Host-Bacterial Mutualism in the Human Intestine
Abstract
The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
Increased gut permeability is thought to facilitate the movement of inflammatory mediators from the gut into the circulation, promoting systemic insulin resistance.
“Increased gut permeability is thought to facilitate the movement of inflammatory mediators from the gut into the circulation, promoting systemic insulin resistance [134,136].”
From The Pathophysiology of Gestational Diabetes Mellitus (2018) · cites this paper as [136]
Most animal and human studies have reported that obesity and insulin resistance are associated with an altered ratio of Firmicutes and Bacteroidetes.
“Most of the animal and human studies have reported that obesity and insulin resistance are associated with an altered ratio of Firmicutes and Bacteroidetes [8,9].”
From Effects of Regular Kefir Consumption on Gut Microbiota in Patients with Metabolic Syndrome: A Parallel-Group, Randomized, Controlled Study (2019) · cites this paper as [9]
The gut microbiota is integral to human physiology and contributes to metabolism, immune function, and gut homeostasis.
“It is now understood that the gut microbiota coevolved with the human host over thousands of years and are integral to overall human physiology, playing a pivotal role in metabolism, immune system function and maintenance of gut homeostasis.1, 2”
From Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms, and Outlook (2015) · cites this paper as [1]
The number of drugs metabolized by the gut microbiota is likely greater than 50 because systematic analyses are lacking and the microbiome is genetically diverse.
“This number is likely an underestimate given the lack of any systematic analyses of the gut microbial metabolism of drugs and the vast genetic diversity within the microbiome34.”
From The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism (2016) · cites this paper as [34]
A primary role of the gut microbiota is to assist in digesting food and extracting nutrients that the host cannot metabolize without microbial help.
“A major function of the gut microbiota is to aid in host food digestion, harvesting key nutrients that the host is incapable of metabolizing without the help of microbes (Backhed et al., 2005).”
From The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy (2018) · cites this paper as Backhed et al., 2005
Under healthy conditions, the microbiota influences numerous physiological processes within the host, including protection against pathogens, nutrient digestion and absorption, development, and education of multiple host organs and the immune system.
“Under healthy conditions, the microbiota influences numerous physiological processes within the host, such as protection against pathogens, nutrient digestion and absorption, development, and education of multiple host organs and the immune system (3–6).”
From The gut-brain axis: how microbiota and host inflammasome influence brain physiology and pathology (2020) · cites this paper as [4]
Cites
The gut microbiota as an environmental factor that regulates fat storage
Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245 · see citing works
Self-citationProkaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871 · see citing works
Energy conservation in chemotrophic anaerobic bacteria
Thauer, R. K., Jungermann, K., & Decker, K. (1977) · Bacteriological Reviews · doi:10.1128/br.41.1.100-180.1977 · Cited by 4,146 · see citing works
Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis
Yachi, S., & Loreau, M. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.4.1463 · Cited by 3,211 · see citing works
The diversity–stability debate
McCann, K. S. (2000) · Nature · doi:10.1038/35012234 · Cited by 3,110 · see citing works
MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT
Savage, D. C. (1977) · Annual Review of Microbiology · doi:10.1146/annurev.mi.31.100177.000543 · Cited by 2,436 · see citing works
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
Hugenholtz, P., Goebel, B. M., & Pace, N. R. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.18.4765-4774.1998 · Cited by 2,429 · see citing works
Marine viruses and their biogeochemical and ecological effects
Fuhrman, J. A. (1999) · Nature · doi:10.1038/21119 · Cited by 2,257 · see citing works
Zoetendal, E. G., Akkermans, A. D. L., & de Vos, W. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3854-3859.1998 · Cited by 1,360 · 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
Self-citationGlycan 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
Self-citationHuman Fecal Flora: The Normal Flora of 20 Japanese-Hawaiians
Moore, W. E. C., & Holdeman, L. V. (1974) · Applied Microbiology · doi:10.1128/am.27.5.961-979.1974 · Cited by 1,144 · see citing works
Metagenomic Analyses of an Uncultured Viral Community from Human Feces
Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton, J., Salamon, P., & Rohwer, F. L. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.20.6220-6223.2003 · Cited by 828 · see citing works
Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
Seksik, P., Rigottier‐Gois, L., Gramet, G., BRIEND‐SUTREN, M., Pochart, P., Marteau, P. R., Jian, R., & Dore, J. M. (2003) · Gut · doi:10.1136/gut.52.2.237 · Cited by 746 · see citing works
Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut
Suzuki, K., Meek, B., Doi, Y., Muramatsu, M., Chiba, T., Honjo, T., & Fagarasan, S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307317101 · Cited by 721 · see citing works
The contribution of the large intestine to energy supplies in man
N I, M. (1984) · The American Journal of Clinical Nutrition · doi:10.1093/ajcn/39.2.338 · Cited by 691 · see citing works
Metabolic interactions between anaerobic bacteria in methanogenic environments
Stams, A. J. M. (1994) · Antonie van Leeuwenhoek · doi:10.1007/bf00871644 · Cited by 584 · see citing works
Evolution of cooperation and conflict in experimental bacterial populations
Rainey, P. B., & Rainey, K. (2003) · Nature · doi:10.1038/nature01906 · Cited by 568 · see citing works
The Host Genotype Affects the Bacterial Community in the Human Gastronintestinal Tract
Zoetendal, A. D. L. A. E. G. (2001) · Microbial Ecology in Health and Disease · doi:10.1080/089106001750462669 · Cited by 558 · see citing works
Changes in the distribution of body mass index of adults and children in the US population
Flegal, K. M., & Troiano, R. P. (2000) · International Journal of Obesity · doi:10.1038/sj.ijo.0801232 · Cited by 512 · see citing works
Sonnenburg, J. L., Angenent, L. T., & Gordon, J. I. (2004) · Nature Immunology · doi:10.1038/ni1079 · Cited by 406 · see citing works
Self-citationEmpirical and Theoretical Bacterial Diversity in Four Arizona Soils
Dunbar, J., Barns, S. M., Ticknor, L. O., & Kuske, C. R. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.6.3035-3045.2002 · Cited by 368 · see citing works
Scavino, A. F., Hashsham, S. A., Dollhopf, S. L., Raskin, L. M., Glagoleva, O. B., Dazzo, F. B., Hickey, R. F., Criddle, C. S., & Tiedje, J. M. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.9.4058-4067.2000 · Cited by 338 · see citing works
Extensive DNA Inversions in the B. fragilis Genome Control Variable Gene Expression
Cerdeño-Tárraga, A. M., Patrick, S., Crossman, L. C., Blakely, G., Abratt, V. R., Lennard, N. J., Poxton, I. R., Duerden, B. I., Harris, B. R., Quail, M. A., et al. (2005) · Science · doi:10.1126/science.1107008 · Cited by 298 · see citing works
Goebel, B. M., & Stackebrandt, E. (1994) · Applied and Environmental Microbiology · doi:10.1128/aem.60.5.1614-1621.1994 · Cited by 294 · see citing works
Kuwahara, T., Yamashita, A., Hirakawa, H., Nakayama, H., Toh, H., Okada, N., Kuhara, S., Hattori, M., Hayashi, T., & Ohnishi, Y. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404172101 · Cited by 271 · see citing works
Strategies of microbial cheater control
Travisano, M., & Velicer, G. J. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2003.12.009 · Cited by 265 · see citing works
Microecology of the termite gut: structure and function on a microscale
Brune, A., & Friedrich, M. W. (2000) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(00)00087-4 · Cited by 245 · see citing works
Johne's Disease, Inflammatory Bowel Disease, and Mycobacterium paratuberculosis
Chacón, O., Bermudez, L. E., & Barletta, R. G. (2004) · Annual Review of Microbiology · doi:10.1146/annurev.micro.58.030603.123726 · Cited by 232 · see citing works
Shipman, J. A., Berleman, J. E., & Salyers, A. A. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.19.5365-5372.2000 · Cited by 214 · see citing works
Enumeration of Methanobrevibacter smithii in human feces
Miller, T. L., & Wolin, M. J. (1982) · Archives of Microbiology · doi:10.1007/bf00451492 · Cited by 203 · see citing works
Winter, C., Smit, A., Herndl, G. J., & Weinbauer, M. G. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.2.804-813.2004 · Cited by 111 · see citing works
The Molecular Biology Database Collection: 2004 update
Galperin, M. Y. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh143 · Cited by 103 · see citing works
To be a mutator, or how pathogenic and commensal bacteria can evolve rapidly
Taddéi, F., Matić, I., Godelle, B., & Radman, M. (1997) · Trends in Microbiology · doi:10.1016/s0966-842x(97)01157-8 · Cited by 88 · see citing works
Glucose and cAMP: Adversaries in the regulation of hepatic gene expression
Towle, H. C. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.251530798 · Cited by 47 · see citing works
The Effect of Pectin on Hepatic Lipogenesis in the Enterally-Fed Rat
Rolandelli, R. H., Koruda, M. J., Settle, R. G., Leskiw, M. J., Stein, T. P., & Rombeau, J. L. (1989) · Journal of Nutrition · doi:10.1093/jn/119.1.89 · Cited by 11 · see citing works
Influence of intestinal microbes on heat production in germ-free, gnotobiotic and conventional mice.
