MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT

Savage, D. C.

doi:10.1146/annurev.mi.31.100177.000543

Cited by 2,436Gut microbiota and healthMicrobial Community Ecology and PhysiologyInfant Nutrition and Health

MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT

Savage, D. C.·1977·Annual Review of Microbiology

DOI 10.1146/annurev.mi.31.100177.000543

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Abstract

CONTENTS INTRODUCTION 107 MICROBIAL ECOLOGY AS APPLIED TO THE GASTROINTESTINAL TRACT 108 MICROBIAL HABITATS IN THE MAMMALIAN GASTROINTESTINAL TRACT ........ 110 COMPOSITION AND LOCALIZATION OF CLIMAX COMMUNITIES IN ADULTS ...... 111 Some Comments on Methods 111 The Stomach (Esophagus) 112 The Small Bowel 115 The Large Bowel 116 The Feces 118 SUCCESSION IN BABIES 119 FACTORS INFLUENCING COMPOSITION OF THE MICROBIOTA 121 Forces Exerted by the Host and Its Diet and Environment 121 Forces Resulting from Activities of the Microbes Themselves 126 HOW MICROBES IN THE BIOTA MAKE THEIR LIVING (NICHES) 127 SUMMARY AND CONCLUSIONS 129

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From Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions (2013) · cites this paper as [10]

Genetics of the Evolutionary Process.
Dobzhansky, T. (1970) · doi:10.5281/zenodo.10742832 · Cited by 1,617 · see citing works
The Microbial World
Stanier, R. Y., Doudoroff, M., & Adelberg, E. A. (1957) · AIBS Bulletin · doi:10.2307/1292492 · Cited by 475 · see citing works
The normal microbial flora of man
(1975) · Food and Cosmetics Toxicology · doi:10.1016/0015-6264(75)90162-5 · Cited by 232 · see citing works
Comparative physiology of the digestive system
Stevens, C. (1977) · Medical Entomology and Zoology · Cited by 55 · see citing works

