The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
Open accessAbstract
Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.
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Cites
A Global Measure of Perceived Stress
Cohen, S., Kamarck, T., & Mermelstein, R. (1983) · Journal of Health and Social Behavior · doi:10.2307/2136404 · Cited by 32,807 · see citing works
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,770 · see citing works
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
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
A 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
A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762 · 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
Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis
Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., et al. (2013) · Nature Medicine · doi:10.1038/nm.3145 · Cited by 4,386 · see citing works
Unravelling the pathogenesis of inflammatory bowel disease
Xavier, R. J., & Podolsky, D. K. (2007) · Nature · doi:10.1038/nature06005 · Cited by 4,364 · see citing works
The Treatment-Naive Microbiome in New-Onset Crohn’s Disease
Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220 · see citing works
Loftus, E. V. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.01.063 · Cited by 3,115 · see citing works
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058 · see citing works
Ford Alexander, C., Paul, M., Hanauer Steven, B., 谭蓓, & Dong, W. Z. (2001) · Cited by 3,021 · see citing works
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., Reyes, J. A., Shah, S. A., LeLeiko, N., Snapper, S. B., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-9-r79 · Cited by 2,713 · 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
A framework for human microbiome research
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11209 · Cited by 2,650 · see citing works
Genetics and pathogenesis of inflammatory bowel disease
Khor, B., Gardet, A., & Xavier, R. J. (2011) · Nature · doi:10.1038/nature10209 · Cited by 2,629 · see citing works
Intrauterine infection and preterm delivery
Goldenberg, R. L., Hauth, J. C., & Andrews, W. W. (2000) · New England Journal of Medicine · doi:10.1056/nejm200005183422007 · Cited by 2,548 · 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
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
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277 · see citing works
Baumgart, D. C., & Sandborn, W. J. (2012) · The Lancet · doi:10.1016/s0140-6736(12)60026-9 · Cited by 2,205 · see citing works
Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy
Koren, O., Goodrich, J. K., Cullender, T. C., Spor, A., Laitinen, K., Kling Bäckhed, H., Gonzalez, A., Werner, J. J., Angenent, L. T., Knight, R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.008 · Cited by 2,165 · see citing works
Ordás, Í., Eckmann, L., Talamini, M. A., Baumgart, D. C., & Sandborn, W. J. (2012) · The Lancet · doi:10.1016/s0140-6736(12)60150-0 · Cited by 2,095 · see citing works
Inflammation as a link between obesity, metabolic syndrome and type 2 diabetes
Esser, N., Legrand-Poels, S., Piette, J., Scheen, A. J., & Paquot, N. (2014) · Diabetes Research and Clinical Practice · doi:10.1016/j.diabres.2014.04.006 · Cited by 1,981 · see citing works
Correlation of mRNA and protein in complex biological samples
Maier, T., Güell, M., & Serrano, L. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.036 · Cited by 1,802 · see citing works
Reciprocal interactions of the intestinal microbiota and immune system
Maynard, C. L., Elson, C. O., Hatton, R. D., & Weaver, C. T. (2012) · Nature · doi:10.1038/nature11551 · Cited by 1,598 · cited 2× · see citing works
“…and the intestinal epithelium, host cells isolated from primary biopsy samples will be cultured and perturbed in vitro (Gallo and Hooper, 2012; Maynard et al., 2012; Stappenbeck et al., 1998) to determine the relative contribution of metabolites and host epithelial cells in this…”
BackgroundEconomic costs of diabetes in the U.S. in 2007
American Diabetes Association (2008) · Diabetes Care · doi:10.2337/dc08-9017 · Cited by 1,323 · see citing works
Ott, S. J., Musfeldt, M., Wenderoth, D. F., Hampe, J., Brant, O., Fölsch, U. R., Timmis, K. N., & Schreiber, S. (2004) · Gut · doi:10.1136/gut.2003.025403 · Cited by 1,311 · see citing works
Personal omics profiling reveals dynamic molecular and medical phenotypes
Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y. K., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.009 · Cited by 1,291 · see citing works
Low counts of Faecalibacterium prausnitzii in colitis microbiota
Sokol, H., Seksik, P., Furet, J. P., Firmesse, O., Nion-Larmurier, I., Beaugerie, L., Cosnes, J., Corthier, G., Marteau, P., & Doré, J. (2009) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20903 · Cited by 1,275 · see citing works
