Codiversification of gut microbiota with humans
Open accessPublished version of a preprint
Abstract
The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Multiple bacterial species' phylogenies resemble their human host populations' phylogenies, highlighting that geographical stratification in those species is unlikely to be driven by lifestyle alone.
“Moreover, it has also been observed that multiple bac terial species' phylogenies resemble their human host popula tions' phylogenies, highlighting that geographical stratification in those species is unlikely to be driven by lifestyle alone. 15”
From Global genetic diversity of human gut microbiome species is related to geographic location and host health (2025) · cites this paper as [15]
Clostridiales is part of the phylum Bacillota, which was previously observed to be the top phylum showing co-diversification with human populations.
“Interestingly, Clostridiales is part of the phylum Bacillota (formerly known as Firmicutes), which was previously observed to be the top phylum showing co-diversification with human populations.”
From Global genetic diversity of human gut microbiome species is related to geographic location and host health (2025) · cites this paper as [15]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Classification and Regression by randomForest
Liaw, A. I., & Wiener, M. C. (2007) · Cited by 18,594 · see citing works
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,426 · see citing works
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
Letunic, I., & Bork, P. (2021) · Nucleic Acids Res. · doi:10.1093/nar/gkab301 · Cited by 9,899 · see citing works
phytools: an R package for phylogenetic comparative biology (and other things)
Revell, L. J. (2011) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00169.x · Cited by 9,143 · see citing works
Feature Selection with the <b>Boruta</b> Package
Kursa, M. B., & Rudnicki, W. R. (2010) · Journal of Statistical Software · doi:10.18637/jss.v036.i11 · Cited by 5,659 · see citing works
Genetic Structure of Human Populations
Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kídd, K. K., Анатольевич, Ж. Л., & Feldman, M. W. (2002) · Science · doi:10.1126/science.1078311 · Cited by 3,000 · see citing works
Personalized nutrition by prediction of glycemic responses
Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., Ben-Yacov, O., Lador, D., Avnit-Sagi, T., Lotan-Pompan, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.001 · Cited by 2,929 · see citing works
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx148 · Cited by 2,709 · see citing works
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
Jia, B., Raphenya, A. R., Alcock, B. P., Waglechner, N., Guo, P., Tsang, K. K., Lago, B. A., Dave, B. M., Pereira, S. K., Sharma, A. N., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1004 · Cited by 2,671 · see citing works
Alterations of the human gut microbiome in liver cirrhosis
Qin, N., Yang, F., Li, A., Prifti, E., Chen, Y., Shao, L., Guo, J., Le Chatelier, E., Yao, J., Wu, L., et al. (2014) · Nature · doi:10.1038/nature13568 · Cited by 2,177 · 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-citationLarge-scale association analyses identify host factors influencing human gut microbiome composition
Kurilshikov, A., Medina-Gomez, C., Bacigalupe, R., Radjabzadeh, D., Wang, J., Demirkan, A., Le Roy, C. I., Raygoza Garay, J. A., Finnicum, C. T., Liu, X., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00763-1 · Cited by 1,786 · see citing works
Self-citationThe gut microbiome in atherosclerotic cardiovascular disease
Jie, Z., Xia, H., Zhong, S.-L., Feng, Q., Li, S., Liang, S., Zhong, H., Liu, Z., Gao, Y., Zhao, H., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00900-1 · Cited by 1,638 · see citing works
Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works
Genes mirror geography within Europe
Novembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., Indap, A., King, K. S., Bergmann, S., Nelson, M. R., et al. (2008) · Nature · doi:10.1038/nature07331 · Cited by 1,479 · see citing works
Extreme genome reduction in symbiotic bacteria
McCutcheon, J. P., & Moran, N. A. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2670 · Cited by 1,464 · see citing works
Potential of fecal microbiota for early-stage detection of colorectal cancer
Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., Amiot, A., Böhm, J., Brunetti, F., Habermann, N., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145645 · Cited by 1,375 · see citing works
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
Tanizawa, Y., Fujisawa, T., & Nakamura, Y. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx713 · Cited by 1,302 · 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
The first 1000 cultured species of the human gastrointestinal microbiota
Rajilić-Stojanović, M., & de Vos, W. M. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12075 · Cited by 1,182 · see citing works
A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models
Ho, L. S. T., & Ané, C. (2014) · Systematic Biology · doi:10.1093/sysbio/syu005 · Cited by 1,081 · see citing works
Gupta, V. K., Paul, S., & Dutta, C. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01162 · Cited by 1,019 · see citing works
Community-led, integrated, reproducible multi-omics with anvi’o
Eren, A. M., Kiefl, E., Shaiber, A., Veseli, I., Miller, S. E., Schechter, M. S., Fink, I., Pan, J. N., Yousef, M., Fogarty, E. C., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-00834-3 · Cited by 940 · see citing works
Stochastic Mapping of Morphological Characters
Huelsenbeck, J. P., Nielsen, R., & Bollback, J. P. (2003) · Systematic Biology · doi:10.1080/10635150390192780 · Cited by 930 · see citing works
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., et al. (2017) · Science · doi:10.1126/science.aan4834 · Cited by 886 · see citing works
Walk on the Wild Side: Estimating the Global Magnitude of Visits to Protected Areas
Balmford, A. P., Green, J., Anderson, M., Beresford, J., Huang, C., Naidoo, R., Walpole, M., & Manica, A. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002074 · Cited by 869 · see citing works
Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869 · 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
The Late Pleistocene Dispersal of Modern Humans in the Americas
Goebel, T., Waters, M. R., & O’Rourke, D. H. (2008) · Science · doi:10.1126/science.1153569 · Cited by 773 · see citing works
Roseburia Spp.: A Marker of Health?