YAMANAKA, M., Nomura, T., & Kametaka, M. (1977) · Journal of Nutritional Science and Vitaminology · doi:10.3177/jnsv.23.221 · Cited by 11 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · see citing works
Self-citationA human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
Changes of Intestinal Functions in Liver Cirrhosis
Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820 · see citing works
Metabolic Endotoxemia Initiates Obesity and Insulin Resistance
Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A. M., Fava, F., Tuohy, K. M., Chabo, C., et al. (2007) · Diabetes · doi:10.2337/db06-1491 · Cited by 6,638 · see citing works
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176 · see citing works
Self-citationGut flora metabolism of phosphatidylcholine promotes cardiovascular disease
Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., DuGar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., et al. (2011) · Nature · doi:10.1038/nature09922 · Cited by 5,597 · see citing works
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works
Revised Estimates for the Number of Human and Bacteria Cells in the Body
Sender, R., Fuchs, S., & Milo, R. (2016) · PLOS Biology · doi:10.1371/journal.pbio.1002533 · Cited by 5,425 · see citing works
Cani, P. D., Bibiloni, R., Knauf, C., Waget, A., Neyrinck, A. M., Delzenne, N. M., & Burcelin, R. (2008) · Diabetes · doi:10.2337/db07-1403 · Cited by 4,819 · see citing works
Metagenomic Analysis of the Human Distal Gut Microbiome
Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E. (2006) · Science · doi:10.1126/science.1124234 · Cited by 4,699 · see citing works
Self-citationRichness of human gut microbiome correlates with metabolic markers
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works
Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works
Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour
Cryan, J. F., & Dinan, T. G. (2012) · Nature Reviews Neuroscience · doi:10.1038/nrn3346 · Cited by 4,572 · see citing works
Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria
Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554 · 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
Proteobacteria: Microbial signature of dysbiosis in gut microbiota
Shin, N.-R., Whon, T. W., & Bae, J.-W. (2015) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.06.011 · Cited by 3,954 · see citing works
Introduction to the human gut microbiota
Thursby, E., & Juge, N. (2017) · Biochemical Journal · doi:10.1042/bcj20160510 · Cited by 3,600 · see citing works
Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine
Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.02.017 · Cited by 3,358 · see citing works
Self-citationKeystone taxa as drivers of microbiome structure and functioning
Banerjee, S., Schlaeppi, K., & van der Heijden, M. G. A. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0024-1 · Cited by 3,044 · see citing works
Neutrophils and immunity: challenges and opportunities
Nathan, C. (2006) · Nature reviews. Immunology · doi:10.1038/nri1785 · Cited by 2,971 · see citing works
The ecology of the microbiome: Networks, competition, and stability
Coyte, K. Z., Schlüter, J., & Foster, K. R. (2015) · Science · doi:10.1126/science.aad2602 · Cited by 2,722 · see citing works
Abraham, C., & Cho, J. H. (2009) · New England Journal of Medicine · doi:10.1056/nejmra0804647 · Cited by 2,712 · see citing works
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C., & Siuzdak, G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812874106 · Cited by 2,677 · see citing works
Mechanisms underlying the resistance to diet-induced obesity in germ-free mice
Bäckhed, F., Manchester, J. K., Semenkovich, C. F., & Gordon, J. I. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605374104 · Cited by 2,615 · see citing works
Self-citationThe gut microbiota of insects – diversity in structure and function
Engel, P., & Moran, N. A. (2013) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12025 · Cited by 2,594 · see citing works
Influence of diet on the gut microbiome and implications for human health
Singh, R. K., Chang, H.-W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., et al. (2017) · Journal of Translational Medicine · doi:10.1186/s12967-017-1175-y · Cited by 2,599 · see citing works
The gut microbiota influences blood-brain barrier permeability in mice
Braniste, V., Al-Asmakh, M., Kowal, C., Anuar, F., Abbaspour, A., Tóth, M., Korecka, A., Bakocevic, N., Ng, L. G., Kundu, P., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3009759 · Cited by 2,530 · see citing works