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Host-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277 · see citing works
Gut microbiota in health and disease
Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182 · see citing works
Bacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231 · see citing works
Bile salt biotransformations by human intestinal bacteria
Ridlon, J. M., Kang, D.-J., & Hylemon, P. B. (2006) · Journal of Lipid Research · doi:10.1194/jlr.r500013-jlr200 · Cited by 2,829 · see citing works
Gut–brain axis: How the microbiome influences anxiety and depression
Foster, J. A., & McVey Neufeld, K.-A. (2013) · Trends in Neurosciences · doi:10.1016/j.tins.2013.01.005 · Cited by 2,460 · see citing works
Commensal Host-Bacterial Relationships in the Gut
Hooper, L. V., & Gordon, J. I. (2001) · Science · doi:10.1126/science.1058709 · Cited by 2,362 · see citing works
The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon
Donohoe, D. R., Garge, N., Zhang, X., Sun, W., O'Connell, T. M., Bunger, M. K., & Bultman, S. J. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.02.018 · Cited by 2,003 · see citing works
“The vast majority of microbes are bacteria that reside in the gut and are estimated to number 100 trillion, which is 10-fold greater than all of somatic and germ cells in the human body (Savage, 1977; Turnbaugh and Gordon, 2009).”
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Mariat, D., Firmesse, O., Levenez, F., Guimarăes, V., Sokol, H., Doré, J., Corthier, G., & Furet, J.-P. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-123 · Cited by 1,755 · see citing works
Dysbiosis of the gut microbiota in disease
Carding, S., Verbeke, K., Vipond, D. T., Corfe, B. M., & Owen, L. J. (2015) · Microbial Ecology in Health & Disease · doi:10.3402/mehd.v26.26191 · Cited by 1,710 · see citing works
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Schwabe, R. F., & Jobin, C. (2013) · Nature Reviews Cancer · doi:10.1038/nrc3610 · Cited by 1,689 · see citing works
The Application of Ecological Theory Toward an Understanding of the Human Microbiome
Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M., & Relman, D. A. (2012) · Science · doi:10.1126/science.1224203 · Cited by 1,437 · see citing works
A Genomic View of the Human- <i>Bacteroides thetaiotaomicron</i> Symbiosis
Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K., Chiang, H. C., Hooper, L. V., & Gordon, J. I. (2003) · Science · doi:10.1126/science.1080029 · Cited by 1,353 · see citing works
Human oral, gut, and plaque microbiota in patients with atherosclerosis
Koren, O., Spor, A., Felin, J., Fåk, F., Stombaugh, J., Tremaroli, V., Behre, C. J., Knight, R., Fagerberg, B., Ley, R. E., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011383107 · Cited by 1,196 · see citing works
Glycan foraging in vivo by an intestine-adapted bacterial symbiont
Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1109051 · Cited by 1,184 · see citing works
Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity
Clarke, T. B., Davis, K. M., Lysenko, E. S., Zhou, A. Y., Yu, Y., & Weiser, J. N. (2010) · Nature Medicine · doi:10.1038/nm.2087 · Cited by 1,154 · see citing works
Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut
Artis, D. (2008) · Nature reviews. Immunology · doi:10.1038/nri2316 · Cited by 1,136 · see citing works
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r42 · Cited by 1,076 · see citing works
Role of gastrointestinal microbiota in fish
Nayak, S. K. (2010) · Aquaculture Research · doi:10.1111/j.1365-2109.2010.02546.x · Cited by 1,073 · see citing works
Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity
Leclercq, S., Matamoros, S., Cani, P. D., Neyrinck, A. M., Jamar, F., Stärkel, P., Windey, K., Tremaroli, V., Bäckhed, F., Verbeke, K., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1415174111 · Cited by 972 · see citing works
Microorganisms with Claimed Probiotic Properties: An Overview of Recent Literature
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Towards the human intestinal microbiota phylogenetic core
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J., Ugarte, E., Muñoz‐Tamayo, R., Paslier, D. L. E., Nalin, R., et al. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01982.x · Cited by 927 · see citing works