Danese, S., & Fiocchi, C. (2011) · New England Journal of Medicine · doi:10.1056/nejmra1102942 · Cited by 1,113 · see citing works
Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives
Joossens, M., Huys, G., Cnockaert, M., De Preter, V., Verbeke, K., Rutgeerts, P., Vandamme, P., & Vermeire, S. (2011) · Gut · doi:10.1136/gut.2010.223263 · Cited by 1,063 · see citing works
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Abubucker, S., Segata, N., Goll, J. B., Schubert, A. M., Izard, J., Cantarel, B. L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002358 · Cited by 1,050 · see citing works
Willing, B. P., Dicksved, J., Halfvarson, J., Andersson, A. F., Lucio, M., Zheng, Z., Järnerot, G., Tysk, C., Jansson, J. K., & Engstrand, L. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.08.049 · Cited by 1,032 · see citing works
Epithelial antimicrobial defence of the skin and intestine
Gallo, R. L., & Hooper, L. V. (2012) · Nature reviews. Immunology · doi:10.1038/nri3228 · Cited by 959 · 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
Romero, R., Hassan, S. S., Gajer, P., Tarca, A. L., Fadrosh, D. W., Nikita, L., Galuppi, M., Lamont, R. F., Chaemsaithong, P., Miranda, J., et al. (2014) · Microbiome · doi:10.1186/2049-2618-2-4 · Cited by 852 · see citing works
Xenobiotics shape the physiology and gene expression of the active human gut microbiome
Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J. (2013) · Cell · doi:10.1016/j.cell.2012.10.052 · Cited by 811 · see citing works
Economic Costs of Diabetes in the U.S. in 2007
Leahy, J. L. (2008) · Yearbook of Endocrinology · doi:10.1016/s0084-3741(08)79219-9 · Cited by 781 · see citing works
A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy
Aagaard, K. M., Riehle, K. P., Ma, J., Segata, N., Mistretta, T., Coarfa, C., Raza, S., Rosenbaum, S., den Veyver, I. B. V., Milosavljevic, A., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036466 · Cited by 714 · 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
Haiser, H. J., Gootenberg, D. B., Chatman, K., Sirasani, G., Balskus, E. P., & Turnbaugh, P. J. (2013) · Science · doi:10.1126/science.1235872 · Cited by 704 · see citing works
RELIABILITY AND VALIDITY OF THE INTERNATIONAL PHYSICAL ACTIVITY QUESTIONNAIRE (IPAQ)
Hallal, P. C., & Victora, C. G. (2004) · Medicine & Science in Sports & Exercise · doi:10.1249/01.mss.0000117161.66394.07 · Cited by 562 · 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
The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
Gevers, D., Knight, R., Petrosino, J. F., Huang, K., McGuire, A. L., Birren, B. W., Nelson, K. E., White, O., Methé, B. A., & Huttenhower, C. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001377 · Cited by 493 · see citing works
Molecular analysis of the gut microbiota of identical twins with Crohn's disease
Dicksved, J., Halfvarson, J., Rosenquist, M., Järnerot, G., Tysk, C., Apajalahti, J., Engstrand, L. G., & Jansson, J. K. (2008) · The ISME Journal · doi:10.1038/ismej.2008.37 · Cited by 459 · see citing works
Willing, B., Halfvarson, J., Dicksved, J., Rosenquist, M., Järnerot, G., Engstrand, L., Tysk, C., & Jansson, J. K. (2009) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20783 · Cited by 455 · see citing works
Romero, R. J., Hassan, S. S., Gajer, P., Tarca, A. L., Fadrosh, D. W., Bieda, J., Chaemsaithong, P., Miranda, J., Chaiworapongsa, T., & Ravel, J. (2014) · Microbiome · doi:10.1186/2049-2618-2-18 · Cited by 403 · see citing works
Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
Erickson, A. R., Cantarel, B. L., Lamendella, R., Darzi, Y., Mongodin, E. F., Pan, C., Shah, M., Halfvarson, J., Tysk, C., Henrissat, B., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049138 · Cited by 395 · see citing works
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
Packey, C. D., & Sartor, R. B. (2009) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0b013e32832a8a5d · Cited by 319 · see citing works
McHardy, I. H., Goudarzi, M., Tong, M., Ruegger, P. M., Schwager, E., Weger, J. R., Graeber, T. G., Sonnenburg, J. L., Horvath, S., Huttenhower, C., et al. (2013) · Microbiome · doi:10.1186/2049-2618-1-17 · Cited by 316 · see citing works
Walters, T. D., Kim, M., Denson, L. A., Griffiths, A. M., Dubinsky, M. C., Markowitz, J. F., Baldassano, R. N., Crandall, W., Rosh, J. R., Pfefferkorn, M. D., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.10.027 · Cited by 275 · see citing works
Hudson, M. E., Pozdnyakova, I., Haines, K., Mor, G., & Snyder, M. P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708572104 · Cited by 260 · see citing works
Analysis of bacterial bowel communities of IBD patients: What has it revealed?