Next-Generation DNA Sequencing Methods
Mardis, E. R. (2008) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164359 · Cited by 2,371 · see citing works
Singh, N., Gurav, A., Sivaprakasam, S., Brady, E., Padia, R., Shi, H., Thangaraju, M., Prasad, P. D., Manicassamy, S., Munn, D. H., et al. (2014) · Immunity · doi:10.1016/j.immuni.2013.12.007 · Cited by 2,368 · see citing works
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works
Bacteroides : the Good, the Bad, and the Nitty-Gritty
Wexler, H. M. (2007) · Clinical Microbiology Reviews · doi:10.1128/cmr.00008-07 · Cited by 2,318 · see citing works
Sayin, S. I., Wahlström, A., Felin, J., Jäntti, S., Marschall, H.-U., Bamberg, K., Angelin, B., Hyötyläinen, T., Orešič, M., & Bäckhed, F. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.01.003 · Cited by 2,331 · see citing works
The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria
Johansson, M. E. V., Phillipson, M., Petersson, J., Velcich, A., Holm, L., & Hansson, G. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803124105 · Cited by 2,200 · see citing works
Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome
Chassaing, B., Koren, O., Goodrich, J. K., Poole, A. C., Srinivasan, S., Ley, R. E., & Gewirtz, A. T. (2015) · Nature · doi:10.1038/nature14232 · Cited by 2,055 · see citing works
Self-citationThe Pathophysiology of Gestational Diabetes Mellitus
Plows, J. F., Stanley, J. L., Baker, P. N., Reynolds, C. M., & Vickers, M. H. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19113342 · Cited by 1,874 · see citing works
“Increased gut permeability is thought to facilitate the movement of inflammatory mediators from the gut into the circulation, promoting systemic insulin resistance [134,136].”
BackgroundThe keystone-pathogen hypothesis
Hajishengallis, G., Darveau, R. P., & Curtis, M. A. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2873 · Cited by 1,790 · see citing works
Cani, P. D., Neyrinck, A. M., Fava, F., Knauf, C., Burcelin, R., Tuohy, K. M., Gibson, G. R., & Delzenne, N. M. (2007) · Diabetologia · doi:10.1007/s00125-007-0791-0 · Cited by 1,770 · see citing works
Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770 · see citing works
Intestinal permeability – a new target for disease prevention and therapy
Bischoff, S. C., Barbara, G., Buurman, W., Ockhuizen, T., Schulzke, J.-D., Serino, M., Tilg, H., Watson, A., & Wells, J. M. (2014) · BMC Gastroenterology · doi:10.1186/s12876-014-0189-7 · Cited by 1,755 · see citing works
The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age
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
Bercik, P., Denou, E., Collins, J., Jackson, W., Lu, J., Jury, J., Deng, Y., Blennerhassett, P., Macri, J., McCoy, K. D., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.04.052 · Cited by 1,748 · see citing works
Rivière, A., Selak, M., Lantin, D., Leroy, F., & Vuyst, L. D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00979 · Cited by 1,746 · see citing works
Schwabe, R. F., & Jobin, C. (2013) · Nature Reviews Cancer · doi:10.1038/nrc3610 · Cited by 1,689 · see citing works
Worlds within worlds: evolution of the vertebrate gut microbiota
Ley, R. E., Lozupone, C., Hamady, M., Knight, R. D., & Gordon, J. I. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1978 · Cited by 1,652 · see citing works
Self-citationGut microbiota in cardiovascular health and disease
Tang, W. H. W., Kitai, T., & Hazen, S. L. (2017) · Circulation Research · doi:10.1161/circresaha.117.309715 · Cited by 1,670 · see citing works
Antibiotics in early life alter the murine colonic microbiome and adiposity
Cho, I., Yamanishi, S., Cox, L., Methé, B. A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012) · Nature · doi:10.1038/nature11400 · Cited by 1,613 · see citing works
Bacteria as vitamin suppliers to their host: A gut microbiota perspective
LeBlanc, J. G., Milani, C., de Giori, G. S., Sesma, F., van Sinderen, D., & Ventura, M. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.08.005 · Cited by 1,613 · see citing works
Gut-Residing Segmented Filamentous Bacteria Drive Autoimmune Arthritis via T Helper 17 Cells
Wu, H.-J., Ivanov, I. I., Darce, J., Hattori, K., Shima, T., Umesaki, Y., Littman, D. R., Benoist, C., & Mathis, D. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.001 · Cited by 1,577 · see citing works
The impact of diet and lifestyle on gut microbiota and human health
Conlon, M., & Bird, A. (2014) · Nutrients · doi:10.3390/nu7010017 · Cited by 1,567 · see citing works
Algae as nutritional and functional food sources: revisiting our understanding.