The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardio-metabolic health
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Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes
Magnúsdóttir, S., Ravcheev, D., de Crécy-Lagard, V., & Thiele, I. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00148 · Cited by 876 · see citing works
Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity
Cani, P. D., Osto, M., Geurts, L., & Everard, A. (2012) · Gut Microbes · doi:10.4161/gmic.19625 · Cited by 864 · see citing works
Mesenchymal Stem/Stromal Cells (MSCs): Role as Guardians of Inflammation
Prockop, D. J., & Youn Oh, J. (2012) · Molecular Therapy · doi:10.1038/mt.2011.211 · Cited by 816 · see citing works
“Bone marrow stromal cells attenuate sepsis via prostaglandin E(2)-dependent reprogramming of host macrophages to increase their interleukin-10 production.”
BackgroundInfluential
The human microbiome: Our second genome
Grice, E. A., & Segre, J. A. (2012) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090711-163814 · Cited by 759 · see citing works
The biology and future prospects of antivirulence therapies
Cegelski, L., Marshall, G. R., Eldridge, G. R., & Hultgren, S. J. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1818 · Cited by 788 · see citing works
Candida albicans biofilms: development, regulation, and molecular mechanisms
Gulati, M., & Nobile, C. J. (2016) · Microbes and Infection · doi:10.1016/j.micinf.2016.01.002 · Cited by 738 · see citing works
Nitrate, bacteria and human health
Lundberg, J. O., Weitzberg, E., Cole, J. A., & Benjamin, N. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro929 · Cited by 739 · see citing works
The human gut microbiome: ecology and recent evolutionary changes
Walter, J., & Ley, R. (2011) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090110-102830 · Cited by 720 · see citing works
Intestinal microbiota in human health and disease: the impact of probiotics
Gerritsen, J., Smidt, H., Rijkers, G. T., & de Vos, W. M. (2011) · Genes & Nutrition · doi:10.1007/s12263-011-0229-7 · Cited by 724 · see citing works
Intestinal Permeability in Inflammatory Bowel Disease: Pathogenesis, Clinical Evaluation, and Therapy of Leaky Gut
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Conducting a microbiome study
Goodrich, J. K., Di Rienzi, S. C., Poole, A. C., Koren, O., Walters, W. A., Caporaso, J. G., Knight, R., & Ley, R. E. (2014) · Cell · doi:10.1016/j.cell.2014.06.037 · Cited by 714 · see citing works
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Martens, E. C., Neumann, M., & Desai, M. S. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0036-x · Cited by 711 · see citing works
The role of the microbiome in cancer development and therapy
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Adler, C. J., Dobney, K., Weyrich, L. S., Kaidonis, J., Walker, A. W., Haak, W., Bradshaw, C. J. A., Townsend, G., Sołtysiak, A., Alt, K. W., et al. (2013) · Nature Genetics · doi:10.1038/ng.2536 · Cited by 621 · see citing works
Drug resistance and new therapies in colorectal cancer
Jeught, K. V. D., Xu, H.-C., Li, Y.-J., Lu, X.-B., & Ji, G. (2018) · World Journal of Gastroenterology · doi:10.3748/wjg.v24.i34.3834 · Cited by 597 · see citing works
Extensive transmission of microbes along the gastrointestinal tract
Schmidt, T. S., Hayward, M. R., Coelho, L. P., Li, S. S., Costea, P. I., Voigt, A. Y., Wirbel, J., Maistrenko, O. M., Alves, R. J., Bergsten, E., et al. (2019) · eLife · doi:10.7554/elife.42693 · Cited by 596 · see citing works
Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans
Hagan, T., Cortese, M., Rouphael, N., Boudreau, C., Linde, C., Maddur, M. S., Das, J., Wang, H., Guthmiller, J., Zheng, N.-Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.010 · Cited by 572 · see citing works
Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing
Kasai, C., Sugimoto, K., Moritani, I., Tanaka, J., Oya, Y., Inoue, H., Tameda, M., Shiraki, K., Ito, M., Takei, Y., et al. (2015) · BMC Gastroenterology · doi:10.1186/s12876-015-0330-2 · Cited by 581 · see citing works
Polysaccharide Utilization Loci: Fueling Microbial Communities
Grondin, J. M., Tamura, K., Déjean, G., Abbott, D. W., & Brumer, H. (2017) · Journal of Bacteriology · doi:10.1128/jb.00860-16 · Cited by 554 · see citing works