Sokol, H., Lay, C., Seksik, P., & Tannock, G. W. (2008) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20392 · Cited by 220 · see citing works
Sequence Analysis of the Human Virome in Febrile and Afebrile Children
Wylie, K. M., Mihindukulasuriya, K. A., Sodergren, E., Weinstock, G. M., & Storch, G. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0027735 · Cited by 193 · see citing works
Species-level classification of the vaginal microbiome
Fettweis, J. M., Serrano, M. G., Sheth, N. U., Mayer, C. M., Glascock, A. L., Brooks, J. P., Jefferson, K. K., & Buck, G. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s8-s17 · Cited by 187 · see citing works
Tong, M., Li, X., Parfrey, L. W., Roth, B. E., Ippoliti, A., Wei, B., Borneman, J., McGovern, D. P. B., Frank, D. N., Li, E., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080702 · Cited by 176 · see citing works
Gene-environment interactions in chronic inflammatory disease
Renz, H., von Mutius, E., Brandtzæg, P., Cookson, W., Autenrieth, I. B., & Haller, D. (2011) · Nature Immunology · doi:10.1038/ni0411-273 · Cited by 169 · see citing works
The immune system's involvement in obesity-driven type 2 diabetes
Shu, C. J., Benoist, C. O., & Mathis, D. J. (2012) · Seminars in Immunology · doi:10.1016/j.smim.2012.12.001 · Cited by 165 · see citing works
Notes from some crypt watchers: regulation of renewal in the mouse intestinal epithelium
Stappenbeck, T. S., Wong, M. H., Saam, J. R., Mysorekar, I. U., & Gordon, J. I. (1998) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(98)80110-5 · Cited by 160 · see citing works
Genomic sequence analysis and characterization of Sneathia amnii sp. nov
Harwich, M. D., Serrano, M. G., Fettweis, J. M., Alves, J. M. P., Reimers, M. A., Buck, G. A., & Jefferson, K. K. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s8-s4 · Cited by 150 · see citing works
Emerging View of the Human Virome
Wylie, K., Weinstock, G., & Storch, G. (2012) · Translational Research: The Journal of Laboratory and Clinical Medicine · doi:10.1016/j.trsl.2012.03.006 · Cited by 145 · see citing works
An Update on The Diabetes Prevention Program
Ratner, R. E. (2006) · Endocrine Practice · doi:10.4158/ep.12.s1.20 · Cited by 141 · see citing works
Metabolomics in diabetes research
Friedrich, N. (2012) · Journal of Endocrinology · doi:10.1530/joe-12-0120 · Cited by 132 · see citing works
Romero, R. J., Hassan, S. S., Gajer, P., Tarca, A. L., Fadrosh, D. W., Nikita, L., Galuppi, M., Lamont, R., Chaemsaithong, P., Miranda, J., et al. (2014) · Microbiome · doi:10.1186/2049-2618-2-10 · Cited by 120 · see citing works
Detecting and annotating genetic variations using the HugeSeq pipeline
Lam, H. Y. K., Pan, C., Clark, M. J., Lacroute, P., Chen, R., Haraksingh, R., O’Huallachain, M., Gerstein, M., Kidd, J. M., Bustamante, C. D., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2134 · Cited by 114 · see citing works
Molodecky, N. A., Panaccione, R., Ghosh, S., Barkema, H. W., & Kaplan, G. G. (2011) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21511 · Cited by 109 · see citing works
Wijesinghe, D. S., Allegood, J. C., Gentile, L. B., Fox, T. E., KESTER, M. A., & Chalfant, C. E. (2009) · Journal of Lipid Research · doi:10.1194/jlr.d000430 · Cited by 97 · see citing works
Ananthakrishnan, A. N., Huang, H., Nguyen, D. D., Sauk, J. S., Yajnik, V., & Xavier, R. J. (2014) · The American Journal of Gastroenterology · doi:10.1038/ajg.2013.464 · Cited by 89 · see citing works
Presley, L. L., Ye, J., Li, X., LeBlanc, J. F., Zhang, Z., Ruegger, P. M., Allard, J., McGovern, D. P. B., Ippoliti, A., Roth, B. E., et al. (2011) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21793 · Cited by 85 · see citing works
de Weerth, C., Fuentes, S., & de Vos, W. M. (2013) · Gut Microbes · doi:10.4161/gmic.26041 · Cited by 82 · see citing works
The Microbiome and Development: A Mother's Perspective
Prince, A., Antony, K. M., Ma, J., & Aagaard, K. M. (2014) · Seminars in Reproductive Medicine · doi:10.1055/s-0033-1361818 · Cited by 74 · see citing works
Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments
Cantarel, B. L., Erickson, A. R., VerBerkmoes, N. C., Erickson, B. K., Carey, P. A., Pan, C., Shah, M. B., Mongodin, E. F., Jansson, J. K., Fraser, C. M., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027173 · Cited by 63 · see citing works
Martin, J. C., Sykes, S. M., Young, S., Kota, K., Sanka, R., Sheth, N. U., Orvis, J., Sodergren, E. J., Wang, Z., Weinstock, G. M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036427 · Cited by 50 · see citing works
An Overview of Valuable Scientific Models for Diabetes Mellitus
Akash, M. S. H., Rehman, K., & Chen, S. (2013) · Current Diabetes Reviews · doi:10.2174/15733998113099990062 · Cited by 50 · see citing works
Alves, J. M. P., & Buck, G. A. (2007) · Chemistry & Biodiversity · doi:10.1002/cbdv.200790212 · Cited by 31 · see citing works
