Zhang Z, Xu D, Wang L, Hao J, Wang J, Zhou X, et al. Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol. 2016;26(14):1873–9.
Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019;365(6452):eaaw4361.
Campbell C, McKenney PT, Konstantinovsky D, Isaeva OI, Schizas M, Verter J, et al. Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells. Nature. 2020;581(7809):475–9.
Gill SK, Rossi M, Bajka B, Whelan K. Dietary fibre in gastrointestinal health and disease. Nat Rev Gastroenterol Hepatol. 2021;18(2):101–16.
Kundu P, Blacher E, Elinav E, Pettersson S. Our gut microbiome: the evolving inner self. Cell. 2017;171(7):1481–93.
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.e20.
Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat Biotechnol. 2021;39(1):105–14.
Levin D, Raab N, Pinto Y, Rotshchild D, Zanir G, Godneva A, et al. Diversity and functional landscapes in the microbiota of animals in the wild. Science. 2021;372:eabb5352.
Zhou Z, Deng T. The Tibetan Plateau is a natural laboratory for studying organic evolution and environmental change. Sci China Earth Sci. 2020;63(2):169–71.
Deng T, Wu F, Zhou Z, Su T. Tibetan Plateau: an evolutionary junction for the history of modern biodiversity. Sci China Earth Sci. 2020;63(2):16.
Qiang Li, Tao Deng, Joel E. et al. Out of Tibet: Pliocene woolly rhino suggests high-plateau origin of ice age megaherbivores. Science. 2011;333(Sep.2 TN.6047):1285–8.
Cortes-Ortiz L, Amato KR. Host genetics influence the gut microbiome. Science. 2021;373(6551):159–60.
Moeller AH, Suzuki TA, Phifer-Rixey M, Nachman MW. Transmission modes of the mammalian gut microbiota. Science. 2018;362(6413):453–7.
Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, et al. Gut microbiome heritability is nearly universal but environmentally contingent. Science. 2021;373(6551):181–6.
Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24(1):133-45.e5.
Brucker RM, Bordenstein SR. The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities. Evolution. 2012;66(2):349–62.
Groussin M, Mazel F, Alm EJ. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe. 2020;28(1):12–22.
Mazel F, Davis KM, Loudon A, Kwong WK, Groussin M, Parfrey LW. Is host filtering the main driver of phylosymbiosis across the tree of life? mSystems. 2018. https://doi.org/10.1128/msystems.00097-18.
Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, et al. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun. 2017;8(1):14319.
Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, Muller MN, et al. Cospeciation of gut microbiota with hominids. Science. 2016;353(6297):380–2.
Gaulke CA, Arnold HK, Humphreys IR, Kembel SW, O’Dwyer JP, Sharpton TJ. Ecophylogenetics clarifies the evolutionary association between mammals and their gut microbiota. MBio. 2018. https://doi.org/10.1128/mBio.01348-18.
Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, et al. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat Commun. 2019;10(1):2200.
Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. Universal trees based on large combined protein sequence data sets. Nat Genet. 2001;28(3):281–5.
Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005;6(5):361–75.
Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, et al. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc Natl Acad Sci U S A. 2014;111(52):18655–60.
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, et al. The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014;344(6188):1168–73.
Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, et al. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science. 2019. https://doi.org/10.1126/science.aav6202.
Humphreys AM, Barraclough TG. The evolutionary reality of higher taxa in mammals. Proc Biol Sci. 2014;281(1783):20132750.
Mattock J, Watson M. A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination. Nat Methods. 2023;20(8):1170–3.
Xie F, Jin W, Si H, Yuan Y, Tao Y, Liu J, et al. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. Microbiome. 2021;9(1):137.
Rühlemann MC, Wacker EM, Ellinghaus D, Franke A. Magscot: a fast, lightweight and accurate bin-refinement tool. Bioinformatics. 2022;38(24):5430–3.
Kang DD, Li F, Kirton E, Thomas A, Wang Z. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7(7):e7359.
Wu Y-W, Simmons BA, Singer SW. Maxbin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32(4):605–7.
Alneberg J, Bjarnason BS, De Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11(11):1144–6.
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol. 2021;39(4):499–509.
Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil PA, Hugenholtz P. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 2022;50(D1):D785–94.
Stewart RD, Auffret MD, Warr A, Walker AW, Roehe R, Watson M. Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. Nat Biotechnol. 2019;37(8):953–61.
Tong F, Wang T, Gao NL, Liu Z, Cui K, Duan Y, et al. The microbiome of the buffalo digestive tract. Nat Commun. 2022;13(1):823.
Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, et al. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell. 2023;186(14):3111-24.e13.
Youngblut ND, Cuesta-Zuluaga J, Reischer GH, Dauser S, Schuster N, Walzer C, et al. Large-scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity. mSystems. 2020;5(6):e01045–20.
Glendinning L, Gen B, Wallace RJ, Watson M. Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. Sci Rep. 2021;11(1):1990.
Csurös M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26(15):1910–2.
Halpern D, Gruss A. A sensitive bacterial-growth-based test reveals how intestinal Bacteroides meet their porphyrin requirement. BMC Microbiol. 2015;15(1):282.
Signore AV, Storz JF. Biochemical pedomorphosis and genetic assimilation in the hypoxia adaptation of Tibetan antelope. Sci Adv. 2020. https://doi.org/10.1126/sciadv.abb5447.
David LA, Alm EJ. Rapid evolutionary innovation during an Archaean genetic expansion. Nature. 2011;469(7328):93–6.