The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
(2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.08.014 · Cited by 536 · see citing works
Specialized metabolites from the microbiome in health and disease
Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P. C., & Mazmanian, S. K. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.10.016 · Cited by 544 · see citing works
Bacterial contributions to mammalian gut development
Hooper, L. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.01.001 · Cited by 541 · see citing works
Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function
Mao, S., Zhang, M., Liu, J., & Zhu, W. (2015) · Scientific Reports · doi:10.1038/srep16116 · Cited by 532 · see citing works
Assembly of the human intestinal microbiota
Dethlefsen, L., Eckburg, P. B., Bik, E. M., & Relman, D. A. (2006) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.06.013 · Cited by 509 · see citing works
Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases
Peterson, D. A., Frank, D. N., Pace, N. R., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.05.001 · Cited by 503 · see citing works
The effects of fermentation acids on bacterial growth
Russell, J. B., & Diez-Gonzalez, F. (1997) · Advances in Microbial Physiology · doi:10.1016/s0065-2911(08)60017-x · Cited by 498 · see citing works
Sex, body mass index, and dietary fiber intake influence the human gut microbiome
Dominianni, C., Sinha, R., Goedert, J. J., Pei, Z., Yang, L., Hayes, R. B., & Ahn, J. (2015) · PLOS ONE · doi:10.1371/journal.pone.0124599 · Cited by 468 · see citing works
Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice
Kashyap, P. C., Marcobal, A., Ursell, L. K., Larauche, M., Duboc, H., Earle, K. A., Sonnenburg, E. D., Ferreyra, J. A., Higginbottom, S. K., Million, M., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.01.047 · Cited by 451 · see citing works
Dysbiosis Signature of Fecal Microbiota in Colorectal Cancer Patients
Wu, N., Yang, X., Zhang, R., Li, J., Xiao, X., Hu, Y., Chen, Y., Yang, F., Lu, N., Wang, Z., et al. (2013) · Microbial Ecology · doi:10.1007/s00248-013-0245-9 · Cited by 454 · see citing works
A vegan or vegetarian diet substantially alters the human colonic faecal microbiota
Zimmer, J., Lange, B., Frick, J.-S., Sauer, H., Zimmermann, K., Schwiertz, A., Rusch, K., Klosterhalfen, S., & Enck, P. (2012) · European Journal of Clinical Nutrition · doi:10.1038/ejcn.2011.141 · Cited by 465 · see citing works
Circadian disorganization alters intestinal microbiota
Voigt, R. M., Forsyth, C. B., Green, S. J., Mutlu, E., Engen, P., Vitaterna, M. H., Turek, F. W., & Keshavarzian, A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097500 · Cited by 439 · see citing works
Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas
Shen, X. J., Rawls, J. F., Randall, T. A., Burcall, L., Mpande, C., Jenkins, N., Jovov, B., Abdo, Z., Sandler, R. S., & Keku, T. O. (2010) · Gut Microbes · doi:10.4161/gmic.1.3.12360 · Cited by 418 · see citing works
The blood exposome and its role in discovering causes of disease
Rappaport, S. M., Barupal, D. K., Wishart, D., Vineis, P., & Scalbert, A. (2014) · Environmental Health Perspectives · doi:10.1289/ehp.1308015 · Cited by 393 · see citing works
Microbiota conservation and BMI signatures in adult monozygotic twins
Tims, S., Derom, C., Jonkers, D. M., Vlietinck, R., Saris, W. H., Kleerebezem, M., de Vos, W. M., & Zoetendal, E. G. (2013) · The ISME Journal · doi:10.1038/ismej.2012.146 · Cited by 367 · see citing works
The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease
O’Dwyer, D. N., Dickson, R. P., & Moore, B. B. (2016) · The Journal of Immunology · doi:10.4049/jimmunol.1600279 · Cited by 362 · see citing works
Endocannabinoids–at the crossroads between the gut microbiota and host metabolism
Cani, P. D., Plovier, H., Van Hul, M., Geurts, L., Delzenne, N. M., Druart, C., & Everard, A. (2016) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2015.211 · Cited by 367 · see citing works
Probiotic agents and infectious diseases: a modern perspective on a traditional therapy
Alvarez-Olmos, M. I., & Oberhelman, R. A. (2001) · Clinical Infectious Diseases · doi:10.1086/320518 · Cited by 359 · see citing works