Meyer, F., Trimble, W. L., Chang, E. B., & Handley, K. M. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-169 · Cited by 17 · see citing works
Meyer, F., Trimble, W. L., Chang, E. B., et al. (2012) · Genome biology · doi:10.1186/gb4042 · Cited by 13 · see citing works
Wijesinghe, D. S., Mayton, E. K., Mietla, J. A., Mukherjee, A., Wu, J., Fang, X., & Chalfant, C. E. (2011) · Analytical Methods · doi:10.1039/c1ay05459g · Cited by 12 · see citing works
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- Behrman RE Butler AS 2007 Preterm Birth: Causes Washington DC Consequences, and Prevention 20669423
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Current understanding of the human microbiome
Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018) · Nature Medicine · doi:10.1038/nm.4517 · Cited by 2,609 · see citing works
Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis
Chong, J., Wishart, D. S., & Xia, J. (2019) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.86 · Cited by 2,144 · see citing works
Best practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030 · 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
Gut microbiota-derived metabolites as key actors in inflammatory bowel disease
Lavelle, A., & Sokol, H. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0258-z · Cited by 2,015 · see citing works
Species-level functional profiling of metagenomes and metatranscriptomes
Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0176-y · Cited by 1,693 · see citing works
Chong, J., Liu, P., Zhou, G., & Xia, J. (2020) · Nature Protocols · doi:10.1038/s41596-019-0264-1 · Cited by 1,670 · see citing works
The Integrative Human Microbiome Project
The Integrative HMP (iHMP) Research Network Consortium, Proctor, L. M., Creasy, H. H., Fettweis, J. M., Lloyd-Price, J., Mahurkar, A., Zhou, W., Buck, G. A., Snyder, M. P., Strauss, J. F., et al. (2019) · Nature · doi:10.1038/s41586-019-1238-8 · Cited by 1,381 · see citing works
Integrative omics for health and disease
Karczewski, K. J., & Snyder, M. P. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2018.4 · Cited by 1,158 · see citing works
A defined commensal consortium elicits CD8 T cells and anti-cancer immunity
Tanoue, T., Morita, S., Plichta, D. R., Skelly, A. N., Suda, W., Sugiura, Y., Narushima, S., Vlamakis, H., Motoo, I., Sugita, K., et al. (2019) · Nature · doi:10.1038/s41586-019-0878-z · Cited by 1,145 · see citing works
Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0405-7 · Cited by 1,030 · see citing works
The gut microbiota at the intersection of diet and human health
Gentile, C. L., & Weir, T. L. (2018) · Science · doi:10.1126/science.aau5812 · Cited by 1,049 · see citing works
RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Poore, G. D., Kopylova, E., Zhu, Q., Carpenter, C., Fraraccio, S., Wandro, S., Kosciolek, T., Janssen, S., Metcalf, J., Song, S. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2095-1 · Cited by 989 · see citing works
RetractedThe vaginal microbiome and preterm birth
Fettweis, J. M., Serrano, M. G., Brooks, J. P., Edwards, D. J., Girerd, P. H., Parikh, H. I., Huang, B., Arodz, T. J., Edupuganti, L., Glascock, A. L., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0450-2 · Cited by 983 · see citing works
Next-Generation Machine Learning for Biological Networks
Camacho, D. M., Collins, K. M., Powers, R. K., Costello, J. C., & Collins, J. J. (2018) · Cell · doi:10.1016/j.cell.2018.05.015 · Cited by 974 · see citing works
The Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites
Kaiko, G. E., Ryu, H., Koues, O. I., Collins, P. L., Solnica‐Krezel, L., Pearce, E. J., Pearce, E. L., Oltz, E. M., & Stappenbeck, T. S. (2016) · Cell · doi:10.1016/j.cell.2016.05.018 · Cited by 738 · see citing works
Microbiome-wide association studies link dynamic microbial consortia to disease
Gilbert, J. A., Quinn, R. A., Debelius, J. W., Xu, Z. Z., Morton, J. T., Garg, N., Jansson, J. K., Dorrestein, P. C., & Knight, R. D. (2016) · Nature · doi:10.1038/nature18850 · Cited by 714 · see citing works
A microfluidics-based in vitro model of the gastrointestinal human–microbe interface
Shah, P., Fritz, J. V., Glaab, E., Desai, M. S., Greenhalgh, K., Frachet, A., Niegowska, M., Estes, M., Jäger, C., Seguin-Devaux, C., et al. (2016) · Nature Communications · doi:10.1038/ncomms11535 · Cited by 660 · see citing works
Karkman, A., Pärnänen, K., & Larsson, D. G. J. (2019) · Nature Communications · doi:10.1038/s41467-018-07992-3 · Cited by 628 · see citing works
The Microbiome Quality Control Project Consortium, Sinha, R., Abu-Ali, G., Vogtmann, E., Fodor, A. A., Ren, B., Amir, A., Schwager, E., Crabtree, J., Ma, S., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3981 · Cited by 587 · see citing works
Longitudinal multi-omics of host–microbe dynamics in prediabetes