Tamanai‐Shacoori, Z., Smida, I., Bousarghin, L., Loréal, O., Meuric, V., Fong, S. B., Bonnaure‐Mallet, M., & Jolivet‐Gougeon, A. (2017) · Future Microbiology · doi:10.2217/fmb-2016-0130 · Cited by 751 · 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
Tracing the peopling of the world through genomics
Nielsen, R., Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S., & Willerslev, E. (2017) · Nature · doi:10.1038/nature21347 · Cited by 728 · see citing works
Helicobacter pylori in Health and Disease
Cover, T. L., & Blaser, M. J. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.01.073 · Cited by 716 · see citing works
Interconnected microbiomes and resistomes in low-income human habitats
Pehrsson, E. C., Tsukayama, P., Patel, S., Mejía-Bautista, M., Sosa-Soto, G., Navarrete, K. M., Calderon, M., Cabrera, L., Hoyos-Arango, W., Bertoli, M. T., et al. (2016) · Nature · doi:10.1038/nature17672 · Cited by 607 · see citing works
Youngblut, N. D., Reischer, G. H., Walters, W. A., Schuster, N., Walzer, C., Stalder, G. L., Ley, R. E., & Farnleitner, A. H. (2019) · Nature Communications · doi:10.1038/s41467-019-10191-3 · Cited by 595 · see citing works
Self-citationSubsistence strategies in traditional societies distinguish gut microbiomes
Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms7505 · Cited by 587 · see citing works
Cospeciation of gut microbiota with hominids
Moeller, A. H., Caro‐Quintero, A., Mjungu, D. C., Georgiev, A. V., Lonsdorf, E. V., Muller, M. N., Pusey, A. E., Peeters, M., Hahn, B. H., & Ochman, H. (2016) · Science · doi:10.1126/science.aaf3951 · Cited by 570 · see citing works
Coadaptation of Helicobacter pylori and humans: ancient history, modern implications
Atherton, J. C., & Blaser, M. J. (2009) · Journal of Clinical Investigation · doi:10.1172/jci38605 · Cited by 549 · see citing works
SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data
Lee, T., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-162 · Cited by 549 · see citing works
Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera
Powell, J. E., Martinson, V. G., Urban‐Mead, K. R., & Moran, N. A. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.01861-14 · Cited by 547 · see citing works
Olm, M. R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B. A., Morowitz, M. J., & Banfield, J. F. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00797-0 · Cited by 537 · see citing works
Social networks predict gut microbiome composition in wild baboons
Tung, J., Barreiro, L. B., Burns, M. B., Grenier, J., Lynch, J., Grieneisen, L., Jeanne Altmann, A., Alberts, S. C., Blekhman, R., & Archie, E. A. (2015) · eLife · doi:10.7554/elife.05224 · Cited by 524 · see citing works
Self-citationThe Hologenome Concept: Helpful or Hollow?
Moran, N. A., & Sloan, D. B. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002311 · Cited by 508 · see citing works
Bischl, B., Lang, M., Kotthoff, L., Schratz, P., Schiffner, J., Richter, J., Jones, Z., Casalicchio, G., Gallo, M., & Binder, M. (2013) · doi:10.32614/cran.package.mlr · Cited by 506 · see citing works
A Statistical Test for Host–Parasite Coevolution
Legendre, P., Desdevises, Y., & Bazin, É. (2002) · Systematic Biology · doi:10.1080/10635150252899734 · Cited by 501 · see citing works
Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Groussin, M., Mazel, F., Sanders, J. G., Smillie, C. S., Lavergne, S., Thuiller, W., & Alm, E. J. (2017) · Nature Communications · doi:10.1038/ncomms14319 · Cited by 491 · see citing works
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · 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
Falush, D., Kraft, C., Taylor, N. S., Correa, P., Fox, J. G., Achtman, M., & Suerbaum, S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.251396098 · Cited by 429 · see citing works
Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota
Rampelli, S., Schnorr, S. L., Consolandi, C., Turroni, S., Severgnini, M., Peano, C., Brigidi, P., Crittenden, A. N., Henry, A. G., & Candela, M. (2015) · Current Biology · doi:10.1016/j.cub.2015.04.055 · Cited by 399 · see citing works
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
Schirmer, M., D’Amore, R., Ijaz, U. Z., Hall, N., & Quince, C. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0976-y · Cited by 376 · see citing works
Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes
Amato, K. R., Sanders, J. G., Song, S. J., Nute, M., Metcalf, J. L., Thompson, L., Morton, J. T., Amir, A., McKenzie, V. J., Humphrey, G., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0175-0 · Cited by 368 · see citing works
The initial state of the human gut microbiome determines its reshaping by antibiotics
Raymond, F., Ouameur, A. A., Déraspe, M., Iqbal, N., Gingras, H., Dridi, B., Leprohon, P., Plante, P.-L., Giroux, R., Bérubé, È., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.148 · Cited by 359 · see citing works
Moran, N., & Bennett, G. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091213-112901 · Cited by 357 · see citing works
Xie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.004 · Cited by 341 · see citing works
Self-citationThe effect of heritability and host genetics on the gut microbiota and metabolic syndrome
Lim, M. Y., You, H. J., Yoon, H. S., Kwon, B., Lee, J. Y., Lee, S., Song, Y., Lee, K., Sung, J., & Ko, G. (2016) · Gut · doi:10.1136/gutjnl-2015-311326 · Cited by 340 · see citing works
