The shrinking human gut microbiome

QIIME allows analysis of high-throughput community sequencing data

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An obesity-associated gut microbiome with increased capacity for energy harvest

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A core gut microbiome in obese and lean twins

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Human gut microbiome viewed across age and geography

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Linking long-term dietary patterns with gut microbial enterotypes

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Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

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Revised Estimates for the Number of Human and Bacteria Cells in the Body

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Richness of human gut microbiome correlates with metabolic markers

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Evolution of mammals and their gut microbes

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The expensive-tissue hypothesis: The brain and the digestive system in human and primate evolution

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How colonization by microbiota in early life shapes the immune system

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Interactions between the microbiota, immune and nervous systems in health and disease

Fung, T. C., Olson, C. A., & Hsiao, E. Y. (2017) · Nature Neuroscience · doi:10.1038/nn.4476 · Cited by 1,900 · see citing works

Diet-induced extinctions in the gut microbiota compound over generations

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Gut microbiome of the Hadza hunter-gatherers

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Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells

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Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017) · Nature Medicine · doi:10.1038/nm.4272 · Cited by 1,063 · see citing works

Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section

Jakobsson, H. E., Abrahamsson, T. R., Jenmalm, M. C., Harris, K., Quince, C., Jernberg, C., Björkstén, B., Engstrand, L., & Andersson, A. F. (2014) · Gut · doi:10.1136/gutjnl-2012-303249 · Cited by 1,011 · see citing works

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

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Early life antibiotic‐driven changes in microbiota enhance susceptibility to allergic asthma

Russell, S. L., Gold, M. J., Hartmann, M., Willing, B. P., Thorson, L., Wlodarska, M., Gill, N., Blanchet, M., Mohn, W. W., McNagny, K. M., et al. (2012) · The EMBO Reports · doi:10.1038/embor.2012.32 · Cited by 883 · see citing works

The microbiome of uncontacted Amerindians

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Antibiotic use and its consequences for the normal microbiome

Blaser, M. J. (2016) · Science · doi:10.1126/science.aad9358 · Cited by 836 · see citing works

Gut Microbiota Orchestrates Energy Homeostasis during Cold

Chevalier, C., Stojanović, O., Colin, D. J., Suarez-Zamorano, N., Tarallo, V., Veyrat-Durebex, C., Rigo, D., Fabbiano, S., Stevanović, A., Hagemann, S., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.004 · Cited by 829 · see citing works

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

Korpela, K., Salonen, A., Virta, L. J., Kekkonen, R. A., Forslund, K., Bork, P., & de Vos, W. M. (2016) · Nature Communications · doi:10.1038/ncomms10410 · Cited by 698 · see citing works

Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans

Ou, J., Carbonero, F., Zoetendal, E. G., DeLany, J. P., Wang, M., Newton, K., Gaskins, H. R., & O’Keefe, S. J. (2013) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.112.056689 · Cited by 646 · see citing works

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome

Tap, J., Derrien, M., Törnblom, H., Brazeilles, R., Cools-Portier, S., Doré, J., Störsrud, S., Le Nevé, B., Öhman, L., & Simrén, M. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.09.049 · Cited by 642 · see citing works

Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing <i>Clostridium difficile</i> Infection

Youngster, I., Russell, G. H., Pindar, C., Ziv-Baran, T., Sauk, J., & Hohmann, E. L. (2014) · JAMA · doi:10.1001/jama.2014.13875 · Cited by 629 · see citing works

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues

Krautkramer, K. A., Kreznar, J. H., Romano, K. A., Vivas, E. I., Barrett-Wilt, G. A., Rabaglia, M. E., Keller, M. P., Attie, A. D., Rey, F. E., & Denu, J. M. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.025 · Cited by 607 · see citing works

The Origins of Agriculture in the Near East

Zeder, M. A. (2011) · Current Anthropology · doi:10.1086/659307 · Cited by 593 · see citing works

Subsistence 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

The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

Martínez, I., Stegen, J. C., Maldonado-Gómez, M. X., Eren, A. M., Siba, P. M., Greenhill, A. R., & Walter, J. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.049 · Cited by 576 · 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

Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity

Bruce-Keller, A. J., Salbaum, J. M., Luo, M., Blanchard, E., Taylor, C. M., Welsh, D. A., & Berthoud, H.-R. (2015) · Biological Psychiatry · doi:10.1016/j.biopsych.2014.07.012 · Cited by 563 · 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

Captivity humanizes the primate microbiome

Clayton, J. B., Vangay, P., Huang, H., Ward, T., Hillmann, B., Al‐Ghalith, G. A., Travis, D. A., Long, H. T., Tuan, B. V., Minh, V. V., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521835113 · Cited by 510 · see citing works

Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter

Greenwood, C., Morrow, A. L., Lagomarcino, A. J., Altaye, M., Taft, D. H., Yu, Z., Newburg, D. S., Ward, D. V., & Schibler, K. R. (2014) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2014.01.010 · Cited by 410 · 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

Rapid changes in the gut microbiome during human evolution

Moeller, A. H., Li, Y., Ngole, E. M., Ahuka‐Mundeke, S., Lonsdorf, E. V., Pusey, A. E., Peeters, M., Hahn, B. H., & Ochman, H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419136111 · Cited by 336 · see citing works

Food and evolution : toward a theory of human food habits

Harris, M., & Ross, E. B. (1987) · Project Muse (Johns Hopkins University) · Cited by 335 · 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

Human gut microbiota community structures in urban and rural populations in Russia

Tyakht, A., Kostryukova, E., Popenko, A., Belenikin, M. S., Pavlenko, A. V., Larin, A. K., Karpova, I. Y., Selezneva, O. V., Semashko, T. A., Ospanova, E. A., et al. (2013) · Nature Communications · doi:10.1038/ncomms3469 · Cited by 283 · see citing works

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns

Gomez, A., Petrzelkova, K. J., Burns, M. B., Yeoman, C. J., Amato, K. R., Vlckova, K., Modry, D., Todd, A., Jost Robinson, C. A., Remis, M. J., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.02.013 · Cited by 248 · see citing works

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

Morton, E. R., Lynch, J., Froment, A., Lafosse, S., Heyer, E., Przeworski, M., Blekhman, R., & Ségurel, L. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005658 · Cited by 231 · see citing works

Earliest Archaeological Evidence of Persistent Hominin Carnivory

Ferraro, J. V., Plummer, T. W., Pobiner, B. L., Oliver, J. S., Bishop, L. C., Braun, D. R., Ditchfield, P. W., Seaman, J. W., Binetti, K. M., Seaman, J. W., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062174 · Cited by 224 · see citing works

Insights from Characterizing Extinct Human Gut Microbiomes

Tito, R. Y., Knights, D., Metcalf, J. L., Obregón-Tito, A. J., Cleeland, L. M., Najar, F. Z., Roe, B. A., Reinhard, K. J., Sobolik, K. D., Belknap, S. L., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051146 · Cited by 217 · see citing works

Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection

Youngster, I., Mahabamunuge, J., Systrom, H. K., Sauk, J. S., Khalili, H., Levin, J., Kaplan, J. L., & Hohmann, E. L. (2016) · BMC Medicine · doi:10.1186/s12916-016-0680-9 · Cited by 184 · see citing works

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species

Amato, K. R., Martínez‐Mota, R., Righini, N., Raguet-Schofield, M., Corcione, F. P., Marini, E., Humphrey, G. C., Gogul, G., Gaffney, J., Lovelace, E., et al. (2015) · Oecologia · doi:10.1007/s00442-015-3507-z · Cited by 123 · see citing works

Comparative Analysis of Gut Microbiota of Native Tibetan and Han Populations Living at Different Altitudes

Li, K., Dan, Z., Gesang, L., Wang, H., Zhou, Y., Du, Y., Ren, Y., Shi, Y., & Nie, Y. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155863 · Cited by 119 · 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

The Gut Microbiome of Wild Lemurs: A Comparison of Sympatric Lemur catta and Propithecus verreauxi

Fogel, A. T. (2015) · Folia Primatologica · doi:10.1159/000369971 · Cited by 64 · see citing works

The Microbiome and Asthma

Huang, Y. J., & Boushey, H. A. (2014) · Annals of the American Thoracic Society · doi:10.1513/annalsats.201306-187mg · Cited by 45 · see citing works

