Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320(5879):1034–9.
Article
CAS
PubMed
Google Scholar
Kinross JM, Darzi AW, Nicholson JK. Gut microbiome-host interactions in health and disease. Genome Med. 2011;3(3):14.
Article
PubMed
PubMed Central
Google Scholar
Knight R, Callewaert C, Marotz C, Hyde ER, Debelius JW, McDonald D, et al. The microbiome and human biology. Annu Rev Genomics Hum Genet. 2017;18:65–86.
Article
CAS
PubMed
Google Scholar
Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;38(9):1079–86.
Article
CAS
PubMed
Google Scholar
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C. Minimum information about an uncultivated virus genome (MIUViG). Nature biotechnology. 2019;37(1):29-37.
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woese CR. There must be a prokaryote somewhere: microbiology’s search for itself. Microbiol Mol Biol Rev. 1994;58(1):1–9.
CAS
Google Scholar
Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 2016;165(6):1332–45.
Article
CAS
PubMed
Google Scholar
Roager HM, Hansen LB, Bahl MI, Frandsen HL, Carvalho V, Gøbel RJ, et al. Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nat Microbiol. 2016;1(9):1–9.
Article
Google Scholar
Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AA, et al. Genome-centric view of carbon processing in thawing permafrost. Nature. 2018;560(7716):49–54.
Article
CAS
PubMed
Google Scholar
Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, et al. Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem. Nat Microbiol. 2018;3(11):1274–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martinez-Guryn K, Hubert N, Frazier K, Urlass S, Musch MW, Ojeda P, et al. Small intestine microbiota regulate host digestive and absorptive adaptive responses to dietary lipids. Cell Host Microbe. 2018;23(4):458–69.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2(11):1533–42.
Article
CAS
PubMed
Google Scholar
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3(7):804–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. 2019;176(3):649–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, et al. A new genomic blueprint of the human gut microbiota. Nature. 2019;568(7753):499.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. New insights from uncultivated genomes of the global human gut microbiome. Nature. 2019;568(7753):505–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol. 2018;3(8):870–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shkoporov AN, Clooney AG, Sutton TD, Ryan FJ, Daly KM, Nolan JA, et al. The human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe. 2019;26(4):527–41.
Article
CAS
PubMed
Google Scholar
Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell. 2019a;177(5):1109–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell host & microbe. 2020;28(5):724-40.
Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Massive expansion of human gut bacteriophage diversity. Cell. 2021;184(4):1098–109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K. Genomic variation landscape of the human gut microbiome. Nature. 2013;493(7430):45–50.
Article
PubMed
Google Scholar
García-García N, Tamames J, Linz AM, Pedrós-Alió C, Puente-Sánchez F. Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions. ISME J. 2019;13(12):2969–83.
Article
PubMed
PubMed Central
Google Scholar
Cordero OX, Polz MF. Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol. 2014;12(4):263–73.
Article
CAS
PubMed
Google Scholar
Caro-Quintero A, Konstantinidis KT. Bacterial species may exist, metagenomics reveal. Environ Microbiol. 2012;14(2):347–55.
Article
CAS
PubMed
Google Scholar
Gregory AC, Solonenko SA, Ignacio-Espinoza JC, LaButti K, Copeland A, Sudek S, et al. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics. 2016;17(1):1–3.
Article
Google Scholar
Bobay LM, Ochman H. Biological species in the viral world. Proc Natl Acad Sci U S A. 2018;115(23):6040–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olm MR, Crits-Christoph A, Bouma-Gregson K, Firek BA, Morowitz MJ, Banfield JF. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol. 2021:1–0.
Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, et al. Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ. 2019;7:e6800.
Article
PubMed
PubMed Central
Google Scholar
Moss EL, Maghini DG, Bhatt AS. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nat Biotechnol. 2020:1–7.
Ahn T-H, Chai J, Pan C. Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance. Bioinformatics. 2015;31:170–7.
Article
CAS
PubMed
Google Scholar
Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, et al. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome. 2014;2:33.
Article
PubMed
PubMed Central
Google Scholar
Sankar A, Malone B, Bayliss SC, Pascoe B, Méric G, Hitchings MD, et al. Bayesian identification of bacterial strains from sequencing data. Microb Genom. 2016;2(8):e000075.
PubMed
PubMed Central
Google Scholar
Albanese D, Donati C. Strain profiling and epidemiology of bacterial species from metagenomic sequencing. Nat Commun. 2017;8:2260.
Article
PubMed
PubMed Central
Google Scholar
Tamburini FB, Andermann TM, Tkachenko E, Senchyna F, Banaei N, Bhatt AS. Precision identification of diverse bloodstream pathogens in the gut microbiome. Nat Med. 2018;24(12):1809–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D. ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol. 2015;33:1045–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sahl JW, Schupp JM, Rasko DA, Colman RE, Foster JT, Keim P. Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data. Genome Med. 2015;7:52.
Article
PubMed
PubMed Central
Google Scholar
Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 2016;26(11):1612–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, et al. DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biology. 2017;18(1):1–22.
Article
Google Scholar
Fischer M, Strauch B, Renard BY. Abundance estimation and differential testing on strain level in metagenomics data. Bioinformatics. 2017;33(14):i124–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. metaSNV: A tool for metagenomic strain level analysis. PLoS One. 2017;12(7):e0182392.