Hurst LD. The ka/ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002;18(9):486–7.
Qiu J. China: the third pole. Nature. 2008;454(7203):393–6.
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.
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):499–504.
Liu Y, Ji M, Yu T, Zaugg J, Anesio AM, Zhang Z, et al. A genome and gene catalog of glacier microbiomes. Nat Biotechnol. 2022;40(9):1341–8.
Li C, Li X, Guo R, Ni W, Liu K, Liu Z, et al. Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse. Microbiome. 2023;11(1):7.
Zeng S, Patangia D, Almeida A, Zhou Z, Mu D, Paul Ross R, et al. A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. Nat Commun. 2022;13(1):5139.
Chen C, Zhou Y, Fu H, Xiong X, Fang S, Jiang H, et al. Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome. Nat Commun. 2021;12(1):1106.
de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME, Giraud T. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. New Phytol. 2013;198(2):347–85.
Li J, Sauers L, Zhuang D, Ren H, Guo J, Wang L, et al. Divergence and convergence of gut microbiomes of wild insect pollinators. mBio. 2023;14(4):e01270–23.
Song SJ, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, et al. Comparative analyses of vertebrate gut microbiomes reveal convergence between birds and bats. MBio. 2020. https://doi.org/10.1128/mbio.02901-19.
Gomez de Agüero M, Ganal-Vonarburg SC, Fuhrer T, Rupp S, Uchimura Y, Li H, et al. The maternal microbiota drives early postnatal innate immune development. Science. 2016;351(6279):1296–302.
Larke JA, Heiss BE, Ehrlich AM, Taft DH, Raybould HE, Mills DA, et al. Milk oligosaccharide-driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice. Microbiome. 2023;11(1):194.
Lawson MAE, O’Neill IJ, Kujawska M, Gowrinadh Javvadi S, Wijeyesekera A, Flegg Z, et al. Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. ISME J. 2020;14(2):635–48.
Keady MM, Jimenez RR, Bragg M, Wagner JCP, Bornbusch SL, Power ML, et al. Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life. Proc Natl Acad Sci U S A. 2023;120(28):e2218900120.
Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9(5):313–23.
Slack E, Hapfelmeier S, Stecher B, Velykoredko Y, Stoel M, Lawson MAE, et al. Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism. Science. 2009;325(5940):617–20.
Sanidad KZ, Amir M, Ananthanarayanan A, Singaraju A, Shiland NB, Hong HS, et al. Maternal gut microbiome–induced IgG regulates neonatal gut microbiome and immunity. Sci Immunol. 2022;7(72):eabh3816.
Laursen MF, Roager HM. Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy. ISME J. 2023;17(12):2452–7.
Garrido D, Barile D, Mills DA. A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract. Adv Nutr. 2012;3(3):415S-S421.
Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol. 2021;12:567408. https://doi.org/10.3389/fmicb.2021.567408.
Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D, et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature. 2023;614(7946):125–35.
Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H. Social behavior shapes the chimpanzee pan-microbiome. Sci Adv. 2016;2(1):e1500997.
Lee N-K, Kim W-S, Paik H-D. Bacillus strains as human probiotics: characterization, safety, microbiome, and probiotic carrier. Food Sci Biotechnol. 2019;28(5):1297–305.
Ji L, Zhang L, Liu H, Shen J, Zhang Y, Lu L, Zhang X, Ma X. Bacillus subtilis M6 improves intestinal barrier, antioxidant capacity and gut microbial composition in AA broiler. Front Nutr. 2022;9:965310. https://doi.org/10.3389/fnut.2022.965310.
Garvey SM, Mah E, Blonquist TM, Kaden VN, Spears JL. The probiotic Bacillus subtilis BS50 decreases gastrointestinal symptoms in healthy adults: a randomized, double-blind, placebo-controlled trial. Gut Microbes. 2022;14(1):2122668.
Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–90.
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics. 2015;31(10):1674–6. https://doi.org/10.1093/bioinformatics/btv033.
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11(12):2864–8.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043–55.
Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 2021;22(1):178.
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64.
Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2019;36(6):1925–7.
Segata N, Börnigen D, Morgan XC, Huttenhower C. Phylophlan is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013;4:2304.
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–50.
Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ. 2015;3:e1029-e.
Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, et al. Mash screen: high-throughput sequence containment estimation for genome discovery. Genome Biol. 2019;20(1):232.
Wood DE, Lu J, Langmead B. Improved metagenomic analysis with kraken 2. Genome Biol. 2019;20(1):257.
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55–60.
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:1–11.
Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35(11):1026–8.
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60.
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46(W1):W95–101.
Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 2021;49(W1):W29-w35.
Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, et al. A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol. 2020;16(1):60–8.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. Qiime allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.
Kwong WK, Medina LA, Koch H, Sing K-W, Soh EJY, Ascher JS, et al. Dynamic microbiome evolution in social bees. Sci Adv. 2017;3(3):e1600513.
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):238.
Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. Kaks_calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 2010;8(1):77–80.
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;39(6):727–36.
Keck F, Rimet F, Bouchez A, Franc A. Phylosignal: an R package to measure, test, and explore the phylogenetic signal. Ecol Evol. 2016;6(9):2774–80.
Symonds MR, Blomberg SP. A primer on phylogenetic generalised least squares. Modern phylogenetic comparative methods and their application in evolutionary biology: concepts and practice. 2014 p. 105–30.