Zhou, W., Sailani, M. R., Contrepois, K., Zhou, Y., Ahadi, S., Leopold, S. R., Zhang, M. J., Rao, V., Avina, M., Mishra, T., et al. (2019) · Nature · doi:10.1038/s41586-019-1236-x · Cited by 583 · see citing works
A Longitudinal Big Data Approach for Precision Health
Schüssler-Fiorenza Rose, S. M., Contrepois, K., Moneghetti, K. J., Zhou, W., Mishra, T., Mataraso, S., Dagan-Rosenfeld, O., Ganz, A. B., Dunn, J., Hornburg, D., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0414-6 · Cited by 494 · see citing works
Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies
Aggarwal, N., Kitano, S., Puah, G. R. Y., Kittelmann, S., Hwang, I. Y., & Chang, M. W. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.2c00431 · Cited by 544 · see citing works
Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis
Aguiar‐Pulido, V., Huang, W., Suárez-Ulloa, V., Cickovski, T., Mathee, K., & Narasimhan, G. (2016) · Evolutionary Bioinformatics · doi:10.4137/ebo.s36436 · Cited by 514 · see citing works
The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems
Willis, J. R., & Gabaldón, T. (2020) · Microorganisms · doi:10.3390/microorganisms8020308 · Cited by 474 · see citing works
Ananthakrishnan, A. N., Luo, C., Yajnik, V., Khalili, H., Garber, J. J., Stevens, B. W., Cleland, T., & Xavier, R. J. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.04.010 · Cited by 451 · see citing works
Multi-Omics Profiling for Health
Babu, M., & Snyder, M. P. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100561 · Cited by 419 · see citing works
Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System
Van Belleghem, J. D., Dąbrowska, K., Vaneechoutte, M., Barr, J. J., & Bollyky, P. L. (2018) · Viruses · doi:10.3390/v11010010 · Cited by 408 · see citing works
The dormant blood microbiome in chronic, inflammatory diseases
Potgieter, M., Bester, J., Kell, D. B., & Pretorius, E. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv013 · Cited by 377 · see citing works
Thomas, S., Izard, J., Walsh, E. K., Batich, K. A., Chongsathidkiet, P., Clarke, G. A., Sela, D. A., Muller, A. J., Mullin, J. M., Albert, K., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-2929 · Cited by 369 · see citing works
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
Wallen, Z. D., Demirkan, A., Twa, G., Cohen, G., Dean, M. N., Standaert, D. G., Sampson, T. R., & Payami, H. (2022) · Nature Communications · doi:10.1038/s41467-022-34667-x · Cited by 346 · see citing works
A practical guide to the oral microbiome and its relation to health and disease
Krishnan, K., Chen, T., & Paster, B. (2017) · Oral Diseases · doi:10.1111/odi.12509 · Cited by 347 · see citing works
A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology
Chen, H., Nwe, P.-K., Yang, Y., Rosen, C. E., Bielecka, A. A., Kuchroo, M. R., Cline, G. W., Kruse, A. C., Ring, A. M., Crawford, J. M., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.036 · Cited by 339 · see citing works
Exploring the emerging role of the microbiome in cancer immunotherapy
Fessler, J. L., Matson, V. Z., & Gajewski, T. F. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0574-4 · Cited by 318 · see citing works
MetaboAnalystR 2.0: From Raw Spectra to Biological Insights
Chong, J., Yamamoto, M., & Xia, J. (2019) · Metabolites · doi:10.3390/metabo9030057 · Cited by 317 · see citing works
Host Genetics and Gut Microbiome: Challenges and Perspectives
Kurilshikov, A., Wijmenga, C., Fu, J., & Zhernakova, A. (2017) · Trends in Immunology · doi:10.1016/j.it.2017.06.003 · Cited by 309 · see citing works
MicrobiotaProcess: A comprehensive R package for deep mining microbiome
Xu, S., Zhan, L., Tang, W., Dai, Z., Zhou, L., Feng, T., Chen, M., Liu, S., Wu, T., Hu, E., et al. (2023) · The Innovation · doi:10.1016/j.xinn.2023.100388 · Cited by 306 · see citing works
Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy
Serrano, M. G., Parikh, H. I., Brooks, J. P., Edwards, D. J., Arodz, T. J., Edupuganti, L., Huang, B., Girerd, P. H., Bokhari, Y. A., Bradley, S. P., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0465-8 · Cited by 300 · see citing works
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences
Mallick, H., Franzosa, E. A., Mclver, L. J., Banerjee, S., Sirota‐Madi, A., Kostic, A. D., Clish, C. B., Vlamakis, H. C., Xavier, R. J., & Huttenhower, C. (2019) · Nature Communications · doi:10.1038/s41467-019-10927-1 · Cited by 279 · see citing works
Drug-microbiota interactions: an emerging priority for precision medicine
Zhao, Q. C., Chen, Y., Huang, W., Zhou, H., & Zhang, W. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01619-w · Cited by 296 · see citing works
Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer
Bultman, S. J. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500902 · Cited by 269 · see citing works
Ma, Z., Zuo, T., Frey, N., & Rangrez, A. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01946-6 · Cited by 297 · see citing works
Ketogenic Diet and Microbiota: Friends or Enemies?