Elucidating the richness of bacterial groups in the gut of Nicobarese tribal community – Perspective on their lifestyle transition

Maile, A., Kumar, K. V., Muruganandam, N., Chander, M. P., Kartick, C., & Vijayachari, P. (2016) · Anaerobe · doi:10.1016/j.anaerobe.2016.03.002 · Cited by 18 · see citing works

The gut microbiota and its biogeography

McCallum, G., & Tropini, C. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00969-0 · Cited by 342 · see citing works

Potential Effects of Horizontal Gene Exchange in the Human Gut

Lerner, A., Matthias, T., & Aminov, R. I. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01630 · Cited by 200 · see citing works

Viral Infections, the Microbiome, and Probiotics

Harper, A., Vijayakumar, V., Ouwehand, A. C., ter Haar, J., Obis, D., Espadaler, J., Binda, S., Desiraju, S., & Day, R. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.596166 · Cited by 177 · see citing works

Roles of the gut microbiota in the adaptive evolution of mammalian species

Moeller, A. H., & Sanders, J. G. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0597 · Cited by 170 · see citing works

Dysbiosis revisited: Understanding the role of the oral microbiome in the pathogenesis of gingivitis and periodontitis: A critical assessment

Scannapieco, F. A., & Dongari‐Bagtzoglou, A. I. (2021) · Journal of Periodontology · doi:10.1002/jper.21-0120 · Cited by 125 · see citing works

Gut microbiota and old age: Modulating factors and interventions for healthy longevity

Coman, V., & Vodnar, D. C. (2020) · Experimental Gerontology · doi:10.1016/j.exger.2020.111095 · Cited by 124 · see citing works

The Hygiene Hypothesis – Learning From but Not Living in the Past

Pfefferle, P. I., Keber, C. U., Cohen, R. M., & Garn, H. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.635935 · Cited by 103 · see citing works

The mother–offspring dyad: microbial transmission, immune interactions and allergy development

Jenmalm, M. C. (2017) · Journal of Internal Medicine · doi:10.1111/joim.12652 · Cited by 95 · see citing works

Interrogating the microbiome: experimental and computational considerations in support of study reproducibility

Poussin, C., Sierro, N., Boué, S., Battey, J. N. D., Scotti, E., Belcastro, V., Peitsch, M. C., Ivanov, N. V., & Hoeng, J. (2018) · Drug Discovery Today · doi:10.1016/j.drudis.2018.06.005 · Cited by 89 · see citing works

Probiotics: Current Landscape and Future Horizons

Day, R. L., Harper, A. J., Woods, R. M., Davies, O. G., & Heaney, L. M. (2019) · Future Science OA · doi:10.4155/fsoa-2019-0004 · Cited by 88 · see citing works

Effects of domestication on the gut microbiota parallel those of human industrialization

Reese, A. T., Chadaideh, K. S., Diggins, C. E., Schell, L. D., Beckel, M., Callahan, P., Ryan, R., Thompson, M. E., & Carmody, R. N. (2021) · eLife · doi:10.7554/elife.60197 · Cited by 88 · see citing works

Potential contribution of beneficial microbes to face the COVID-19 pandemic

Antunes, A. E. C., Vinderola, G., Xavier-Santos, D., & Sivieri, K. (2020) · Food Research International · doi:10.1016/j.foodres.2020.109577 · Cited by 84 · see citing works

Effects of Low and High FODMAP Diets on Human Gastrointestinal Microbiota Composition in Adults with Intestinal Diseases: A Systematic Review

Vandeputte, D., & Joossens, M. (2020) · Microorganisms · doi:10.3390/microorganisms8111638 · Cited by 83 · see citing works

Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health

Kok, C. R., Rose, D. J., & Hutkins, R. W. (2022) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-060721-015516 · Cited by 79 · see citing works

Whole Blueberry and Isolated Polyphenol-Rich Fractions Modulate Specific Gut Microbes in an In Vitro Colon Model and in a Pilot Study in Human Consumers

Ntemiri, A., Ghosh, T. S., Gheller, M. E., Tran, T. T. T., Blum, J., Pellanda, P., Vlčková, K., Neto, M. C., Howell, A. B., Thalacker‐Mercer, A. E., et al. (2020) · Nutrients · doi:10.3390/nu12092800 · Cited by 71 · see citing works