Cirrhosis, bile acids and gut microbiota: Unraveling a complex relationship
Ridlon, J. M., Alves, J. M., Hylemon, P. B., & Bajaj, J. S. (2013) · Gut Microbes · doi:10.4161/gmic.25723 · Cited by 336 · see citing works
Gut microflora as a target for energy and metabolic homeostasis
Cani, P. D., & Delzenne, N. M. (2007) · Current Opinion in Clinical Nutrition and Metabolic Care · doi:10.1097/mco.0b013e3282efdebb · Cited by 332 · see citing works
Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn's Disease
Scanlan, P. D., Shanahan, F., O'Mahony, C., & Marchesi, J. R. (2006) · Journal of Clinical Microbiology · doi:10.1128/jcm.00312-06 · Cited by 330 · see citing works
Antagonistic activity exerted in vitro and in vivo by Lactobacillus casei (strain GG) against Salmonella typhimurium C5 infection
Hudault, S., Liévin, V, Bernet-Camard, M. F., & Servin, A. L. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.2.513-518.1997 · Cited by 329 · see citing works
Gut microbiota role in irritable bowel syndrome: New therapeutic strategies
Distrutti, E., Monaldi, L., Ricci, P., & Fiorucci, S. (2016) · World Journal of Gastroenterology · doi:10.3748/wjg.v22.i7.2219 · Cited by 320 · see citing works
The gastrointestinal ecosystem: a precarious alliance among epithelium, immunity and microbiota. Microreview
McCracken, V. J., & Lorenz, R. G. (2001) · Cellular Microbiology · doi:10.1046/j.1462-5822.2001.00090.x · Cited by 314 · see citing works
The oral microbiome diversity and its relation to human diseases
He, J., Li, Y., Cao, Y., Xue, J., & Zhou, X. (2015) · Folia Microbiologica · doi:10.1007/s12223-014-0342-2 · Cited by 314 · see citing works
Antibiotics-induced depletion of mice microbiota induces changes in host serotonin biosynthesis and intestinal motility
Ge, X., Ding, C., Zhao, W., Xu, L., Tian, H., Gong, J., Zhu, M., Li, J., & Li, N. (2017) · Journal of Translational Medicine · doi:10.1186/s12967-016-1105-4 · Cited by 274 · see citing works
Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients
Kerckhoffs, A. P., Samsom, M., Rest, M. E. V. D., Vogel, J. D., Knol, J., Ben-Amor, K., & Akkermans, L. M. (2009) · World Journal of Gastroenterology · doi:10.3748/wjg.15.2887 · Cited by 289 · see citing works
Fecal Microbiota Transplantation: Indications, Methods, Evidence, and Future Directions
Borody, T. J., Paramsothy, S., & Agrawal, G. (2013) · Current Gastroenterology Reports · doi:10.1007/s11894-013-0337-1 · Cited by 275 · see citing works
Impact of dietary protein on microbiota composition and activity in the gastrointestinal tract of piglets in relation to gut health: a review
Rist, V. T. S., Weiss, E., Eklund, M., & Mosenthin, R. (2013) · Animal · doi:10.1017/s1751731113000062 · Cited by 269 · see citing works
Myd88-dependent positioning of Ptgs2-expressing stromal cells maintains colonic epithelial proliferation during injury
Brown, S. L., Riehl, T. E., Walker, M. R., Geske, M. J., Doherty, J. M., Stenson, W. F., & Stappenbeck, T. S. (2007) · Journal of Clinical Investigation · doi:10.1172/jci29159 · Cited by 263 · see citing works
A Molecular Analysis of Fecal and Mucosal Bacterial Communities in Irritable Bowel Syndrome
Codling, C., O’Mahony, L., Shanahan, F., Quigley, E. M. M., & Marchesi, J. R. (2010) · Digestive Diseases and Sciences · doi:10.1007/s10620-009-0934-x · Cited by 243 · see citing works
Culture‐independent analysis of the gut microbiota in colorectal cancer and polyposis
Scanlan, P. D., Shanahan, F., Clune, Y., Collins, J. K., O'Sullivan, G. C., O'Riordan, M., Holmes, E., Wang, Y., & Marchesi, J. R. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01503.x · Cited by 245 · see citing works
The Bacterial Flora in Inflammatory Bowel Disease: Current Insights in Pathogenesis and the Influence of Antibiotics and Probiotics
Linskens, R. K., Huijsdens, X. W., Savelkoul, P. H. M., Vandenbroucke-Grauls, C. M. J. E., & Meuwissen, S. G. M. (2001) · Scandinavian Journal of Gastroenterology · doi:10.1080/003655201753265082 · Cited by 233 · see citing works
Fecal microbiota transplantation broadening its application beyond intestinal disorders
Xu, M.-Q. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i1.102 · Cited by 231 · see citing works
Respiration of <i>Escherichia coli</i> in the Mouse Intestine