Self-citationEzeji, J. C., Sarikonda, D. K., Hopperton, A., Erkkila, H. L., Cohen, D. E., Martinez, S. P., Cominelli, F., Kuwahara, T., Dichosa, A. E. K., Good, C. E., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1922241 · Cited by 333 · see citing works
PACo: A Novel Procrustes Application to Cophylogenetic Analysis
Balbuena, J., Míguez-Lozano, R., & Blasco-Costa, I. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061048 · Cited by 315 · see citing works
The Relationship Between the Human Genome and Microbiome Comes into View
Goodrich, J. K., Davenport, E. R., Clark, A. G., & Ley, R. E. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155532 · Cited by 311 · see citing works
Self-citationThe Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri
Frese, S. A., Benson, A. K., Tannock, G. W., Loach, D. M., Kim, J., Zhang, M., Oh, P. L., Heng, N. C. K., Patil, P. B., Juge, N., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001314 · Cited by 309 · see citing works
Social behavior shapes the chimpanzee pan-microbiome
Moeller, A. H., Foerster, S., Wilson, M. L., Pusey, A. E., Hahn, B. H., & Ochman, H. (2016) · Science Advances · doi:10.1126/sciadv.1500997 · Cited by 296 · see citing works
Mobile genes in the human microbiome are structured from global to individual scales
Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., et al. (2016) · Nature · doi:10.1038/nature18927 · Cited by 288 · see citing works
Transmission modes of the mammalian gut microbiota
Moeller, A. H., Suzuki, T. A., Phifer‐Rixey, M., & Nachman, M. W. (2018) · Science · doi:10.1126/science.aat7164 · Cited by 285 · see citing works
Self-citationCo-evolution and Co-speciation of Host-Gut Bacteria Systems
Groussin, M., Mazel, F., & Alm, E. J. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.06.013 · Cited by 278 · see citing works
Evolutionary and Ecological Consequences of Gut Microbial Communities
Moran, N. A., Ochman, H., & Hammer, T. J. (2019) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110617-062453 · Cited by 271 · see citing works
Louis, S., Tappu, R.-M., Damms-Machado, A., Huson, D. H., & Bischoff, S. C. (2016) · PLoS ONE · doi:10.1371/journal.pone.0149564 · Cited by 269 · see citing works
Transmission of human-associated microbiota along family and social networks
Brito, I., Gurry, T., Zhao, S., Huang, K. H., Young, S., Shea, T. P., Naisilisili, W., Jenkins, A., Jupiter, S. D., Gevers, D., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0409-6 · Cited by 239 · see citing works
Reconstruction of ancient microbial genomes from the human gut
Wibowo, M. C., Yang, Z., Borry, M., Hübner, A., Huang, K. D., Tierney, B. T., Zimmerman, S. E., Barajas-Olmos, F. M., Contreras-Cubas, C., Garcia‐Ortíz, H., et al. (2021) · Nature · doi:10.1038/s41586-021-03532-0 · Cited by 237 · see citing works
Public human microbiome data are dominated by highly developed countries
Abdill, R. J., Adamowicz, E. M., & Blekhman, R. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001536 · Cited by 221 · see citing works
Self-citationDhakan, D. B., Maji, A., Sharma, A. K., Saxena, R., Pulikkan, J., Grace, T., Gomez, A. M., Scaria, J., Amato, K. R., & Sharma, V. K. (2019) · GigaScience · doi:10.1093/gigascience/giz004 · Cited by 213 · see citing works
Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans
David, L. A., Weil, A. A., Ryan, E. T., Calderwood, S. B., Harris, J. B., Chowdhury, F., Begum, Y. A., Qadri, F., LaRocque, R. C., & Turnbaugh, P. J. (2015) · mBio · doi:10.1128/mbio.00381-15 · Cited by 192 · see citing works
Evaluation of saliva as a source of human DNA for population and association studies
Quinque, D., Kittler, R., Kayser, M., Stoneking, M., & Nasidze, I. (2006) · Analytical Biochemistry · doi:10.1016/j.ab.2006.03.021 · Cited by 191 · see citing works
Barratt, M. J., Nuzhat, S., Ahsan, K., Frese, S. A., Arzamasov, A. A., Sarker, S. A., Islam, M. M., Palit, P., Islam, M. R., Hibberd, M. C., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abk1107 · Cited by 169 · see citing works
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
Weimann, A., Mooren, K., Frank, J. A., Pope, P., Bremges, A., & Mchardy, A. (2016) · mSystems · doi:10.1128/msystems.00101-16 · Cited by 157 · 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
Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis
Liu, W., Zhang, J., Wu, C., Cai, S., Huang, W., Chen, J., Xi, X., Liang, Z., Hou, Q., Zhou, B., et al. (2016) · Scientific Reports · doi:10.1038/srep34826 · Cited by 119 · see citing works
Karcher, N., Pasolli, E., Asnicar, F., Huang, K. D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S. H., Louis, P., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-02042-y · Cited by 116 · see citing works
The developing infant gut microbiome: A strain-level view
Enav, H., Bäckhed, F., & Ley, R. E. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.009 · Cited by 115 · see citing works
Self-citationThe role of the microbiota in human genetic adaptation
Suzuki, T. A., & Ley, R. E. (2020) · Science · doi:10.1126/science.aaz6827 · Cited by 110 · see citing works
Self-citationBlowing Hot and Cold: Body Temperature and the Microbiome
Huus, K. E., & Ley, R. E. (2021) · mSystems · doi:10.1128/msystems.00707-21 · Cited by 107 · see citing works
Self-citationA Justification for Reporting the Majority-Rule Consensus Tree in Bayesian Phylogenetics