Paoli, A., Mancin, L., Bianco, A., Thomas, E., Mota, J. F., & Piccini, F. (2019) · Genes · doi:10.3390/genes10070534 · Cited by 265 · see citing works
Williamson, I., Arnold, J. W., Samsa, L. A., Gaynor, L. T., DiSalvo, M., Cocchiaro, J. L., Carroll, I. M., Azcárate-Peril, M. A., Rawls, J. F., Allbritton, N. L., et al. (2018) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2018.05.004 · Cited by 248 · see citing works
Resveratrol, Metabolic Syndrome, and Gut Microbiota
Chaplin, A. M. L., Carpéné, C., & Mercader, J. (2018) · Nutrients · doi:10.3390/nu10111651 · Cited by 248 · see citing works
Gut microbiota dysbiosis in a cohort of patients with psoriasis
Hidalgo‐Cantabrana, C., Gómez, J., Delgado, S., Requena‐López, S., Queiro‐Silva, R., Margolles, A., Coto, E., Sánchez, B., & Coto‐Segura, P. (2019) · British Journal of Dermatology · doi:10.1111/bjd.17931 · Cited by 236 · see citing works
Baseline human gut microbiota profile in healthy people and standard reporting template
King, C. H., Desai, H., Sylvetsky, A. C., LoTempio, J. E., Ayanyan, S., Carrie, J., Crandall, K. A., Fochtman, B. C., Gasparyan, L., Gulzar, N., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0206484 · Cited by 230 · see citing works
Vindigni, S. M., Zisman, T. L., Suskind, D. L., & Damman, C. J. (2016) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x16644242 · Cited by 228 · see citing works
Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases
Armstrong, H., Alipour, M., Valcheva, R. S., Bording‐Jorgensen, M., Jovel, J., Zaidi, D., Shah, P., Lou, Y., Ebeling, C., Mason, A. L., et al. (2019) · Microbiome · doi:10.1186/s40168-018-0604-3 · Cited by 228 · see citing works
Dąbrowska, K., & Abedon, S. T. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00012-19 · Cited by 214 · see citing works
Integrative Personal Omics Profiles during Periods of Weight Gain and Loss
Piening, B., Zhou, W., Contrepois, K., Röst, H. L., Gu, G. J., Mishra, T., Hanson, B., Bautista, E. J., Leopold, S. R., Yeh, C. Y., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2017.12.013 · Cited by 210 · see citing works
NIH Human Microbiome Portfolio Analysis Team (2019) · Microbiome · doi:10.1186/s40168-019-0620-y · Cited by 207 · see citing works
Tools for Analysis of the Microbiome
Galloway-Peña, J., & Hanson, B. (2020) · Digestive Diseases and Sciences · doi:10.1007/s10620-020-06091-y · Cited by 206 · see citing works
Effects of Rare Microbiome Taxa Filtering on Statistical Analysis
Cao, Q., Sun, X., Rajesh, K., Chalasani, N., Gelow, K., Katz, B. P., Shah, V. H., Sanyal, A. J., & Smirnova, E. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.607325 · Cited by 202 · see citing works
CAMISIM: simulating metagenomes and microbial communities
Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., Lesker, T. R., Belmann, P., DeMaere, M. Z., Darling, A. E., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0633-6 · Cited by 194 · see citing works
Chong, J., & Xia, J. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0239-3_17 · Cited by 192 · see citing works
Worby, C. J., Schreiber, H. L., Straub, T. J., van Dijk, L. R., Bronson, R. A., Olson, B. S., Pinkner, J. S., Obernuefemann, C. L. P., Muñoz, V. L., Paharik, A. E., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01107-x · Cited by 188 · see citing works
Duran-Pinedo, A. E., & Frias-Lopez, J. (2015) · Microbes and Infection · doi:10.1016/j.micinf.2015.03.014 · Cited by 187 · see citing works
MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities
Cao, K. L., Costello, M., Lakis, V., Bartolo, F., Chua, X., Brazeilles, R., & Rondeau, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0160169 · Cited by 178 · see citing works
Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus
Hidalgo-Cantabrana, C., Goh, Y. J., Pan, M., Sanozky-Dawes, R., & Barrangou, R. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1905421116 · Cited by 186 · see citing works
Undisclosed, unmet and neglected challenges in multi-omics studies
Tarazona, S., Arzalluz-Luque, Á., & Conesa, A. (2021) · Nature Computational Science · doi:10.1038/s43588-021-00086-z · Cited by 177 · see citing works
Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry?
