Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
Open accessAbstract
The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenic archaea. Studies in gnotobiotic mice indicate that Methanobrevibacter smithii , the dominant archaeon in the human gut ecosystem, affects the specificity and efficiency of bacterial digestion of dietary polysaccharides, thereby influencing host calorie harvest and adiposity. Metagenomic studies of the gut microbial communities of genetically obese mice and their lean littermates have shown that the former contain an enhanced representation of genes involved in polysaccharide degradation, possess more archaea, and exhibit a greater capacity to promote adiposity when transplanted into germ-free recipients. These findings have led to the hypothesis that M. smithii may be a therapeutic target for reducing energy harvest in obese humans. To explore this possibility, we have sequenced its 1,853,160-bp genome and compared it to other human gut-associated M. smithii strains and other Archaea. We have also examined M. smithii 's transcriptome and metabolome in gnotobiotic mice that do or do not harbor Bacteroides thetaiotaomicron , a prominent saccharolytic bacterial member of our gut microbiota. Our results indicate that M. smithii is well equipped to persist in the distal intestine through ( i ) production of surface glycans resembling those found in the gut mucosa, ( ii ) regulated expression of adhesin-like proteins, ( iii ) consumption of a variety of fermentation products produced by saccharolytic bacteria, and ( iv ) effective competition for nitrogenous nutrient pools. These findings provide a framework for designing strategies to change the representation and/or properties of M. smithii in the human gut microbiota.
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M. smithii increases the fermentation efficiency of many bacterial taxa in the gut, including those that ferment complex polysaccharides.
“M. smithii increases the fermentation efficiency of many bacterial taxa in the gut, including those that ferment complex polysaccharides [223].”
From The athletic gut microbiota (2020) · cites this paper as [223]
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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-citationDiversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · 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-citationConsed: a graphical tool for sequence finishing.Preprint
Gordon, D., Abajian, C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.195 · Cited by 3,706 · see citing works
STRING: a database of predicted functional associations between proteins
von Mering, C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg034 · Cited by 2,942 · see citing works
An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System
Mazmanian, S. K., Liu, C. H., Tzianabos, A. O., & Kasper, D. L. (2005) · Cell · doi:10.1016/j.cell.2005.05.007 · Cited by 2,910 · 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-citationMedini, D., Donati, C., Tettelin, H., Masignani, V., & Rappuoli, R. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.09.006 · Cited by 1,307 · 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
Self-citationRecent Advances in Carbohydrate Bioengineering
Gilbert, H. J. (1999) · Medical Entomology and Zoology · Cited by 790 · 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
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism
Samuel, B. S., & Gordon, J. I. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602187103 · Cited by 674 · see citing works
Self-citationDiversity of Microbial Sialic Acid Metabolism
Vimr, E. R., Kalivoda, K. A., Deszo, E. L., & Steenbergen, S. M. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.1.132-153.2004 · Cited by 580 · see citing works
Enzymatic analysis; a practical guide
(1993) · General Pharmacology The Vascular System · doi:10.1016/0306-3623(93)90404-l · Cited by 522 · see citing works
Nitrate reduction and the nitrogen cycle in archaea
Cabello, P., Roldán, M. D., & Moreno‐Vivián, C. (2004) · Microbiology · doi:10.1099/mic.0.27303-0 · Cited by 321 · see citing works
Human Symbionts Use a Host-Like Pathway for Surface Fucosylation
Coyne, M. J., Reinap, B., Lee, M. M., & Comstock, L. E. (2005) · Science · doi:10.1126/science.1106469 · Cited by 304 · see citing works
Passonneau, J. V., & Lowry, O. H. (1993) · Humana Press eBooks · doi:10.1007/978-1-60327-407-4 · Cited by 300 · see citing works