Holder, M. T., Sukumaran, J., & Lewis, P. O. (2008) · Systematic Biology · doi:10.1080/10635150802422308 · Cited by 104 · see citing works
Youngblut, N. D., de la Cuesta‐Zuluaga, J., Reischer, G. H., Dauser, S., Schuster, N., Walzer, C., Stalder, G. L., Farnleitner, A. H., & Ley, R. E. (2020) · mSystems · doi:10.1128/msystems.01045-20 · Cited by 100 · see citing works
Self-citationLokmer, A., Cian, A., Froment, A., Gantois, N., Viscogliosi, É., Chabé, M., & Ségurel, L. (2019) · PLoS ONE · doi:10.1371/journal.pone.0211139 · Cited by 71 · see citing works
Self-citationHost adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle
Browne, H. P., Almeida, A., Kumar, N., Vervier, K., Adoum, A., Viciani, E., Dawson, N. J. R., Forster, S. C., Cormie, C., Goulding, D., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02428-6 · Cited by 71 · see citing works
Even, G., Lokmer, A., Rodrigues, J., Audebert, C., Viscogliosi, É., Ségurel, L., & Chabé, M. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.533528 · Cited by 62 · see citing works
Self-citationCaptivity and the co-diversification of great ape microbiomes
Nishida, A. H., & Ochman, H. (2021) · Nature Communications · doi:10.1038/s41467-021-25732-y · Cited by 48 · see citing works
Human population history revealed by a supertree approach
Duda, P., & Zrzavý, J. (2016) · Scientific Reports · doi:10.1038/srep29890 · Cited by 39 · see citing works
Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut MicrobesPreprint
Merrill, B. D., Carter, M. M., Olm, M. R., Dahan, D., Tripathi, S. M., Spencer, S. P., Yu, F. B., Jain, S., Neff, N. F., Jha, A. R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.30.486478 · Cited by 20 · see citing works
Strong influence of vertebrate host phylogeny on gut archaeal diversityPreprint
Youngblut, N. D., Reischer, G. H., Dauser, S., Walzer, C., Stalder, G. L., Farnleitner, A. H., & Ley, R. E. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.10.376293 · Cited by 7 · see citing works
Self-citationSynTracker: a synteny based tool for tracking microbial strainsPreprint
Enav, H., & Ley, R. E. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.06.463341 · Cited by 6 · see citing works
Self-citationnick-youngblut/gtdb_to_taxdump: Improved docs
Youngblut, N., Borry, M., Portik, D. M., & Shen, W. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.3696963 · Cited by 3 · see citing works
Self-citationleylabmpi/codiversification: Zenodo release
Fitzstevens, L., Suzuki, T. A., Huus, K. E., & Youngblut, N. D. (2022) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.6947453 · Cited by 1 · see citing works
Self-citationPhylogenies related to: Codiversification of gut microbiota with humans
Suzuki, T., Fitzstevens, L., Youngblut, N., et al. (2022) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5061/dryad.qrfj6q5k2
Self-citation
Flagged first, then by citations
Research works printed but not linked: 2
- [6]Merrill BD bioRxiv 2022.03.30.486478 [ Preprint] (2022). 10.1101/2022.03.30.48647. · DOI
- [26]Tung J eLife 4, e05224 (2015).25774601
Cited by
Sorted by citations
Ma, Z., Zuo, T., Frey, N., & Rangrez, A. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01946-6 · Cited by 297 · see citing works
Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes
Carter, M. M., Olm, M. R., Merrill, B. D., Dahan, D., Tripathi, S. M., Spencer, S. P., Yu, F. B., Jain, S., Neff, N. F., Jha, A. R., et al. (2023) · Cell · doi:10.1016/j.cell.2023.05.046 · Cited by 230 · see citing works
Western diets and chronic diseases
Adolph, T. E., & Tilg, H. (2024) · Nature Medicine · doi:10.1038/s41591-024-03165-6 · Cited by 203 · see citing works
Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions
Nam, N. N., Do, H. D. K., Trinh, K. T. L., & Lee, N. Y. (2023) · Foods · doi:10.3390/foods12112140 · Cited by 203 · see citing works
Critical role of the gut microbiota in immune responses and cancer immunotherapy
Li, Z., Xiong, W., Zhu, L. W., Wang, J., Zeng, Z., Kołat, D., Li, X., Zhou, D., Xu, X., & Zhao, L.-Y. (2024) · Journal of Hematology & Oncology · doi:10.1186/s13045-024-01541-w · Cited by 188 · see citing works
Host genetic regulation of human gut microbial structural variation
Zhernakova, D. V., Wang, D., Liu, L., Andreu-Sánchez, S., Zhang, Y., Ruiz-Moreno, A. J., Peng, H., Plomp, N., Del Castillo-Izquierdo, Á., Gacesa, R., et al. (2024) · Nature · doi:10.1038/s41586-023-06893-w · Cited by 174 · see citing works
Host control of the microbiome: Mechanisms, evolution, and disease
Wilde, J., Slack, E. M. C., & Foster, K. R. (2024) · Science · doi:10.1126/science.adi3338 · Cited by 159 · see citing works
Xu, Y., Liu, L., Zhu, J.-Y., Zhu, S., Ye, B., Yang, J.-L., Huang, J.-Y., Huang, Z.-H., You, Y., Li, W., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.02.001 · Cited by 141 · see citing works
The developing infant gut microbiome: A strain-level view
Enav, H., Bäckhed, F., & Ley, R. E. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.009 · Cited by 115 · see citing works
Self-citationGut microbiota reshapes cancer immunotherapy efficacy: Mechanisms and therapeutic strategies
Xie, J., Liu, M., Deng, X., Tang, Y., Zheng, S., Ou, X., Tang, H., Xie, X., Wu, M., & Zou, Y. (2024) · iMeta · doi:10.1002/imt2.156 · Cited by 99 · see citing works
The old friends hypothesis: evolution, immunoregulation and essential microbial inputs
Rook, G. A. W. (2023) · Frontiers in Allergy · doi:10.3389/falgy.2023.1220481 · Cited by 93 · see citing works