Swanson, H. I. (2015) · Drug Metabolism and Disposition · doi:10.1124/dmd.115.065714 · Cited by 179 · see citing works
Multi-omic approaches for host-microbiome data integration
Chetty, A., & Blekhman, R. (2024) · Gut Microbes · doi:10.1080/19490976.2023.2297860 · Cited by 184 · see citing works
Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities
Jiang, D., Armour, C. R., Hu, C., Meng, M., Tian, C., Sharpton, T. J., & Jiang, Y. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00995 · Cited by 164 · see citing works
Cueva, C., Gil‐Sánchez, I., Ayuda‐Durán, B., González‐Manzano, S., Gonzaléz‐Paramás, A. M., Santos‐Buelga, C., Bartolomé, B., & Moreno-Arribas, M. V. (2017) · Molecules · doi:10.3390/molecules22010099 · Cited by 171 · see citing works
González, N., Prieto, I., del Puerto‐Nevado, L., Portal‐Núñez, S., Ardura, J. A., Cortón, M., Fernández‐Fernández, B., Aguilera, Ó., Gómez‐Guerrero, C., Mas, S., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.14472 · Cited by 169 · see citing works
Metagenomic Approaches for Understanding New Concepts in Microbial Science
Alves, L. D. F., Westmann, C. A., Lovate, G. L., de Siqueira, G. M. V., Borelli, T. C., & Guazzaroni, M. (2018) · International Journal of Genomics · doi:10.1155/2018/2312987 · Cited by 162 · see citing works
Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench
Wu, W., Chen, C., Panyod, S., Chen, R.-A., Wu, M., Sheen, L., & Chang, S. (2018) · Journal of the Formosan Medical Association · doi:10.1016/j.jfma.2018.02.005 · Cited by 162 · see citing works
Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity
Chen, L., Collij, V., Jaeger, M., van den Munckhof, I., Vila, A. V., Kurilshikov, A., Gaćeša, R., Sinha, T., Oosting, M., Joosten, L. A. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17840-y · Cited by 154 · see citing works
The Role of the Gut Microbiota in Lipid and Lipoprotein Metabolism
Yu, Y., Raka, F., & Adeli, K. (2019) · Journal of Clinical Medicine · doi:10.3390/jcm8122227 · Cited by 158 · see citing works
Bioactive compounds for human and planetary health
Kussmann, M., Cunha, D. H. A., & Berciano, S. (2023) · Frontiers in Nutrition · doi:10.3389/fnut.2023.1193848 · Cited by 178 · see citing works
Lu, H., Ren, Z., Li, A., Li, J., Xu, S., Zhang, H., Jiang, J., Yang, J., Luo, Q., Zhou, K., et al. (2019) · Journal of Oral Microbiology · doi:10.1080/20002297.2018.1563409 · Cited by 142 · see citing works
Machine learning for data integration in human gut microbiome
Li, P., Luo, H., Ji, B., & Nielsen, J. (2022) · Microbial Cell Factories · doi:10.1186/s12934-022-01973-4 · Cited by 150 · see citing works
Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome
Das, P., Babaei, P., & Nielsen, J. (2019) · BMC Genomics · doi:10.1186/s12864-019-5591-7 · Cited by 139 · see citing works
Exploring and Understanding the Biochemical Diversity of the Human Microbiota
Koppel, N., & Balskus, E. P. (2016) · Cell chemical biology · doi:10.1016/j.chembiol.2015.12.008 · Cited by 138 · see citing works
‘Multi-omics’ data integration: applications in probiotics studies
Kwoji, I. D., Aiyegoro, O. A., Okpeku, M., & Adeleke, M. A. (2023) · npj Science of Food · doi:10.1038/s41538-023-00199-x · Cited by 135 · see citing works
Ganda, E., Bisinotto, R. S., Lima, S. F., Kronauer, K., Decter, D. H., Oikonomou, G., Schukken, Y. H., & Bicalho, R. C. (2016) · Scientific Reports · doi:10.1038/srep37565 · Cited by 129 · see citing works
Specific Gut Microbiome and Serum Metabolome Changes in Lung Cancer Patients
Zhao, F., An, R., Wang, L., Shan, J., & Wang, X. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.725284 · Cited by 127 · see citing works
Ahmadi, S., Nagpal, R., Wang, S., Gagliano, J., Kitzman, D. W., Soleimanian-Zad, S., Sheikh-Zeinoddin, M., Read, R., & Yadav, H. (2019) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2019.01.011 · Cited by 124 · see citing works
Host and microbiome multi-omics integration: applications and methodologies
Wang, Q., Wang, K., Wu, W., Giannoulatou, E., Ho, J. W. K., & Li, L. (2019) · Biophysical Reviews · doi:10.1007/s12551-018-0491-7 · Cited by 122 · see citing works
Metatranscriptome of the Oral Microbiome in Health and Disease
Solbiati, J., & Frias‐Lopez, J. (2018) · Journal of Dental Research · doi:10.1177/0022034518761644 · Cited by 119 · see citing works
Zhang, X., & Yi, N. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03803-z · Cited by 117 · see citing works
Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity
Gupta, P., Singh, M. P., & Goyal, K. (2020) · Frontiers in Public Health · doi:10.3389/fpubh.2020.00326 · Cited by 119 · see citing works
Computational methods for chromosome-scale haplotype reconstruction
Garg, S. (2021) · Genome Biology · doi:10.1186/s13059-021-02328-9 · Cited by 116 · see citing works