Wells, M. L., Potin, P., Craigie, J. S., Raven, J. A., Merchant, S. S., Helliwell, K. E., Smith, A. G., Camire, M. E., & Brawley, S. H. (2017) · Journal of Applied Phycology · doi:10.1007/s10811-016-0974-5 · Cited by 1,562 · see citing works
Shin, N.-R., Lee, J.-C., Lee, H.-Y., Kim, M.-S., Whon, T. W., Lee, M.-S., & Bae, J.-W. (2014) · Gut · doi:10.1136/gutjnl-2012-303839 · Cited by 1,550 · see citing works
Takahashi, S., Tomita, J., Nishioka, K., Hisada, T., & Nishijima, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0105592 · Cited by 1,514 · see citing works
An insight into gut microbiota and its functionalities
Adak, A., & Khan, M. R. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-018-2943-4 · Cited by 1,485 · see citing works
Johansson, M., Larsson, J. M. H., & Hansson, G. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006451107 · Cited by 1,459 · see citing works
Gaboriau-Routhiau, V., Rakotobe, S., Lécuyer, E., Mulder, I., Lan, A., Bridonneau, C., Rochet, V., Pisi, A., De Paepe, M., Brandi, G., et al. (2009) · Immunity · doi:10.1016/j.immuni.2009.08.020 · Cited by 1,452 · see citing works
The gastrointestinal mucus system in health and disease
Johansson, M. E. V., Sjövall, H., & Hansson, G. C. (2013) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2013.35 · Cited by 1,438 · see citing works
The role of gut microbiota in immune homeostasis and autoimmunity
Wu, H.-J., & Wu, E. (2012) · Gut Microbes · doi:10.4161/gmic.19320 · Cited by 1,426 · see citing works
The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy
Gopalakrishnan, V., Helmink, B. A., Spencer, C. N., Reuben, A., & Wargo, J. A. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.03.015 · Cited by 1,392 · see citing works
Neufeld, K. M., Kang, N., Bienenstock, J., & Foster, J. A. (2011) · Neurogastroenterology & Motility · doi:10.1111/j.1365-2982.2010.01620.x · Cited by 1,392 · see citing works
Microbes in Gastrointestinal Health and Disease
Neish, A. S. (2008) · Gastroenterology · doi:10.1053/j.gastro.2008.10.080 · Cited by 1,388 · see citing works
Symptomatic atherosclerosis is associated with an altered gut metagenome
Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012) · Nature Communications · doi:10.1038/ncomms2266 · Cited by 1,371 · see citing works
Pelaseyed, T., Bergström, J. H., Gustafsson, J. K., Ermund, A., Birchenough, G. M. H., Schütte, A., van der Post, S., Svensson, F., Rodríguez‐Piñeiro, A. M., Nyström, E. E. L., et al. (2014) · Immunological Reviews · doi:10.1111/imr.12182 · Cited by 1,363 · see citing works
Environmental and Gut Bacteroidetes: The Food Connection
Thomas, F., Hehemann, J., Rebuffet, E., Czjzek, M., & Michel, G. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00093 · Cited by 1,329 · see citing works
Proteobacteria: A Common Factor in Human Diseases
Rizzatti, G., Lopetuso, L. R., Gibiino, G., Binda, C., & Gasbarrini, A. (2017) · BioMed Research International · doi:10.1155/2017/9351507 · Cited by 1,264 · see citing works
Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis
Bevins, C. L., & Salzman, N. H. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2546 · Cited by 1,238 · see citing works
Mucosal vaccines: the promise and the challenge
Neutra, M. R., & Kozlowski, P. A. (2006) · Nature reviews. Immunology · doi:10.1038/nri1777 · Cited by 1,232 · see citing works
A Symbiotic View of Life: We Have Never Been Individuals
Gilbert, S. F., Sapp, J., & Tauber, A. I. (2012) · The Quarterly Review of Biology · doi:10.1086/668166 · Cited by 1,208 · see citing works
The microbiome, cancer, and cancer therapy
Helmink, B. A., Khan, M. A. W., Hermann, A., Gopalakrishnan, V., & Wargo, J. A. (2019) · Nature Medicine · doi:10.1038/s41591-019-0377-7 · Cited by 1,200 · 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
Evidence for a core gut microbiota in the zebrafish