Fricke, W. F., Seedorf, H., Henne, A., Krüer, M., Liesegang, H., Hedderich, R., Gottschalk, G., & Thauer, R. K. (2005) · Journal of Bacteriology · doi:10.1128/jb.188.2.642-658.2006 · Cited by 291 · see citing works
PCAP: A Whole-Genome Assembly ProgramPreprint
Huang, X., Wang, J., Aluru, S., Yang, S., & Hillier, L. (2003) · Genome Research · doi:10.1101/gr.1390403 · Cited by 289 · see citing works
Isolation of Methanobrevibacter smithii from human feces
Miller, T. L., Wolin, M. J., de Macario, E. C., & Macario, A. J. L. (1982) · Applied and Environmental Microbiology · doi:10.1128/aem.43.1.227-232.1982 · Cited by 287 · see citing works
Methanogens in human and animal intestinal Tracts
Miller, T. L., & Wolin, M. J. (1986) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(86)80010-8 · Cited by 195 · see citing works
Sonnenburg, E. D., Sonnenburg, J. L., Manchester, J. K., Hansen, E. E., Chiang, H. C., & Gordon, J. I. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603249103 · Cited by 163 · see citing works
Self-citationRuminal Microbial Metabolism of Peptides and Amino Acids
Wallace, R. J. (1996) · Journal of Nutrition · doi:10.1093/jn/126.suppl_4.1326s · Cited by 159 · see citing works
Berk, H., & Thauer, R. K. (1997) · Archives of Microbiology · doi:10.1007/s002030050514 · Cited by 59 · see citing works
The role of glutaminase in the small intestine
McCauley, R., Kong, S., Fuller, K. A., & Hall, J. C. (1999) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/s1357-2725(98)00121-6 · Cited by 37 · see citing works
Targeting Methanopterin Biosynthesis ToInhibitMethanogenesis
Dumitru, R. V., Palencia, H., Schroeder, S. D., DeMontigny, B. A., Takacs, J. M., Rasche, M. E., Miner, J. L., & Ragsdale, S. W. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.12.7236-7241.2003 · Cited by 37 · see citing works
Wolin, M. J., & Miller, T. L. (2006) · International Congress Series · doi:10.1016/j.ics.2006.01.031 · Cited by 36 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
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
Microbiota and SCFA in lean and overweight healthy subjects
Schwiertz, A., Taras, D., Schäfer, K., Beijer, S., Bos, N. A., Donus, C., & Hardt, P. D. (2010) · Obesity · doi:10.1038/oby.2009.167 · Cited by 2,457 · see citing works
Dao, M. C., Everard, A., Aron-Wisnewsky, J., Sokolovska, N., Prifti, E., Verger, E. O., Kayser, B. D., Levenez, F., Chilloux, J., Hoyles, L., et al. (2016) · Gut · doi:10.1136/gutjnl-2014-308778 · Cited by 1,931 · see citing works
Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016) · Genome Medicine · doi:10.1186/s13073-016-0307-y · Cited by 1,891 · see citing works
The 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
Occurrence, Classification, and Biological Function of Hydrogenases: An Overview
Vignais, P. M., & Billoud, B. (2007) · Chemical Reviews · doi:10.1021/cr050196r · Cited by 1,571 · see citing works
Unravelling the effects of the environment and host genotype on the gut microbiome
Spor, A., Koren, O., & Ley, R. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2540 · Cited by 1,509 · see citing works
<i>Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea</i>
Liu, Y., & Whitman, W. B. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1419.019 · Cited by 1,346 · see citing works
Alterations of the human gut microbiome in multiple sclerosis
Jangi, S., Gandhi, R., Cox, L. M., Li, N., von Glehn, F., Yan, R., Patel, B., Mazzola, M. A., Liu, S., Glanz, B. L., et al. (2016) · Nature Communications · doi:10.1038/ncomms12015 · Cited by 1,307 · see citing works
Effects of gut microbes on nutrient absorption and energy regulation
Krajmalnik‐Brown, R., Ilhan, Z., Kang, D., & DiBaise, J. K. (2012) · Nutrition in Clinical Practice · doi:10.1177/0884533611436116 · Cited by 852 · see citing works
Lewis, J. D., Chen, E. Z., Baldassano, R. N., Otley, A. R., Griffiths, A. M., Lee, D., Bittinger, K., Bailey, A., Friedman, E. S., Hoffmann, C., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.09.008 · Cited by 823 · see citing works
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents
Hoffmann, C., Dollive, S., Grunberg, S., Chen, J., Li, H., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066019 · Cited by 808 · see citing works
“smithii and Bacteroides thetaiotaomicron promoted increased growth of both species compared to mono-colonization [28].”