Carlson, J. M., Leonard, A. B., Hyde, E. R., Petrosino, J., & Primm, T. P. (2017) · Infection and Drug Resistance · doi:10.2147/idr.s129055 · Cited by 114 · see citing works
The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future
Andermann, T. M., Peled, J. U., Ho, C. M., Reddy, P. R., Riches, M., Storb, R. F., Teshima, T., van den Brink, M. R. M., Alousi, A. M., Balderman, S., et al. (2018) · Transplantation and Cellular Therapy · doi:10.1016/j.bbmt.2018.02.009 · Cited by 112 · see citing works
Bronchiectasis: Current Concepts in Pathogenesis, Immunology, and Microbiology
Boyton, R. J., & Altmann, D. M. (2016) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-012615-044344 · Cited by 112 · see citing works
Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients
Galloway-Peña, J., Smith, D. P., Sahasrabhojane, P. V., Wadsworth, W. D., Fellman, B. M., Ajami, N. J., Shpall, E. J., Daver, N. G., Guindani, M., Petrosino, J. F., et al. (2017) · Genome Medicine · doi:10.1186/s13073-017-0409-1 · Cited by 112 · see citing works
Role of gut microbiota in aging-related health decline: insights from invertebrate models
Clark, R. I., & Walker, D. W. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2671-1 · Cited by 111 · see citing works
Hoffmann, A. R., Proctor, L. M., Surette, M. G., & Suchodolski, J. S. (2015) · Veterinary Pathology · doi:10.1177/0300985815595517 · Cited by 112 · see citing works
Nutrients Turned into Toxins: Microbiota Modulation of Nutrient Properties in Chronic Kidney Disease
Fernández-Prado, R., Esteras, R., Pérez-Gómez, M., Gracia-Iguacel, C., González-Parra, E., Sanz, A., Ortiz, A., & Sánchez-Niño, M. (2017) · Nutrients · doi:10.3390/nu9050489 · Cited by 89 · see citing works
Immunity, microbiota and kidney disease
Knauf, F., Brewer, J. R., & Flavell, R. A. (2019) · Nature Reviews Nephrology · doi:10.1038/s41581-019-0118-7 · Cited by 111 · see citing works
Schiebenhoefer, H., Bossche, T. V. D., Fuchs, S., Renard, B. Y., Muth, T., & Martens, L. (2019) · Expert Review of Proteomics · doi:10.1080/14789450.2019.1609944 · Cited by 107 · see citing works
Musella, M., Wathsala, R., Tavella, T., Rampelli, S., Barone, M., Palladino, G., Biagi, E., Brigidi, P., Turroni, S., Franzellitti, S., et al. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.137209 · Cited by 109 · see citing works
Parasite microbiome project: Grand challenges
Dheilly, N. M., Martínez, J. M., Rosario, K., Brindley, P. J., Fichorova, R. N., Kaye, J. Z., Kohl, K. D., Knoll, L. J., Lukeš, J., Perkins, S. L., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1008028 · Cited by 104 · see citing works
Intra‐oral single‐site comparisons of periodontal and peri‐implant microbiota in health and disease
Yu, X., Chan, Y., Zhuang, L., Lai, H., Lang, N. P., Leung, W. K., & Watt, R. M. (2019) · Clinical Oral Implants Research · doi:10.1111/clr.13459 · Cited by 103 · see citing works
OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data
Zhou, G., Ewald, J., & Xia, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab394 · Cited by 102 · see citing works
Systems biology of host–microbe metabolomics
Heinken, A., & Thiele, I. (2015) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1301 · Cited by 96 · see citing works
Qiu, C. C., Caricchio, R., & Gallucci, S. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02608 · Cited by 100 · see citing works
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species
Belcour, A., Frioux, C., Aïte, M., Bretaudeau, A., Hildebrand, F., & Siegel, A. (2020) · eLife · doi:10.7554/elife.61968 · Cited by 99 · see citing works
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2014-09
- Volume
- 16
- Issue
- 3
- Pages
- 276-289
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC5109542
- OpenAlex
- W2624135745
- Cited by
- 536
- References
- 80
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- FWCI
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- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Cell Host & Microbe (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute on Aging (U19AG063744)
- National Human Genome Research Institute (U01HG004866)
- National Institute of Allergy and Infectious Diseases (UH3AI083263)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK102556, U54DK102557)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD080784)
- 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
- human microbiome, host-microbiome interactions, microbiome dynamics, preterm birth, inflammatory bowel disease, type 2 diabetes, multi-omics integration, longitudinal cohort, public data repositories
- MeSH terms
- Bacteria, Diabetes Mellitus, Type 2, Health, Humans, Inflammatory Bowel Diseases, Bacterial Physiological Phenomena, Premature Birth, Microbiota
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 ›
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