The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract
Perdijk, O., Azzoni, R., & Marsland, B. J. (2023) · Physiological Reviews · doi:10.1152/physrev.00020.2023 · Cited by 88 · see citing works
Andreu-Sánchez, S., Blanco-Míguez, A., Wang, D., Golzato, D., Manghi, P., Heidrich, V., Fackelmann, G., Zhernakova, D. V., Kurilshikov, A., Valles-Colomer, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.014 · Cited by 81 · see citing works
Zhu, L.-R., Li, S., Zheng, W.-Q., Ni, W., Cai, M., & Liu, H. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1086078 · Cited by 76 · see citing works
Filippis, F. D., Valentino, V., Sequino, G., Borriello, G., Riccardi, M. G., Pierri, B., Cerino, P., Pizzolante, A., Pasolli, E., Esposito, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48739-7 · Cited by 73 · see citing works
Bornbusch, S. L., Greene, L. K., Rahobilalaina, S., Calkins, S., Rothman, R. S., Clarke, T. A., LaFleur, M., & Drea, C. M. (2022) · Animal Microbiome · doi:10.1186/s42523-022-00176-x · Cited by 63 · see citing works
Widespread extinctions of co-diversified primate gut bacterial symbionts from humans
Sanders, J. G., Sprockett, D. D., Li, Y., Mjungu, D. C., Lonsdorf, E. V., Ndjango, J.-B. N., Georgiev, A. V., Hart, J. A. L., Sanz, C., Morgan, D., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01388-w · Cited by 63 · see citing works
Crosstalk between gut microbiotas and fatty acid metabolism in colorectal cancer
Zhang, H., Tian, Y., Xu, C., Chen, M., Xiang, Z., Gu, L., Xue, H., & Xu, Q. R. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02364-5 · Cited by 52 · see citing works
Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees
Sarton-Lohéac, G., Nunes-Silva, C. G., Mazel, F., Baud, G., de Bakker, V., Das, S., Chazli, Y. E., Ellegaard, K., Garcia‐Garcerà, M., Glover, N., et al. (2023) · mBio · doi:10.1128/mbio.03538-22 · Cited by 45 · see citing works
Ecology of the respiratory tract microbiome
Pérez‐Cobas, A. E., Rodríguez-Beltrán, J., Baquero, F., & Coque, T. M. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.04.006 · Cited by 44 · see citing works
Functional host-specific adaptation of the intestinal microbiome in hominids
Rühlemann, M. C., Bang, C., Gogarten, J. F., Hermes, B. M., Groussin, M., Waschina, S., Poyet, M., Ulrich, M., Akoua-Koffi, C. G., Deschner, T., et al. (2024) · Nature Communications · doi:10.1038/s41467-023-44636-7 · Cited by 45 · see citing works
De Sales-Millán, A., Aguirre-Garrido, J. F., González-Cervantes, R. M., & Velázquez-Aragón, J. A. (2023) · doi:10.20944/preprints202305.1223.v1 · Cited by 44 · see citing works
Human microbiome acquisition and transmission
Heidrich, V., Valles‐Colomer, M., & Segata, N. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01166-x · Cited by 45 · see citing works
Human microbiome variance is underestimated
Shanahan, F., Ghosh, T. S., & O’Toole, P. W. (2023) · Current Opinion in Microbiology · doi:10.1016/j.mib.2023.102288 · Cited by 41 · see citing works
Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease
Su, F., Su, M., Wei, W., Wu, J., Chen, L., Sun, X., Liu, M., Sun, S., Mao, R., Bourgonje, A. R., et al. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2476570 · Cited by 42 · see citing works
Müller, P., de la Cuesta‐Zuluaga, J., Kuhn, M., Arassi, M. B., Treis, T., Blasche, S., Zimmermann, M., Peer Bork, B., Patil, K. R., Typas, A., et al. (2023) · Nature Protocols · doi:10.1038/s41596-023-00926-4 · Cited by 39 · see citing works
Self-citationLi, F., Li, X., Cheng, C. C., Bujdoš, D., Tollenaar, S. L., Simpson, D. J. W., Tasseva, G., Pérez-Muñoz, M. E., Frese, S. A., Gänzle, M. G., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01541-1 · Cited by 36 · see citing works
Dynamics of bacterial recombination in the human gut microbiome
Liu, Z., & Good, B. H. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002472 · Cited by 34 · see citing works
MAIT cells: Conserved watchers on the wall
Germain, L., Veloso, P., Lantz, O. J., & Legoux, F. P. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20232298 · Cited by 36 · see citing works
Within-host evolution of the gut microbiome
Đapa, T., Wong, D. P. G. H., Vasquez, K. S., Xavier, K. B., Huang, K. C., & Good, B. H. (2023) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102258 · Cited by 36 · see citing works
Maier, L., Stein‐Thoeringer, C. K., Ley, R. E., Brötz‐Oesterhelt, H., Link, H., Ziemert, N., Wagner, S., & Peschel, A. (2024) · The Lancet Microbe · doi:10.1016/s2666-5247(24)00049-1 · Cited by 36 · see citing works
Self-citationLongitudinal phage–bacteria dynamics in the early life gut microbiome
Tisza, M. J., Lloyd, R. E., Hoffman, K. L., Smith, D. P., Rewers, M., Cregeen, S. J., & Petrosino, J. F. (2025) · Nature Microbiology · doi:10.1038/s41564-024-01906-4 · Cited by 35 · see citing works
Perez‐Lamarque, B., & Morlon, H. (2024) · Systematic Biology · doi:10.1093/sysbio/syae013 · Cited by 33 · see citing works
Eco-evolutionary feedbacks in the human gut microbiome
Good, B. H., & Rosenfeld, L. B. (2023) · Nature Communications · doi:10.1038/s41467-023-42769-3 · Cited by 33 · see citing works
The gut microbiota links disease to human genome evolution
Quan, Y., Zhang, K., & Zhang, H. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.02.006 · Cited by 32 · see citing works