Microbiome and the immune system: From a healthy steady-state to allergy associated disruption

Mezouar, S., Chantran, Y., Michel, J., Fabre, A., Dubus, J. ‐., Léone, M., Sérémé, Y., Mège, J., Ranque, S., Desnues, B., et al. (2018) · Human Microbiome Journal · doi:10.1016/j.humic.2018.10.001 · Cited by 69 · 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

Finding a needle in a haystack: Bacteroides fragilis polysaccharide A as the archetypical symbiosis factor

Ertürk-Hasdemir, D., & Kasper, D. L. (2018) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13660 · Cited by 65 · see citing works

Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations

Li, A., Vinderola, G., Endo, A., Kantanen, J., Jingfeng, C., Binetti, A. G., Burns, P., Qingmiao, S., Suying, D., Yu, Z., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03116-2 · Cited by 59 · see citing works

Personalized Nutrition Through The Gut Microbiota: Current Insights And Future Perspectives

Vandeputte, D. (2020) · Nutrition Reviews · doi:10.1093/nutrit/nuaa098 · Cited by 58 · see citing works

Effects of Added Dietary Fiber and Rearing System on the Gut Microbial Diversity and Gut Health of Chickens

Hou, L., Sun, B., & Yang, Y. (2020) · Animals · doi:10.3390/ani10010107 · Cited by 46 · see citing works

Scoping review on soil microbiome and gut health—Are soil microorganisms missing from the planetary health plate?

Roslund, M. I., Laitinen, O. H., & Sinkkonen, A. (2024) · People and Nature · doi:10.1002/pan3.10638 · Cited by 31 · see citing works

Primate phageomes are structured by superhost phylogeny and environment

Gogarten, J. F., Rühlemann, M. C., Archie, E. A., Tung, J., Akoua-Koffi, C. G., Bang, C., Deschner, T., Muyembé‐Tamfum, J., Robbins, M. M., Schubert, G., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013535118 · Cited by 28 · see citing works

Early-life food nutrition, microbiota maturation and immune development shape life-long health

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Food System Transformation and Gut Microbiota Transition: Evidence on Advancing Obesity, Cardiovascular Diseases, and Cancers—A Narrative Review

Elechi, J. O. G., Sirianni, R., Conforti, F. L., Cione, E., & PELLEGRINO, M. A. (2023) · Foods · doi:10.3390/foods12122286 · Cited by 25 · see citing works

The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial

Schropp, N., Bauer, A., Stanislas, V., Huang, K. D., Lesker, T.-R., Bielecka, A. A., Strowig, T., & Michels, K. B. (2025) · Microbiome · doi:10.1186/s40168-024-02016-3 · Cited by 25 · see citing works

Confounder or Confederate? The Interactions Between Drugs and the Gut Microbiome in Psychiatric and Neurological Diseases

Michaelis, L., Berg, L., & Maier, L. (2023) · Biological Psychiatry · doi:10.1016/j.biopsych.2023.06.004 · Cited by 17 · see citing works

Bacteria in the ageing gut: did the taming of fire promote a long human lifespan?

Danchin, A. (2018) · Environmental Microbiology · doi:10.1111/1462-2920.14255 · Cited by 16 · see citing works

Lifestyle-Induced Microbial Gradients: An Indian Perspective

Singh, R., Haque, M. M., & Mande, S. S. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02874 · Cited by 13 · see citing works

Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy

Labenz, J., Borkenstein, D., Heil, F. J., Madisch, A., Tappe, U., Schmidt, H., Terjung, B., Klymiuk, I., Horvath, A., Gross, M., et al. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2022.1078315 · Cited by 12 · see citing works

The intersection of social determinants of health, the microbiome, and health outcomes in immigrants: A scoping review

Fanfan, D., Mulligan, C. J., Groer, M. E., Mai, V., Weaver, M. T., Huffman, F. G., & Lyon, D. (2023) · American Journal of Biological Anthropology · doi:10.1002/ajpa.24850 · Cited by 10 · see citing works

Effects of Altered Dietary Fiber on the Gut Microbiota, Short-Chain Fatty Acids and Cecum of Chickens during Different Growth PeriodsPreprint

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Agta hunter–gatherer oral microbiomes are shaped by contact network structure

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Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand

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