Bello, M. G., Knight, R., Gilbert, J. A. & Blaser, M. J. Preserving microbial diversity. Science 362, 33–34 (2018).
Sonnenburg, E. D. & Sonnenburg, J. L. The ancestral and industrialised gut microbiota and implications for human health. Nat. Rev. Microbiol. 17, 383–390 (2019).
Article CAS PubMed Google Scholar
Groussin, M., Mazel, F. & Alm, E. J. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe 28, 12–22 (2020).
Article CAS PubMed Google Scholar
Davenport, E. R. et al. The human microbiome in evolution. BMC Biol. 15, 127 (2017).
Article PubMed PubMed Central Google Scholar
Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016).
Article CAS PubMed PubMed Central Google Scholar
Nishida, A. H. & Ochman, H. Captivity and the co-diversification of great ape microbiomes. Nat. Commun. 12, 5632 (2021).
Article CAS PubMed PubMed Central Google Scholar
Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019).
Article PubMed PubMed Central Google Scholar
Grieneisen, L. et al. Gut microbiome heritability is nearly universal but environmentally contingent. Science 373, 181–186 (2021).
Article CAS PubMed PubMed Central Google Scholar
Goodrich, J. K. et al. Human genetics shape the gut microbiome. Cell 4, 789–799 (2014).
Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).
Article CAS PubMed PubMed Central Google Scholar
Sonnenburg, J. L. & Bäckhed, F. Diet-microbiota interactions as moderators of human metabolism. Nature 535, 56–64 (2016).
Article CAS PubMed PubMed Central Google Scholar
Diaz Heijtz, R. et al. Normal gut microbiota modulates brain development and behavior. Proc. Natl Acad. Sci. USA 108, 3047–3052 (2011).
Youngblut, N. D. et al. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat. Commun. 10, 2200 (2019).
Article PubMed PubMed Central Google Scholar
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Article PubMed PubMed Central Google Scholar
Wu, Y.-W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016).
Article CAS PubMed Google Scholar
Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).
Article CAS PubMed Google Scholar
Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).
Article CAS PubMed PubMed Central Google Scholar
Manara, S. et al. Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species. Genome Biol. 20, 299 (2019).
Article CAS PubMed PubMed Central Google Scholar
Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662.e20 (2019).
Article CAS PubMed PubMed Central Google Scholar
Wibowo, M. C. et al. Reconstruction of ancient microbial genomes from the human gut. Nature 594, 234–239 (2021).
Article CAS PubMed PubMed Central Google Scholar
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).
PubMed PubMed Central Google Scholar
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Article CAS PubMed PubMed Central Google Scholar
Hommola, K., Smith, J. E., Qiu, Y. & Gilks, W. R. A permutation test of host-parasite cospeciation. Mol. Biol. Evol. 26, 1457–1468 (2009).
Article CAS PubMed Google Scholar
Kumar, S., Stecher, G., Suleski, M. & Hedges, S. B. TimeTree: a resource for timelines, timetrees, and divergence times. Mol. Biol. Evol. 34, 1812–1819 (2017).
Article CAS PubMed Google Scholar
de Vienne, D. M. et al. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. New Phytol. 198, 347–385 (2013).
Duchêne, S. et al. Genome-scale rates of evolutionary change in bacteria. Microb. Genom. 2, e000094 (2016).
PubMed PubMed Central Google Scholar
Menardo, F., Duchêne, S., Brites, D. & Gagneux, S. The molecular clock of Mycobacterium tuberculosis. PLoS Pathog. 15, e1008067 (2019).
Article PubMed PubMed Central Google Scholar
Rascovan, N. et al. Emergence and spread of basal lineages of Yersinia pestis during the neolithic decline. Cell 176, 295–305.e10 (2019).
Article CAS PubMed Google Scholar
Ochman, H., Elwyn, S. & Moran, N. A. Calibrating bacterial evolution. Proc. Natl Acad. Sci. USA 96, 12638–12643 (1999).
Article CAS PubMed PubMed Central Google Scholar
Suzuki, T. A. et al. Codiversification of gut microbiota with humans. Science 377, 1328–1332 (2022).
Article CAS PubMed Google Scholar
Moeller, A. H. et al. Rapid changes in the gut microbiome during human evolution. Proc. Natl Acad. Sci. USA 111, 16431–16435 (2014).
Article CAS PubMed PubMed Central Google Scholar
Moeller, A. H. The shrinking human gut microbiome. Curr. Opin. Microbiol. 38, 30–35 (2017).
Article CAS PubMed Google Scholar
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).
Article CAS PubMed PubMed Central Google Scholar
Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463 (2017).
Article CAS PubMed Google Scholar
Sonnenburg, J. L. & Sonnenburg, E. D. Vulnerability of the industrialised microbiota. Science 366, eaaw9255 (2019).
Article CAS PubMed Google Scholar
Pamer, E. G. Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens. Science 352, 535–538 (2016).
Article CAS PubMed PubMed Central Google Scholar
Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021).
Article CAS PubMed Google Scholar
Olson, N. D. et al. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief. Bioinform. 20, 1140–1150 (2019).
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