Gut microbiota reshapes the TNBC immune microenvironment: Emerging immunotherapeutic strategies
Huang, M., Zhang, Y., Chen, Z., Yu, X., Luo, S., Peng, X., & Li, X. (2025) · Pharmacological Research · doi:10.1016/j.phrs.2025.107726 · Cited by 31 · see citing works
Evidence of cospeciation between termites and their gut bacteria on a geological time scale
Arora, J., Buček, A., Hellemans, S., Beránková, T., Arias, J. R., Fisher, B. L., Clitheroe, C., Brune, A., Kinjo, Y., Šobotník, J., et al. (2023) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2023.0619 · Cited by 27 · see citing works
Sun, J., Wang, M., & Kan, Z. (2024) · Frontiers in Endocrinology · doi:10.3389/fendo.2024.1280983 · Cited by 27 · see citing works
A conserved bacterial genetic basis for commensal-host specificity
Gutiérrez-García, K., Aumiller, K., Dodge, R., Obadia, B., Deng, A., Agrawal, S., Yuan, X., Wolff, R., Zhu, H., Hsia, R., et al. (2024) · Science · doi:10.1126/science.adp7748 · Cited by 27 · see citing works
Jian, E., Wang, M., Zhang, Z., Heng, Y., Zhang, C., Chen, Q., Yu, X., Zhu, Y., & Cai, P. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1634803 · Cited by 25 · see citing works
Zhang, H., Jin, K., Xiong, K., Jing, W., Pang, Z., Feng, M., & Cheng, X. (2023) · Cancer Medicine · doi:10.1002/cam4.6194 · Cited by 24 · see citing works
Huang, P., Dong, Q., Wang, Y., Tian, Y., Wang, S., Zhang, C., Yu, L., Tian, F., Gao, X., Guo, H., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100559 · Cited by 24 · see citing works
Integrating natural commensals and pathogens into preclinical mouse models
Rehermann, B., Graham, A. L., Masopust, D., & Hamilton, S. E. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01108-3 · Cited by 23 · see citing works
Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity
Trepka, K. R., Kidder, W. A., Kyaw, T. S., Halsey, T. M., Olson, C. A., Ortega, E. F., Noecker, C. A., Upadhyay, V., Stanfield, D., Steiding, P., et al. (2025) · Science Translational Medicine · doi:10.1126/scitranslmed.adq8870 · Cited by 23 · see citing works
Human-influenced diets affect the gut microbiome of wild baboons
Moy, M. R., Diakiw, L. O., & Amato, K. R. (2023) · Scientific Reports · doi:10.1038/s41598-023-38895-z · Cited by 21 · see citing works
Licata, A. G., Zoppi, M., Dossena, C., Rossignoli, F., Rizzo, D., Marra, M., Gargari, G., Mantegazza, G., Guglielmetti, S., Bergamaschi, L., et al. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.01673-25 · Cited by 22 · see citing works
Enzyme-mediated adaptation of herbivorous insects to host phytochemicals
Dar, S. A., Hasan, W., Devi, Y. K., Gajger, I. T., & John, J. (2024) · Phytochemistry Reviews · doi:10.1007/s11101-024-09933-z · Cited by 21 · see citing works
Effect of diet on the evolution of gut commensal bacteria
Đapa, T., & Xavier, K. B. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2369337 · Cited by 21 · see citing works
Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution
Enav, H., Paz, I., & Ley, R. E. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02276-2 · Cited by 23 · see citing works
Self-citationAnalyzing human gut microbiome data from global populations: challenges and resources
Arif, S. J., Graham, S. P., Abdill, R. J., & Blekhman, R. (2025) · Trends in Microbiology · doi:10.1016/j.tim.2025.05.008 · Cited by 22 · see citing works
Self-citationLuo, S., Hou, Y., Xie, L., Zhang, H., Liu, C., & Chen, T. (2023) · LWT · doi:10.1016/j.lwt.2023.114621 · Cited by 20 · see citing works
Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut MicrobesPreprint
Merrill, B. D., Carter, M. M., Olm, M. R., Dahan, D., Tripathi, S. M., Spencer, S. P., Yu, F. B., Jain, S., Neff, N. F., Jha, A. R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.30.486478 · Cited by 20 · see citing works
Peng, Y., Zhu, J., Wang, S., Liu, Y., Liu, X., DeLeon, O., Zhu, W., Xu, Z., Zhang, X., Zhao, S., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.10.017 · Cited by 20 · see citing works
Human and bacterial genetic variation shape oral microbiomes and health
Kamitaki, N., Handsaker, R. E., Hujoel, M. L. A., Mukamel, R. E., Usher, C. L., McCarroll, S. A., & Loh, P. (2026) · Nature · doi:10.1038/s41586-025-10037-7 · Cited by 22 · see citing works
Assessing co-diversification in host-associated microbiomes
Moeller, A. H., Sanders, J. G., Sprockett, D. D., & Landers, A. A. (2023) · Journal of Evolutionary Biology · doi:10.1111/jeb.14221 · Cited by 19 · see citing works
Jennings, S. A. V., & Clavel, T. (2023) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-021022-025552 · Cited by 19 · see citing works
Pulses: A way to encourage sustainable fiber consumption
Biscarrat, P., Bedu-Ferrari, C., Langella, P., & Cherbuy, C. (2023) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2023.104281 · Cited by 19 · see citing works
Host specificity of gut microbiota associated with social bees: patterns and processes
Mazel, F., Prasad, A., & Engel, P. (2025) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00080-23 · Cited by 20 · see citing works
Maternal Psychosocial Stress Is Associated with Reduced Diversity in the Early Infant Gut Microbiome
Dutton, C. L., Maisha, F. M., Quinn, E. B., Morales, K. L. C., Moore, J. M., & Mulligan, C. J. (2023) · Microorganisms · doi:10.3390/microorganisms11040975 · Cited by 18 · see citing works
Akbuğa-Schön, T., Suzuki, T. A., Jakob, D., Vu, D. L., Waters, J. L., & Ley, R. E. (2023) · mBio · doi:10.1128/mbio.02836-23 · Cited by 17 · see citing works