BackgroundInterplay between the human gut microbiome and host metabolism
Visconti, A., Le Roy, C. I., Rosa, F., Rossi, N., Martin, T. C., Mohney, R. P., Li, W., de Rinaldis, E., Bell, J. T., Venter, J. C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12476-z · Cited by 782 · see citing works
Relating the metatranscriptome and metagenome of the human gut
Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J. A., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319284111 · Cited by 713 · see citing works
Current and Past Strategies for Bacterial Culture in Clinical Microbiology
Lagier, J., Edouard, S., Pagnier, I., Mediannikov, O., Drancourt, M., & Raoult, D. (2015) · Clinical Microbiology Reviews · doi:10.1128/cmr.00110-14 · Cited by 657 · see citing works
Small intestinal bacterial overgrowth syndrome
Bures, J. (2010) · World Journal of Gastroenterology · doi:10.3748/wjg.v16.i24.2978 · Cited by 620 · see citing works
Gut Microbiota and Its Possible Relationship With Obesity
DiBaise, J. K., Zhang, H., Crowell, M. D., Krajmalnik‐Brown, R., Decker, G. A., & Rittmann, B. E. (2008) · Mayo Clinic Proceedings · doi:10.4065/83.4.460 · Cited by 598 · see citing works
Dridi, B., Fardeau, M.-L., Ollivier, B., Raoult, D., & Drancourt, M. (2012) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijs.0.033712-0 · Cited by 596 · see citing works
Salonen, A., Nikkilä, J., Jalanka, J., Immonen, O., Rajilić-Stojanović, M. D., Kekkonen, R. A., Palva, A., & de Vos, W. M. (2010) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2010.02.007 · Cited by 592 · see citing works
Cancer and Inflammation: An Old Intuition with Rapidly Evolving New Concepts
Trinchieri, G. (2012) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-075008 · Cited by 506 · 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
Self-citationGut microbiota: a potential new territory for drug targeting
Jia, W. P., Li, H., Zhao, L., & Nicholson, J. K. (2008) · Nature Reviews Drug Discovery · doi:10.1038/nrd2505 · Cited by 471 · see citing works
Archaea and the Human Gut: New Beginning of an Old Story
Gaci, N., Borrel, G., Tottey, W., O’Toole, P. W., & Brugère, J.-F. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i43.16062 · Cited by 422 · see citing works
Dridi, B., Henry, M., Khéchine, A. E., Raoult, D., & Drancourt, M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007063 · Cited by 384 · see citing works
Mohr, A. E., Jäger, R., Carpenter, K. C., Kerksick, C. M., Purpura, M., Townsend, J. R., West, N. P., Black, K., Gleeson, M., Pyne, D. B., et al. (2020) · Journal of the International Society of Sports Nutrition · doi:10.1186/s12970-020-00353-w · Cited by 378 · see citing works
“smithii increases the fermentation efficiency of many bacterial taxa in the gut, including those that ferment complex polysaccharides [223].”