Jones, S. A., Chowdhury, F. Z., Fabich, A. J., Anderson, A., Schreiner, D. M., House, A. L., Autieri, S. M., Leatham, M. P., Lins, J. J., Jorgensen, M., et al. (2007) · Infection and Immunity · doi:10.1128/iai.00484-07 · Cited by 223 · see citing works
Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children
Laufer, A. S., Metlay, J. P., Gent, J. F., Fennie, K. P., Kong, Y., & Pettigrew, M. M. (2011) · mBio · doi:10.1128/mbio.00245-10 · Cited by 224 · see citing works
What lives on our skin: ecology, genomics and therapeutic opportunities of the skin microbiome
Scharschmidt, T. C., & Fischbach, M. A. (2013) · Drug Discovery Today: Disease Mechanisms · doi:10.1016/j.ddmec.2012.12.003 · Cited by 215 · see citing works
Polyphenol supplementation benefits human health via gut microbiota: a systematic review via meta-analysis
Ma, G., & Chen, Y. (2020) · Journal of Functional Foods · doi:10.1016/j.jff.2020.103829 · Cited by 210 · see citing works
Ecology of Candida albicans gut colonization: inhibition of Candida adhesion, colonization, and dissemination from the gastrointestinal tract by bacterial antagonism
Kennedy, M. J., & Volz, P. A. (1985) · Infection and Immunity · doi:10.1128/iai.49.3.654-663.1985 · Cited by 208 · see citing works
Anaerobic Bacteria Grow within Candida albicans Biofilms and Induce Biofilm Formation in Suspension Cultures
Fox, E. P., Cowley, E. S., Nobile, C. J., Hartooni, N., Newman, D. K., & Johnson, A. D. (2014) · Current Biology · doi:10.1016/j.cub.2014.08.057 · Cited by 207 · see citing works
Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism
Miro-Blanch, J., & Yanes, O. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00638 · Cited by 195 · see citing works
The effect of probiotics on immune regulation, acne, and photoaging
Kober, M.-M., & Bowe, W. P. (2015) · International Journal of Women’s Dermatology · doi:10.1016/j.ijwd.2015.02.001 · Cited by 190 · see citing works
Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species
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Probiotics: interaction with gut microbiome and antiobesity potential.
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Yeoh, N., Burton, J. P., Suppiah, P., Reid, G., & Stebbings, S. (2013) · Current Rheumatology Reports · doi:10.1007/s11926-012-0314-y · Cited by 155 · see citing works
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The human microbiome: A hot spot of microbial horizontal gene transfer
Liu, L., Chen, X., Skogerbø, G., Zhang, P., Chen, R., He, S., & Huang, D.-W. (2012) · Genomics · doi:10.1016/j.ygeno.2012.07.012 · Cited by 131 · see citing works
The microbiome and its potential as a cancer preventive intervention
Bultman, S. J. (2016) · Seminars in Oncology · doi:10.1053/j.seminoncol.2015.09.001 · Cited by 134 · see citing works
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Tight Mucosal Compartmentation of the Murine Immune Response to Antigens of the Enteric Microbiota
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Authors: Savage, D. C.
Corresponding author: Savage, D. C.
Venue: Annual Review of Microbiology
Publisher: Annual Reviews
Published: 1977-10
Volume: 31
Issue: 1
Pages: 107-133
ISSN: 0066-4227 (ISSN-L)
1545-3251
DOI: 10.1146/annurev.mi.31.100177.000543
OpenAlex: W2149351690
Cited by: 2,436
References: 4
Citations by year: 2026: 32 · 2025: 28 · 2024: 47 · 2023: 55 · 2022: 68 · 2021: 92 · 2020: 106 · 2019: 90 · 2018: 101 · 2017: 116 · 2016: 108 · 2015: 153 · 2014: 117 · 2013: 117 · 2012: 109
FWCI: 6.65
Type: journal article
Language: en
Open access: closed
Locations: Annual Review of Microbiology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
Keywords: gut microbiota, microbial ecology, gut microbiota composition, microbial habitats, climax community, stomach, esophagus, small intestine, large intestine, feces, host-microbe interactions, diet, microbial niche
MeSH terms: Animals, Antigens, Bacterial, Bacteria, Bile Acids and Salts, Diet, Ecology, Fatty Acids, Feces, Fermentation, Humans, Infant, Intestine, Large, Intestine, Small, Mammals, Microbiological Techniques, Mucins, Peristalsis, Phagocytosis, Stomach, Temperature, Yeasts

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MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT

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