Roeselers, G., Mittge, E., Stephens, W. Z., Parichy, D. M., Cavanaugh, C. M., Guillemin, K. J., & Rawls, J. F. (2011) · The ISME Journal · doi:10.1038/ismej.2011.38 · Cited by 1,145 · 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
Jones, B. V., Begley, M., Hill, C., Gahan, C. G. M., & Marchesi, J. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804437105 · Cited by 1,098 · see citing works
Genomics of Actinobacteria : Tracing the Evolutionary History of an Ancient Phylum
Ventura, M., Canchaya, C. A., Tauch, A., Chandra, G., Fitzgerald, G. F., Chater, K. F., & van Sinderen, D. (2007) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00005-07 · Cited by 1,093 · see citing works
Bifidobacteria and Their Role as Members of the Human Gut Microbiota
O’Callaghan, A. A., & van Sinderen, D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00925 · Cited by 1,108 · see citing works
Long-term impacts of antibiotic exposure on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2010) · Microbiology · doi:10.1099/mic.0.040618-0 · Cited by 1,067 · see citing works
The influence of diet on the gut microbiota
Scott, K. P., Gratz, S. W., Sheridan, P. O., Flint, H. J., & Duncan, S. H. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.10.020 · Cited by 1,052 · see citing works
A review of the volatiles from the healthy human body
de Lacy Costello, B., Amann, A., Al-Kateb, H., Flynn, C., Filipiak, W., Khalid, T., Osborne, D., & Ratcliffe, N. M. (2014) · Journal of Breath Research · doi:10.1088/1752-7155/8/1/014001 · Cited by 1,042 · see citing works
Dumas, M.-E., Barton, R. H., Toye, A., Cloarec, O., Blancher, C., Rothwell, A., Fearnside, J., Tatoud, R., Blanc, V., Lindon, J. C., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601056103 · Cited by 1,042 · see citing works
Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing
Andersson, A. F., Lindberg, M., Jakobsson, H. E., Bäckhed, F., Nyrén, P., & Engstrand, L. G. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002836 · Cited by 1,037 · see citing works
Characterization of fecal microbial communities in patients with liver cirrhosis
Chen, Y., Yang, F., Lu, H., Wang, B., Chen, Y., Lei, D., Wang, Y., Zhu, B., & Li, L. (2011) · Hepatology · doi:10.1002/hep.24423 · Cited by 1,038 · see citing works
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens
Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B. C., Monack, D. M., et al. (2013) · Nature · doi:10.1038/nature12503 · Cited by 1,035 · see citing works
Self-citationPeripheral education of the immune system by colonic commensal microbiota
Lathrop, S. K., Bloom, S. M., Rao, S. M., Nutsch, K., Lio, C.-W., Santacruz, N., Peterson, D. A., Stappenbeck, T. S., & Hsieh, C.-S. (2011) · Nature · doi:10.1038/nature10434 · Cited by 1,034 · see citing works
Self-citationGenes and Molecules of Lactobacilli Supporting Probiotic Action
Lebeer, S., Vanderleyden, J., & De Keersmaecker, S. C. J. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00017-08 · Cited by 1,013 · see citing works
Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity
Liou, A. P., Paziuk, M., Luevano, J.-M., Machineni, S., Turnbaugh, P. J., & Kaplan, L. M. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3005687 · Cited by 1,007 · see citing works
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
Huse, S. M., Dethlefsen, L., Huber, J. A., Welch, D. B. M., Relman, D. A., & Sogin, M. L. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000255 · Cited by 993 · see citing works
Treating Clostridium difficile infection with fecal microbiota transplantation
Bakken, J. S., Borody, T., Brandt, L. J., Brill, J. V., Demarco, D. C., Franzos, M. A., Kelly, C., Khoruts, A., Louie, T., Martinelli, L. P., et al. (2011) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2011.08.014 · Cited by 1,003 · see citing works