BackgroundCommunity characteristics of the gut microbiomes of competitive cyclists
Petersen, L. M., Bautista, E. J., Nguyen, H., Hanson, B. M., Chen, L., Lek, S. H., Sodergren, E., & Weinstock, G. M. (2017) · Microbiome · doi:10.1186/s40168-017-0320-4 · Cited by 377 · see citing works
Marcobal, A. M., Kashyap, P., Nelson, T. A., Aronov, P. A., Donia, M. S., Spormann, A. M., Fischbach, M. A., & Sonnenburg, J. L. (2013) · The ISME Journal · doi:10.1038/ismej.2013.89 · Cited by 351 · see citing works
Unraveling Microbial Interactions in Food Fermentations: from Classical to Genomics Approaches
Sieuwerts, S., de Bok, F. A. M., Hugenholtz, J., & Vlieg, J. E. T. V. H. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.00113-08 · Cited by 341 · see citing works
Benedict, C., Vogel, H., Jonas, W., Woting, A., Blaut, M., Schürmann, A., & Cedernaes, J. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.10.003 · Cited by 324 · see citing works
Advancing human gut microbiota research by considering gut transit time
Procházková, N., Falony, G., Dragsted, L. O., Licht, T. R., Raes, J., & Roager, H. M. (2022) · Gut · doi:10.1136/gutjnl-2022-328166 · Cited by 322 · see citing works
Leahy, S. C., Kelly, W. J., Altermann, E., Ronimus, R. S., Yeoman, C. J., Pacheco, D. M., Li, D., Kong, Z., McTavish, S. M., Sang, C., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008926 · Cited by 318 · see citing works
Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol
Milani, C., Hevia, A., Foroni, E., Duranti, S., Turroni, F., Lugli, G. A., Sánchez, B., Martín, R., Gueimonde, M., van Sinderen, D., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068739 · Cited by 304 · see citing works
Borrel, G., Parisot, N., Harris, H. M. B., Peyretaillade, É., Gaci, N., Tottey, W., Bardot, O., Raymann, K., Gribaldo, S., Peyret, P., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-679 · Cited by 294 · see citing works
Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD
Matijašić, M., Meštrović, T., Paljetak, H. Č., Perić, M., Barešić, A., & Verbanac, D. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082668 · Cited by 293 · see citing works
Archaea Are Interactive Components of Complex Microbiomes
Moissl‐Eichinger, C., Pausan, M.-R., Taffner, J., Berg, G., Bang, C., & Schmitz, R. A. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.07.004 · Cited by 292 · see citing works
Contributions of the microbial hydrogen economy to colonic homeostasis
Carbonero, F. G., Benefiel, A. C., & Gaskins, H. R. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.85 · Cited by 291 · see citing works
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes
Yassour, M., Lim, M. Y., Yun, H. S., Tickle, T. L., Sung, J., Song, Y., Lee, K., Franzosa, E. A., Morgan, X. C., Gevers, D., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0271-6 · Cited by 286 · see citing works
Gut microbiota in obesity and metabolic disorders
Sanz, Y., Santacruz, A., & Gauffin-Cano, P. (2010) · Proceedings of The Nutrition Society · doi:10.1017/s0029665110001813 · Cited by 281 · see citing works
The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens
Wen, C., Yan, W., Sun, C., Ji, C., Zhou, Q., Zhang, D., Zheng, J., & Yang, N. (2019) · The ISME Journal · doi:10.1038/s41396-019-0367-2 · Cited by 279 · see citing works
Rumen microbial (meta)genomics and its application to ruminant production
Morgavi, D. P., Kelly, W. J., Janssen, P. H., & Attwood, G. T. (2012) · animal · doi:10.1017/s1751731112000419 · Cited by 278 · see citing works