Article
PubMed
PubMed Central
Google Scholar
Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, et al. Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation. Cell Host Microbe. 2018;23(2):229–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.
Article
PubMed
PubMed Central
Google Scholar
Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods. 2016;13(5):435–8.
Article
CAS
PubMed
Google Scholar
Greenblum S, Carr R, Borenstein E. Extensive strain-level copy-number variation across human gut microbiome species. Cell. 2015;160(4):583–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci. 2006;361(1475):1929–40.
Article
PubMed
PubMed Central
Google Scholar
Couto N, Schuele L, Raangs EC, Machado MP, Mendes CI, Jesus TF, et al. Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens. Sci Rep. 2018;8(1):1–3.
Article
CAS
Google Scholar
Nayfach S, Pollard KS. Toward accurate and quantitative comparative metagenomics. Cell. 2016;166(5):1103–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev. 2008;72(4):557–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haegeman B, Hamelin J, Moriarty J, Neal P, Dushoff J, Weitz JS. Robust estimation of microbial diversity in theory and in practice. ISME J. 2013;7(6):1092–101.
Article
PubMed
PubMed Central
Google Scholar
Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985;2(1):13–34.
CAS
PubMed
Google Scholar
Lawrence JG, Ochman H. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A. 1998a;95(16):9413–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shin YC, Bischof GF, Lauer WA, Desrosiers RC. Importance of codon usage for the temporal regulation of viral gene expression. Proc Natl Acad Sci U S A. 2015a;112(45):14030–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sharp PM, Li WH. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987a;15(3):1281–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11(1):119.
Article
PubMed
PubMed Central
Google Scholar
Whitley E, Ball J. Statistics review 1: presenting and summarising data. Crit Care. 2001;6(1):66.
Article
PubMed
PubMed Central
Google Scholar
Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, et al. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol. 2012;30(6):513.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
Google Scholar
Danecek P, McCarthy SA. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics. 2017;33(13):2037–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061.
Article
Google Scholar
Delmont TO, Kiefl E, Kilinc O, Esen OC, Uysal I, Rappe MS, et al. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. Elife. 2019;8:e46497.
Article
PubMed
PubMed Central
Google Scholar
Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975;7(2):256–76.
Article
CAS
PubMed
Google Scholar
Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979;76(10):5269–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wright S. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution. 1965;19(3):395–420.
Article
Google Scholar
Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123(3):585–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, et al. Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017;5(1):10.
Article
PubMed
PubMed Central
Google Scholar
Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 2017;5:e3817.
Article
PubMed
PubMed Central
Google Scholar
Malachowa N, DeLeo FR. Mobile genetic elements of Staphylococcus aureus. Cell Mol Life Sci. 2010;67(18):3057–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alibayov B, Baba-Moussa L, Sina H, Zdeňková K, Demnerová K. Staphylococcus aureus mobile genetic elements. Mol Biol Rep. 2014;41(8):5005–18.
Article
CAS
PubMed
Google Scholar
Karlin S, Mrázek J, Campbell A, Kaiser D. Characterizations of highly expressed genes of four fast-growing bacteria. J Bacteriol. 2001;183(17):5025–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peschel A, Otto M. Phenol-soluble modulins and staphylococcal infection. Nat Rev Microbiol. 2013;11(10):667–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li X, Gerlach D, Du X, Larsen J, Stegger M, Kühner P, Peschel A, Xia G, Winstel V. An accessory wall teichoic acid glycosyltransferase protects Staphylococcus aureus from the lytic activity of Podoviridae. Scientific reports. 2015;5(1):17219. https://doi.org/10.1038/srep17219.
Soufo HJ, Reimold C, Linne U, Knust T, Gescher J, Graumann PL. Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein. Proc Natl Acad Sci U S A. 2010;107(7):3163–8.
Article
CAS
Google Scholar
Bae W, Xia B, Inouye M, Severinov K. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc Natl Acad Sci U S A. 2000;97(14):7784–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duval BD, Mathew A, Satola SW, Shafer WM. Altered growth, pigmentation, and antimicrobial susceptibility properties of Staphylococcus aureus due to loss of the major cold shock gene cspB. Antimicrob Agents Chemother. 2010;54(6):2283–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hsiao EY. Gastrointestinal issues in autism spectrum disorder. Harv Rev Psychiatry. 2014;22(2):104–11.
Article
PubMed
Google Scholar
Hughes AR, Inouye BD, Johnson MT, Underwood N, Vellend M. Ecological consequences of genetic diversity. Ecol Lett. 2008;11(6):609–23.
Article
PubMed
Google Scholar
Tilman D, Isbell F, Cowles JM. Biodiversity and ecosystem functioning. Annu Rev Ecol Evol Syst. 2014;45:471–93.
Article
Google Scholar
Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 2020;21(1):1–6.
Article
Google Scholar
Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, et al. Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol. 2015;7(5):1313–28.
Article
PubMed
PubMed Central
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):1–8.
Article
Google Scholar
Ohio Supercomputer Center. Ohio Supercomputer Center. Columbus: Ohio Supercomputer Center; 1987. http://osc.edu/ark:/19495/f5s1ph73
Google Scholar