Kassinen, A., Krogius-Kurikka, L., Mäkivuokko, H., Rinttilä, T., Paulin, L., Corander, J., Malinen, E., Apajalahti, J., & Palva, A. (2007) · Gastroenterology · doi:10.1053/j.gastro.2007.04.005 · Cited by 1,002 · see citing works
The core gut microbiome, energy balance and obesity
Turnbaugh, P. J., & Gordon, J. I. (2009) · The Journal of Physiology · doi:10.1113/jphysiol.2009.174136 · Cited by 993 · see citing works
Self-citationProbiotics and prebiotics in animal feeding for safe food production
Gaggìa, F., Mattarelli, P., & Biavati, B. (2010) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2010.02.031 · Cited by 992 · see citing works
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
Metformin retards aging in C. elegans by altering microbial folate and methionine metabolism
Cabreiro, F., Au, C., Leung, K.-Y., Vergara-Irigaray, N., Cochemé, H. M., Noori, T., Weinkove, D., Schuster, E., Greene, N. D. E., & Gems, D. (2013) · Cell · doi:10.1016/j.cell.2013.02.035 · Cited by 967 · see citing works
Rawls, J. F., Mahowald, M. A., Ley, R. E., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.08.043 · Cited by 962 · see citing works
Self-citationBacteriophage adhering to mucus provide a non–host-derived immunity
Barr, J. J., Auro, R., Furlan, M., Whiteson, K., Erb, M. L., Pogliano, J., Stotland, A. B., Wolkowicz, R., Cutting, A. S., Doran, K. S., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305923110 · Cited by 942 · see citing works
Commensal bacteria at the interface of host metabolism and the immune system
Brestoff, J. R., & Artis, D. (2013) · Nature Immunology · doi:10.1038/ni.2640 · Cited by 945 · see citing works
Ubeda, C., Taur, Y., Jenq, R. R., Equinda, M. J., Son, T., Samstein, M., Viale, A., Socci, N. D., van den Brink, M. R. M., Kamboj, M., et al. (2010) · Journal of Clinical Investigation · doi:10.1172/jci43918 · Cited by 943 · see citing works
Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling
Shin, S. C., Kim, S., You, H., Kim, B., Kim, A. C., Lee, K., Yoon, J., Ryu, J.-H., & Lee, W. (2011) · Science · doi:10.1126/science.1212782 · Cited by 943 · see citing works
Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System
Garrett, W. S., Lord, G. M., Punit, S., Lugo‐Villarino, G., Mazmanian, S. K., Ito, S., Glickman, J. N., & Glimcher, L. H. (2007) · Cell · doi:10.1016/j.cell.2007.08.017 · Cited by 918 · see citing works
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907 · see citing works
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
Claesson, M. J., O’Sullivan, Ó., Wang, Q., Nikkilä, J., Marchesi, J. R., Smidt, H., de Vos, W. M., Ross, R. P., & O’Toole, P. W. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006669 · Cited by 880 · see citing works
- Authors
- Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I.
- Affiliations
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA.
- Washington University in St. Louis (US)
- Corresponding author
- Ley, Ruth E.
- Gordon, Jeffrey I.
- Venue
- Science
- Published
- 2005-03-25
- Volume
- 307
- Issue
- 5717
- Pages
- 1915-1920
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W1980914602
- Cited by
- 5,277
- References
- 37
- Citations by year
- 2026: 143 · 2025: 225 · 2024: 281 · 2023: 322 · 2022: 363 · 2021: 389 · 2020: 359 · 2019: 344 · 2018: 276 · 2017: 277 · 2016: 313 · 2015: 257 · 2014: 288 · 2013: 243 · 2012: 227
- FWCI
- 10.06
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- gut microbiota, human intestine, microbiome, coevolution, microbial diversity, strain-level diversity, nutrient acquisition, microbiological stability, keystone species, anaerobic bioreactor
- MeSH terms
- Anaerobiosis, Bacteria, Bacteroides, Energy Intake, Energy Metabolism, Biological Evolution, Humans, Intestines, Obesity, Selection, Genetic, Genome, Bacterial, Ecosystem, Bacterial Physiological Phenomena, Gastrointestinal Tract, Biodiversity
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