Wampach, L., Heintz‐Buschart, A., Hogan, A. H., Muller, E. E. L., Narayanasamy, S., Laczny, C. C., Hugerth, L. W., Bindl, L., Bottu, J., Andersson, A. F., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00738 · Cited by 266 · see citing works
Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease
Chehoud, C., Albenberg, L. G., Judge-Golden, C. P., Hoffmann, C., Grunberg, S., Bittinger, K. L., Baldassano, R. N., Lewis, J. D., Bushman, F. D., & Wu, G. D. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000454 · Cited by 265 · see citing works
Understanding the interactions between bacteria in the human gut through metabolic modeling
Shoaie, S., Karlsson, F. H., Mardinoğlu, A., Nookaew, I., Bordel, S., & Nielsen, J. (2013) · Scientific Reports · doi:10.1038/srep02532 · Cited by 260 · see citing works
Li, C., Stražar, M., Mohamed, A. M., Ávila-Pacheco, J., Walker, R. L., Lebar, T., Zhao, S., Lockart, J., Dame, A., Thurimella, K., et al. (2024) · Cell · doi:10.1016/j.cell.2024.03.014 · Cited by 260 · see citing works
Borrel, G., Brugère, J., Gribaldo, S., Schmitz, R. A., & Moissl‐Eichinger, C. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0407-y · Cited by 255 · see citing works
Laursen, M. F., Andersen, L. B. B., Michaelsen, K. F., Mølgaard, C., Trolle, E., Bahl, M. I., & Licht, T. R. (2016) · mSphere · doi:10.1128/msphere.00069-15 · Cited by 252 · see citing works
Zhang, X., Zhong, H., Li, Y., Shi, Z., Ren, H., Zhang, Z., Zhou, X., Tang, S., Han, X., Lin, Y., et al. (2021) · Nature Aging · doi:10.1038/s43587-020-00014-2 · Cited by 250 · see citing works
Sweeney, T. E., & Morton, J. M. (2013) · JAMA Surgery · doi:10.1001/jamasurg.2013.5 · Cited by 250 · see citing works
Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?
Bang, C., Dagan, T., Deines, P., Dubilier, N., Duschl, W. J., Fraune, S., Hentschel, U., Heribert Hirt, A., Hülter, N. F., Lachnit, T., et al. (2018) · Zoology · doi:10.1016/j.zool.2018.02.004 · Cited by 250 · see citing works
Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment
Dollive, S., Chen, Y., Grunberg, S., Bittinger, K. L., Hoffmann, C., Vandivier, L. E., Cuff, C. F., Lewis, J. D., Wu, G. D., & Bushman, F. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071806 · Cited by 236 · see citing works
Koskinen, K., Pausan, M.-R., Perras, A., Beck, M., Bang, C., Mora, M., Schilhabel, A., Schmitz, R. A., & Moissl‐Eichinger, C. (2017) · mBio · doi:10.1128/mbio.00824-17 · Cited by 231 · see citing works
Hansen, E. E., Lozupone, C., Rey, F. E., Wu, M., Guruge, J. L., Narra, A., Goodfellow, J., Zaneveld, J., McDonald, D. T., Goodrich, J. A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000071108 · Cited by 226 · see citing works
Self-citationZhang, Y., Chen, R., Zhang, D., Qi, S., & Liu, Y. (2023) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2023.114295 · Cited by 209 · see citing works
Microbiota Signaling Pathways that Influence Neurologic Disease
Cox, L. M., & Weiner, H. L. (2018) · Neurotherapeutics · doi:10.1007/s13311-017-0598-8 · Cited by 208 · see citing works
Scanlan, P. D., Shanahan, F., & Marchesi, J. R. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-79 · Cited by 206 · see citing works
Gut Microbiome and Obesity: A Plausible Explanation for Obesity
Sanmiguel, C. P., Gupta, A., & Mayer, E. A. (2015) · Current Obesity Reports · doi:10.1007/s13679-015-0152-0 · Cited by 203 · see citing works
iPath: interactive exploration of biochemical pathways and networks
Letunić, I., Yamada, T., Kanehisa, M. I., & Peer Bork, B. (2008) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2008.01.001 · Cited by 201 · see citing works
Studying Bacterial Multispecies Biofilms: Where to Start?