Self-citationThe importance of host physical niches for the stability of gut microbiome composition
Ludington, W. B. (2024) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2023.0066 · Cited by 18 · see citing works
Li, L., Chen, J., Sun, H., Niu, Q., Zhao, Y., Yang, X., & Sun, Q. (2023) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202300236 · Cited by 17 · see citing works
Ameliorative Effects of Korean-Red-Ginseng-Derived Polysaccharide on Antibiotic-Associated Diarrhea
Min, S. J., Kim, H., Yambe, N., & Shin, M. (2024) · Polymers · doi:10.3390/polym16020231 · Cited by 17 · see citing works
Mind over matter: the microbial mindscapes of psychedelics and the gut-brain axis
Caspani, G., Ruffell, S., Tsang, W., Netzband, N., Rohani-Shukla, C., Swann, J. R., & Jefferies, W. A. (2024) · Pharmacological Research · doi:10.1016/j.phrs.2024.107338 · Cited by 18 · see citing works
Gut Microbiome Proteomics in Food Allergies
Abril, A. G., Carrera, M., Sánchez-Pérez, Á., & Villa, T. G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032234 · Cited by 17 · see citing works
Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer
Peng, H., Andreu‐Sánchez, S., Ruiz-Moreno, A. J., Fernández-Pato, A., Wu, J., Gaćeša, R., Zhernakova, A., Wang, D., & Fu, J. (2025) · Nature Communications · doi:10.1038/s41467-025-66612-z · Cited by 18 · see citing works
Human Gut Microbiome Researches Over the Last Decade: Current Challenges and Future Directions
Wu, H., Forslund, S. K., Wang, Z., & Zhao, G. (2023) · Phenomics · doi:10.1007/s43657-023-00131-z · Cited by 18 · see citing works
Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design
Shao, Y., Wang, S., Gichuki, B. M., Stares, M. D., Rozday, T. J., Kumar, N., Browne, H. P., Dawson, N. J. R., Njunge, J. M., Tigoi, C., et al. (2026) · Cell · doi:10.1016/j.cell.2026.01.007 · Cited by 17 · see citing works
The Respiratory Tract Microbiome and Human Health
de Córdoba‐Ansón, P. F., Linares‐Ambohades, I., Baquero, F., Coque, T. M., & Pérez‐Cobas, A. E. (2025) · Microbial Biotechnology · doi:10.1111/1751-7915.70147 · Cited by 13 · see citing works
Evolution of gut microbiota across honeybee species revealed by comparative metagenomics
Prasad, A., Pallujam, A. D., Siddaganga, R., Suryanarayanan, A., Mazel, F., Brockmann, A., Yek, S. H., & Engel, P. (2025) · Nature Communications · doi:10.1038/s41467-025-64115-5 · Cited by 13 · see citing works
The social microbiome: The missing mechanism mediating the sociality-fitness nexus?
Baniel, A., & Charpentier, M. J. E. (2024) · iScience · doi:10.1016/j.isci.2024.109806 · Cited by 14 · see citing works
Tsang, C. T. T., Hui, T. K. L., Chung, N. M., Yuen, W. T., & Tsang, L. M. (2024) · Molecular Ecology · doi:10.1111/mec.17377 · Cited by 13 · see citing works
Tannock, G. W. (2023) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00127-22 · Cited by 14 · see citing works
Zheng, S., Li, K.-Z., Feng, G., Wang, Y.-T., Jia-ning, W. A. N. G., Li, S., & Sun, Y.-D. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02513-5 · Cited by 12 · see citing works
Lunjani, N., Kerbelker, T., Mdletshe, F. B., Hlela, C., & O’Mahony, L. (2024) · Frontiers in Allergy · doi:10.3389/falgy.2023.1203304 · Cited by 13 · see citing works
Rook, G. A. W. (2024) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2024.105653 · Cited by 12 · see citing works
Zhou, J., Yuan, X., & Liu, Y. (2024) · Microbial Pathogenesis · doi:10.1016/j.micpath.2024.106667 · Cited by 12 · see citing works
Siddiqui, R., & Khan, N. A. (2023) · Microorganisms · doi:10.3390/microorganisms11020481 · Cited by 12 · see citing works
Moeller, A. H. (2022) · Science · doi:10.1126/science.ade2879 · Cited by 12 · see citing works
Mah, J. C., Lohmueller, K. E., & Garud, N. R. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf010 · Cited by 11 · see citing works
Ho, P.-Y., & Huang, K. C. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101350 · Cited by 11 · see citing works
From global to local: rethinking the design of probiotic intervention strategies
Vonaesch, P., Garneau, J. R., & Domínguez-Bello, M. G. (2025) · Trends in Microbiology · doi:10.1016/j.tim.2025.11.009 · Cited by 14 · see citing works
Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice
Sprockett, D. D., Dillard, B. A., Landers, A. A., Sanders, J. G., & Moeller, A. H. (2025) · Nature Communications · doi:10.1038/s41467-025-57435-z · Cited by 10 · see citing works
Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly
Caesar, L., Barksdale, C., Valiati, V. H., & Newton, I. L. G. (2025) · Nature Communications · doi:10.1038/s41467-025-66678-9 · Cited by 10 · see citing works
Power, M. L., Muletz‐Wolz, C. R., & Bornbusch, S. L. (2024) · Reproduction and Fertility · doi:10.1530/raf-23-0056 · Cited by 10 · see citing works
Zhao, Y., Li, C., Wu, K., Chen, H., Wang, Q., Xiao, Y., Yao, S., Hong, A., Zhang, M., Lei, S., et al. (2024) · Biomedicines · doi:10.3390/biomedicines12071378 · Cited by 9 · see citing works
Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids
Moeller, A. H. (2025) · Biology Letters · doi:10.1098/rsbl.2024.0454 · Cited by 9 · see citing works
Gencel, M., Cofino, G. M., Hui, C., Sahaf, Z., Gauthier, L., Matta, C., Gagné-Leroux, D., Tsang, D. K. L., Philpott, D. J., Ramathan, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61368-y · Cited by 9 · see citing works
