K., Yahara, K., Berthenet, E., et al. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006730 · Cited by 23 · see citing works
Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen Vibrio shilonii AK1
Strauss, C., Long, H., Patterson, C. E., Te, R., & Lynch, M. (2017) · mBio · doi:10.1128/mbio.01021-17 · Cited by 23 · see citing works
What Microbial Population Genomics Has Taught Us About Speciation
Shapiro, B. J. (2018) · Population genomics · doi:10.1007/13836_2018_10 · Cited by 23 · see citing works
Mu, A., Kwong, J. C., Isles, N. S., da Silva, A. G., Schultz, M. B., Ballard, S. A., Lane, C. R., Carter, G. P., Williamson, D. A., Seemann, T., et al. (2019) · mSphere · doi:10.1128/msphere.00529-18 · Cited by 23 · see citing works
Scholz, B. K., Jakobek, J. L., & Lindgren, P. B. (1994) · Applied and Environmental Microbiology · doi:10.1128/aem.60.4.1093-1100.1994 · Cited by 22 · see citing works
Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics
Denef, V. J. (2018) · Population genomics · doi:10.1007/13836_2018_14 · Cited by 16 · see citing works
Zhou, Z., Luhmann, N., Alikhan, N.-F., Quince, C., & Achtman, M. (2018) · Lecture notes in computer science · doi:10.1007/978-3-319-89929-9_15 · Cited by 16 · see citing works
Shi, X., Shao, C., Luo, C., Chu, Y., Wang, J., Meng, Q., Yu, J. M., Gao, Z., & Kang, Y. (2019) · mSystems · doi:10.1128/msystems.00198-19 · Cited by 16 · see citing works
CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis
Lam, T. J., & Ye, Y. (2019) · The CRISPR Journal · doi:10.1089/crispr.2018.0046 · Cited by 12 · see citing works
Seiler, E., Trappe, K., & Renard, B. Y. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007208 · Cited by 12 · see citing works
Population Genetics of Host-Associated Microbiomes
Bobay, L., & Raymann, K. (2019) · Current Molecular Biology Reports · doi:10.1007/s40610-019-00122-y · Cited by 9 · see citing works
HgsDb: Haplogroups Database to understand migration and molecular risk assessment
Arora, D., Singh, A. B., Sharma, V., et al. (2015) · Bioinformation · doi:10.6026/97320630011272 · Cited by 7 · see citing works
Flagged first, then by citations
Research works printed but not linked: 7
- [22]Brown T Genomes Genomes 2nd edition Oxford: Wiley-Liss 2002 20821850
- [70]Cohan FM Periodic Selection and Ecological Diversity in Bacteria Selective Sweep Springer US 2007 78 93
- [121]Smillie CS Strain Tracking Reveals the Determinants of Bacterial Engraftmen in the Human Gut Following Fecal Microbiota Transplantation Cell Host Microbe 2018 23 229 240.e5 29447696 PMC8318347
- [129]International Committee on Systematics of Prokaryotes. International Code of Nomenclature of Prokaryotes: Prokaryotic Code (2008 Revision) Int J Syst Evol Microbiol 2019 69 S1 S111 26596770
- [143]Ferretti P Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome Cell Host Microbe 2018 24 133 145.e5 30001516 PMC6716579
- [170]Hamilton M Population Genetics Wiley-Blackwell 2009
- [175]Kenneth R George R Sherris JC Medical microbiology: an introduction to infectious diseases McGraw-Hill Medical 2004
Cited by
Sorted by citations
Prevotella Diversity, Niches and Interactions with the Human Host
Tett, A., Pasolli, E., Masetti, G., Ercolini, D., & Segata, N. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00559-y · Cited by 748 · see citing works
The person-to-person transmission landscape of the gut and oral microbiomes
Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449 · see citing works
Ianiro, G., Punčochář, M., Karcher, N., Porcari, S., Armanini, F., Asnicar, F., Beghini, F., Blanco-Míguez, A., Cumbo, F., Manghi, P., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01964-3 · Cited by 366 · see citing works
High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
Zheng, W., Zhao, S., Yin, Y., Zhang, H., Needham, D. M., Evans, E. D., Dai, C. L., Lu, P. J., Alm, E. J., & Weitz, D. A. (2022) · Science · doi:10.1126/science.abm1483 · Cited by 283 · see citing works
Karcher, N., Nigro, E., Punčochář, M., Blanco-Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02427-7 · Cited by 159 · see citing works
Computational methods for chromosome-scale haplotype reconstruction
Garg, S. (2021) · Genome Biology · doi:10.1186/s13059-021-02328-9 · Cited by 116 · see citing works
Podlesny, D., Durdevic, M., Paramsothy, S., Kaakoush, N. O., Högenauer, C., Gorkiewicz, G., Walter, J., & Fricke, W. F. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100711 · Cited by 111 · see citing works
Gut microbiome strain-sharing within isolated village social networks
Beghini, F., Pullman, J., Alexander, M., Shridhar, S. V., Prinster, D., Singh, A., Matute Juárez, R., Airoldi, E. M., Brito, I. L., & Christakis, N. A. (2025) · Nature · doi:10.1038/s41586-024-08222-1 · Cited by 51 · see citing works
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes
Van Rossum, T., Costea, P. I., Paoli, L., Alves, R., Thielemann, R., Sunagawa, S., & Bork, P. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btab789 · Cited by 23 · see citing works
Pangenomes of human gut microbiota uncover links between genetic diversity and stress response
Shoer, S., Reicher, L., Zhao, C., Pollard, K. S., Pilpel, Y., & Segal, E. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.08.017 · Cited by 23 · see citing works
Gizachew, S., & Engidawork, E. (2024) · Genes · doi:10.3390/genes15111389 · Cited by 15 · see citing works
- Authors
- Van Rossum, T., Ferretti, P., Maistrenko, O. M., & Bork, P.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Venue
- Nature Reviews Microbiology
- Published
- 2020-06-04
- Volume
- 18
- Issue
- 9
- Pages
- 491-506
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- PMC
- PMC7610499
- OpenAlex
- W3034087136
- Cited by
- 441
- References
- 193
- Citations by year
- 2026: 59 · 2025: 92 · 2024: 80 · 2023: 64 · 2022: 62 · 2021: 70 · 2020: 14
- FWCI
- 5.16
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- bacterial strain, infraspecific variation, metagenomics, microbial communities, strain typing, population genetics, terminology
- MeSH terms
- Bacteria, Evolution, Molecular, Metagenomics, Microbiota
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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