Røder, H. L., Sørensen, S. J., & Burmølle, M. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.02.019 · Cited by 198 · see citing works
Shetty, S. A., Marathe, N. P., Lanjekar, V. B., Ranade, D. R., & Shouche, Y. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079353 · Cited by 194 · see citing works
Mechanisms of Microbial Hydrogen Disposal in the Human Colon and Implications for Health and Disease
Nakamura, N., Lin, H. C., McSweeney, C. S., Mackie, R. I., & Gaskins, H. R. (2010) · Annual Review of Food Science and Technology · doi:10.1146/annurev.food.102308.124101 · Cited by 194 · see citing works
New Insights in Anorexia Nervosa
Gorwood, P. A. P. M., Blanchet, C., Chartrel, N., Duclos, J., Déchelotte, P., Hanachi, M., Fetissov, S. O., Godart, N. T., Melchior, J., Ramoz, N., et al. (2016) · Frontiers in Neuroscience · doi:10.3389/fnins.2016.00256 · Cited by 193 · see citing works
Archaea as emerging organisms in complex human microbiomes
Dridi, B., Raoult, D., & Drancourt, M. (2011) · Anaerobe · doi:10.1016/j.anaerobe.2011.03.001 · Cited by 190 · see citing works
Freeland, K. R., Wilson, C., & Wolever, T. M. S. (2009) · British Journal Of Nutrition · doi:10.1017/s0007114509991462 · Cited by 187 · see citing works
van Wolferen, M., Orell, A., & Albers, S. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0058-4 · Cited by 187 · see citing works
The Gut Microbiota in Multiple Sclerosis: An Overview of Clinical Trials
Schepici, G., Silvestro, S., Bramanti, P., & Mazzon, E. (2019) · Cell Transplantation · doi:10.1177/0963689719873890 · Cited by 187 · see citing works
Mörkl, S., Lackner, S., Müller, W., Gorkiewicz, G., Kashofer, K., Oberascher, A., Painold, A., Holl, A., Holzer, P., Meinitzer, A., et al. (2017) · International Journal of Eating Disorders · doi:10.1002/eat.22801 · Cited by 181 · see citing works
A road map for the development of community systems (CoSy) biology
Zengler, K., & Palsson, B. Ø. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2763 · Cited by 180 · see citing works
Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon
Nava, G. M., Carbonero, F. G., Croix, J. A., Greenberg, E., & Gaskins, H. R. (2011) · The ISME Journal · doi:10.1038/ismej.2011.90 · Cited by 179 · see citing works
Zhou, M., Hernandez‐Sanabria, E., & Guan, L. L. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00010-10 · Cited by 179 · see citing works
From one amino acid to another: tRNA-dependent amino acid biosynthesis
Sheppard, K., Yuan, J., Hohn, M. J., Jester, B. C., Devine, K. M., & Söll, D. G. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn015 · Cited by 177 · see citing works
How to Make a Living by Exhaling Methane
Ferry, J. G. (2010) · Annual Review of Microbiology · doi:10.1146/annurev.micro.112408.134051 · Cited by 177 · see citing works
Bang, C., Weidenbach, K., Gutsmann, T., Heine, H., & Schmitz, R. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099411 · Cited by 174 · see citing works
Meta‐analysis of the human gut microbiome from urbanized and pre‐agricultural populations
Mancabelli, L., Milani, C., Lugli, G. A., Turroni, F., Ferrario, C., van Sinderen, D., & Ventura, M. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13692 · Cited by 172 · see citing works
Hydrogen cross-feeders of the human gastrointestinal tract
Smith, N. W., Shorten, P. R., Altermann, E., Roy, N. C., & McNabb, W. C. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1546522 · Cited by 165 · see citing works
Cross-Domain and Viral Interactions in the Microbiome
Rowan-Nash, A. D., Korry, B. J., Mylonakis, E. E., & Belenky, P. A. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00044-18 · Cited by 164 · see citing works