Lavrinienko, A., Greppi, A., Häcki, S., Paramonova, D., & Bokulich, N. A. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.105370 · Cited by 9 · see citing works
Selection and transmission of the gut microbiome alone can shift mammalian behavior
Suzuki, T. A., Tanja, A.-S., Waters, J. L., Jakob, D., Vu, D. L., Ballinger, M. A., Rienzi, S. C. D., Chang, H., de Araújo, I. E., Tyakht, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65368-w · Cited by 9 · see citing works
Self-citationA host-centric view of the microbiota metabolome
Yamada, T., & Palm, N. W. (2025) · Immunity · doi:10.1016/j.immuni.2025.11.006 · Cited by 12 · see citing works
Zhao, Y., Chen, L., Yao, S., Chen, L., Huang, J., Chen, S., & Yu, Z. (2023) · Current Research in Food Science · doi:10.1016/j.crfs.2023.100600 · Cited by 11 · see citing works
Stoyanova, M., Gledacheva, V., & Nikolova, S. (2025) · Applied Sciences · doi:10.3390/app15126441 · Cited by 9 · see citing works
Social structuring of the gut microbiome in communally roosting bats
Lebeuf‐Taylor, E., Cosby, A. E., Webber, Q. M. R., & Cottenie, K. (2025) · PLoS ONE · doi:10.1371/journal.pone.0325710 · Cited by 7 · see citing works
Gut microbiota alterations in sleep disturbances: A systematic review and meta-analysis
Wang, Z., Wu, T., Li, J., Dong, G., Kong, L., Zhang, Y., Zhang, Z., Lv, Z., Zhang, Y., Zhan, R., et al. (2026) · Sleep Medicine Reviews · doi:10.1016/j.smrv.2026.102293 · Cited by 7 · see citing works
Intraspecies associations from strain-rich metagenome samples
Qu, E. B., Baker, J. S., Markey, L., Khadka, V. D., Mancuso, C. P., Tripp, A. D., & Lieberman, T. D. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116134 · Cited by 7 · see citing works
Limited codiversification of the gut microbiota with humansPreprint
Good, B. H. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.27.514143 · Cited by 7 · see citing works
metaTraits: a large-scale integration of microbial phenotypic trait information
Podlesny, D., Kim, C. Y., Robbani, S. M., Schudoma, C., Fullam, A., Reimer, L. C., Koblitz, J., Schober, I., Iyappan, A., Rossum, T. V., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1241 · Cited by 6 · see citing works
The Gut Gambit: A Review of How Microbial Imbalance Fuels Metabolic Mayhem
Venkata, L. N. S., Mishra, A. K., Mohanta, Y. K., Rustagi, S., Bahuguna, A., Tomar, A., Baek, K.-H., & Mishra, B. (2026) · Nutrients · doi:10.3390/nu18060888 · Cited by 6 · see citing works
Al-Busaidi, A., Alabri, O., Alomairi, J., Elsharaawy, A., Lawati, A. A., Lawati, H. A., & Das, S. (2024) · Current Diabetes Reviews · doi:10.2174/0115733998281910231231051814 · Cited by 6 · see citing works
- Authors
- Suzuki, T. A., Fitzstevens, J. L., Schmidt, V. T., Enav, H., Huus, K. E., Mbong Ngwese, M., Grießhammer, A., Pfleiderer, A., Adegbite, B. R., Zinsou, J. F., Esen, M., Velavan, T. P., Adegnika, A. A., Song, L. H., Spector, T. D., Muehlbauer, A. L., Marchi, N., Kang, H., Maier, L., Blekhman, R., Ségurel, L., Ko, G., Youngblut, N. D., Kremsner, P., & Ley, R. E.
- Affiliations
- Max Planck Institute for Biology (DE)
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany.
- University of Tübingen (DE)
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany.
- Centre de Recherche Médicales de Lambaréné (GA)
- German Center for Infection Research (DE)
- Vietnamese - German Center of Excellence in Medical Research (VN)
- Vietnamese German Center for Medical Research, Hanoi, Vietnam.
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK.
- University of Minnesota (US)
- Centre National de la Recherche Scientifique (FR)
- Seoul National University (KR)
- Lyon 1 Université (FR)
- Corresponding author
- Suzuki, Taichi A.
- Fitzstevens, J. Liam
- Ley, Ruth E.
- ORCID
- Suzuki, Taichi A.
- Fitzstevens, J. Liam
- Schmidt, Victor T.
- Enav, Hagay
- Huus, Kelsey E.
- Mbong Ngwese, Mirabeau
- Grießhammer, Anne
- Pfleiderer, Anne
- Adegbite, Bayode R.
- Zinsou, Jeannot F.
- Esen, Meral
- Velavan, Thirumalaisamy P.
- Adegnika, Ayola A.
- Song, Le Huu
- Spector, Timothy D.
- Muehlbauer, Amanda L.
- Marchi, Nina
- Kang, Hyena
- Maier, Lisa
- Blekhman, Ran
- Ségurel, Laure
- Ko, GwangPyo
- Youngblut, Nicholas D.
- Kremsner, Peter
- Ley, Ruth E.
- Venue
- Science
- Published
- 2022-09-16
- Volume
- 377
- Issue
- 6612
- Pages
- 1328-1332
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC10777373
- OpenAlex
- W4296032784
- Cited by
- 210
- References
- 95
- Citations by year
- 2026: 48 · 2025: 53 · 2024: 52 · 2023: 48 · 2022: 9
- FWCI
- 13.23
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion, public-domain)
- HAL (submittedVersion, other-oa)
- Pure Amsterdam UMC (submittedVersion)
- Funders
- Wellcome Trust
- National Institute for Health and Care Research
- King's College London
- European Commission
- Agence Nationale de la Recherche (ANR-15-CE02-0003)
- Max-Planck-Gesellschaft
- National Institutes of Health
- Medical Research Council
- National Institute of General Medical Sciences (R35GM128716)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- gut microbiota, co-diversification, core microbiome, host dependency, genome reduction, oxygen sensitivity, temperature sensitivity, mother-child pairs, gut metagenomics, human genome
- MeSH terms
- Gastrointestinal Microbiome, Host Microbial Interactions, Bacteria, Child, Humans, Oxygen, Metagenome
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review