van den Bogert, B., Meijerink, M., Zoetendal, E. G., Wells, J. M., & Kleerebezem, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114277 · Cited by 159 · see citing works
Increased Prevalence of Methanosphaera stadtmanae in Inflammatory Bowel Diseases
Lecours, P. B., Marsolais, D., Cormier, Y. F., Berberi, M., Haché, C., Bourdages, R., & Duchaine, C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087734 · Cited by 154 · see citing works
Microbiota revolution: How gut microbes regulate our lives
Colella, M., Charitos, I. A., Ballini, A., Cafiero, C., Topi, S., Palmirotta, R., & Santacroce, L. (2023) · World Journal of Gastroenterology · doi:10.3748/wjg.v29.i28.4368 · Cited by 153 · see citing works
Linking microbiota to human diseases: a systems biology perspective
Wu, H., Tremaroli, V., & Bäckhed, F. (2015) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2015.09.011 · Cited by 150 · see citing works
Repertoire of Human Breast and Milk Microbiota: A Systematic Review
Togo, A. H., Dufour, J.-C., Lagier, J., Dubourg, G., Raoult, D., & Million, M. (2019) · Future Microbiology · doi:10.2217/fmb-2018-0317 · Cited by 148 · see citing works
The Microbiota of the Human Mammary Ecosystem
Fernández, L., Pannaraj, P. S., Rautava, S., & Rodríguez, J. M. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.586667 · Cited by 143 · see citing works
Methanogenic archaea in health and disease: A novel paradigm of microbial pathogenesis
CONWAYDEMACARIO, E., & Macario, A. J. L. (2008) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2008.06.011 · Cited by 142 · see citing works
Archaea associated with human surfaces: not to be underestimated
Bang, C., & Schmitz, R. A. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv010 · Cited by 139 · see citing works
Lewis, A. L., Desa, N., Hansen, E. E., Knirel, Y. A., Gordon, J. I., Gagneux, P., Nizet, V., & Varki, A. P. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902431106 · Cited by 138 · see citing works
Self-citationArchaea in and on the Human Body: Health Implications and Future Directions
Lurie-Weinberger, M. N., & Gophna, U. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1004833 · Cited by 136 · see citing works
Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome
Borrel, G., McCann, A., Deane, J., Neto, M. C., Lynch, D. B., Brugère, J., & O’Toole, P. W. (2017) · The ISME Journal · doi:10.1038/ismej.2017.72 · Cited by 133 · see citing works
Dridi, B., Fardeau, M., Ollivier, B., Raoult, D., & Drancourt, M. (2011) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkr251 · Cited by 132 · see citing works
The gut microbiome of Mexican children affected by obesity
Maya, O., Murugesan, S., Nirmalkar, K., Alcaraz, L. D., Hoyo‐Vadillo, C., Pizano-Zárate, M. L., & Garcı́a-Mena, J. (2018) · Anaerobe · doi:10.1016/j.anaerobe.2018.10.009 · Cited by 130 · see citing works
Bhute, S. S., Suryavanshi, M. V., Joshi, S. M., Yajnik, C. S., Shouche, Y. S., & Ghaskadbi, S. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00214 · Cited by 129 · see citing works
Methanogens in humans: potentially beneficial or harmful for health
Chaudhary, P. P., Conway, P. L., & Schlundt, J. (2018) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-018-8871-2 · Cited by 129 · see citing works
Harmsen, H. J. M., & de Goffau, M. C. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-31248-4_7 · Cited by 128 · see citing works
Scanlan, P. D., Shanahan, F., & Marchesi, J. R. (2009) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2009.00709.x · Cited by 124 · see citing works
Intestinal methane production in obese individuals is associated with a higher body mass index.
Basseri, R. J., Basseri, B., Pimentel, M., Chong, K., Youdim, A., Low, K., Hwang, L. J., Soffer, E., Chang, C. C.-C., & Mathur, R. (2012) · PubMed Central · Cited by 123 · see citing works
A metagenome-wide association study of gut microbiota in asthma in UK adults
Wang, Q., Li, F., Liang, B., Liang, Y., Chen, S., Mo, X., Ju, Y., Zhao, H., Jia, H., Spector, T. D., et al. (2018) · BMC Microbiology · doi:10.1186/s12866-018-1257-x · Cited by 121 · see citing works
Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology
Khelaifia, S., & Drancourt, M. (2012) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2012.03913.x · Cited by 114 · see citing works
Suryavanshi, M. V., Bhute, S. S., Jadhav, S. D., Bhatia, M. S., Gune, R. P., & Shouche, Y. S. (2016) · Scientific Reports · doi:10.1038/srep34712 · Cited by 113 · see citing works
Hou, Q., Kwok, L., Zheng, Y., Wang, L., Guo, Z., Zhang, J., Huang, W., Wang, Y., Leng, L., Li, H., et al. (2016) · Scientific Reports · doi:10.1038/srep37376 · Cited by 113 · see citing works
Zhou, M., Chung, Y.-H., Beauchemin, K. A., Holtshausen, L., Oba, M., McAllister, T. A., & Guan, L. (2011) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2011.05126.x · Cited by 111 · see citing works
Lifestyle of Lactobacillus plantarum in the mouse caecum
Marco, M. L., Peters, T. H. F., Bongers, R. S., Douwe Molenaar, B., van Hemert, S., Sonnenburg, J. L., Gordon, J. I., & Kleerebezem, M. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02001.x · Cited by 109 · see citing works
Self-citationHost-bacterial coevolution and the search for new drug targets
Zaneveld, J., Turnbaugh, P. J., Lozupone, C., Ley, R. E., Hamady, M., Gordon, J. I., & Knight, R. D. (2008) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2008.01.015 · Cited by 109 · see citing works
Self-citation
- Authors
- Samuel, B. S., Hansen, E. E., Manchester, J. K., Coutinho, P. M., Henrissat, B., Fulton, R., Latreille, P., Kim, K., Wilson, R. K., & Gordon, J. I.
- Affiliations
- Washington University in St. Louis (US)
- *Center for Genome Sciences and
- Centre National de la Recherche Scientifique (FR)
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO 63108; and
- Corresponding author
- Gordon, Jeffrey I.
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2007-06-19
- Volume
- 104
- Issue
- 25
- Pages
- 10643-10648
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1890564
- OpenAlex
- W1982652385
- Semantic Scholar
- 463dd629f64fdb3ab488cc731164b4cb0794bf78
- Cited by
- 549
- References
- 27
- Citations by year
- 2026: 28 · 2025: 27 · 2024: 36 · 2023: 38 · 2022: 37 · 2021: 30 · 2020: 37 · 2019: 25 · 2018: 29 · 2017: 28 · 2016: 28 · 2015: 32 · 2014: 27 · 2013: 31 · 2012: 27
- FWCI
- 8.51
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0202737)
- W. M. Keck Foundation
- San Diego State University
- National Institutes of Health
- University of California, San Diego
- National Institute of Diabetes and Digestive and Kidney Diseases (R37DK030292, DK-30292, DK 70977, R01DK070977, R01DK030292)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- Methanobrevibacter smithii, human gut microbiome, methanogenic archaea, polysaccharide degradation, obesity, adiposity, energy harvesting, gnotobiotic mice, Bacteroides thetaiotaomicron, archaeal genomes, transcriptome, metabolome, nitrogen competition, hydrogen consumption, intestinal colonization
- MeSH terms
- Adaptation, Physiological, Animals, Bacteroides, Fermentation, Germ-Free Life, Humans, Intestines, Male, Models, Biological, Molecular Sequence Data, Genome, Bacterial, Genomics, Methanobrevibacter, Mice
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