The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Stability of the human faecal microbiome in a cohort of adult men
Open accessAbstract
Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
In the citing paper
“Study of short-term longitudinal samplings from half the donors found that individuals are more similar to themselves over time compared with others (Costello et al., 2009; Flores et al., 2014; Mehta et al., 2018).”
From Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers (2021) · cites this paper as Mehta et al., 2018
In the citing paper
“Although stability was the norm, the degree of species stability (quantified as 1 − BC distance; Mehta et al., 2018) was variable across the 413 donors (Fig. 6, B and C)”
From Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers (2021) · cites this paper as Mehta et al., 2018
In the citing paper
“It is possible that higher intake of fiber could reduce the carcinogenic effects of F nucleatum by restoring effective immunosurveillance.173”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [173]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
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
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533
Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.024 · Cited by 3,283
Stool form scale as a useful guide to intestinal transit time
Lewis, S. J., & Heaton, K. W. (1997) · Scandinavian Journal of Gastroenterology · doi:10.3109/00365529709011203 · Cited by 3,244
Bacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231
The diversity–stability debate
McCann, K. S. (2000) · Nature · doi:10.1038/35012234 · Cited by 3,220
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 2,812
Cited by
Sorted by citations
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Shaffer, M., Borton, M., McGivern, B. B., Zayed, A. A., Rosa, S. L. L., Solden, L., Liu, P., Narrowe, A. B., Rodríguez-Ramos, J. A., Bolduc, B., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa621 · Cited by 1,163
Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer
Song, M., Chan, A. T., & Sun, J. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.06.048 · Cited by 752
Self-citationThe person-to-person transmission landscape of the gut and oral microbiomes
Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449
Wang, D. D., Nguyen, L. H., Li, Y., Yan, Y., Ma, W., Rinott, E., Ivey, K. L., Shai, I., Willett, W. C., Hu, F. B., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01223-3 · Cited by 386
Self-citationBacterial antagonism in host-associated microbial communities
García-Bayona, L., & Comstock, L. E. (2018) · Science · doi:10.1126/science.aat2456 · Cited by 372
Gut microbiome composition may be an indicator of preclinical Alzheimer’s disease
Ferreiro, A. L., Choi, J., Ryou, J., Newcomer, E. P., Thompson, R., Bollinger, R. M., Hall-Moore, C. M., Ndao, I. M., Sax, L., Benzinger, T. L. S., et al. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.abo2984 · Cited by 384
d’Enfert, C., Kaune, A.-K., Alaban, L. R., Chakraborty, S., Cole, N. L., Delavy, M., Kosmala, D., Marsaux, B., Fróis-Martins, R., Morelli, M., et al. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa060 · Cited by 377
The Long-Term Genetic Stability and Individual Specificity of the Human Gut Microbiome
Chen, L., Wang, D., Garmaeva, S., Kurilshikov, A., Vila, A. V., Gaćeša, R., Sinha, T., Study, L. C., Segal, E., Weersma, R. K., et al. (2020) · Cell · doi:10.1016/j.cell.2021.03.024 · Cited by 344
Yogurt, cultured fermented milk, and health: A systematic review
Savaiano, D. A., & Hutkins, R. W. (2021) · Nutrition Reviews · doi:10.1093/nutrit/nuaa013 · Cited by 339
Elevated rates of horizontal gene transfer in the industrialized human microbiome
Groussin, M., Poyet, M., Sistiaga, A., Kearney, S. M., Moniz, K., Noel, M., Hooker, J., Gibbons, S. M., Ségurel, L., Froment, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.052 · Cited by 342
Self-citationUnderstanding the impact of antibiotic perturbation on the human microbiome
Schwartz, D. J., Langdon, A. E., & Dantas, G. A. (2020) · Genome Medicine · doi:10.1186/s13073-020-00782-x · Cited by 348
Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms
Sun, J. G., Liao, X., D’Souza, A. W., Boolchandani, M., Li, S., Cheng, K., Martínez, J. L., Li, L., Feng, Y.-J., Fang, L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15222-y · Cited by 287
Metatranscriptome of human faecal microbial communities in a cohort of adult men
Abu-Ali, G., Mehta, R. S., Lloyd‐Price, J., Mallick, H., Branck, T. A., Ivey, K. L., Drew, D. A., DuLong, C. R., Rimm, E. B., Izard, J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0084-4 · Cited by 238
Self-citationAge-dependent changes in GI physiology and microbiota: time to reconsider?
An, R., Wilms, E., Masclee, A. A. M., Smidt, H., Zoetendal, E. G., & Jonkers, D. (2018) · Gut · doi:10.1136/gutjnl-2017-315542 · Cited by 209
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 234
Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention
Dogra, S. K., Dore, J. M., & Damak, S. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.572921 · Cited by 212
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden
Olsson, L. M., Boulund, F., Nilsson, S., Khan, M. T., Gummesson, A., Fagerberg, L., Engstrand, L. G., Perkins, R., Uhlén, M., Bergström, G. M. L., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.002 · Cited by 200
Sharpton, S. R., Schnabl, B., Knight, R., & Loomba, R. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2020.11.010 · Cited by 194
Nguyen, L. H., Ma, W., Wang, D. D., Cao, Y., Mallick, H., Gerbaba, T. K., Lloyd‐Price, J., Abu-Ali, G., Hall, A. B., Sikavi, D. R., et al. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.12.029 · Cited by 186
Self-citationDietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men
Ma, W., Nguyen, L. H., Song, M., Wang, D. D., Franzosa, E. A., Cao, Y., Joshi, A. D., Drew, D. A., Mehta, R. S., Ivey, K. L., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00921-y · Cited by 189
Self-citationGarcía-Bayona, L., & Comstock, L. E. (2019) · mBio · doi:10.1128/mbio.01762-19 · Cited by 181
Examining the healthy human microbiome concept
Joos, R., Boucher, K., Lavelle, A., Arumugam, M., Blaser, M. J., Claesson, M. J., Clarke, G. A., Cotter, P. D., Sordi, L. D., Domínguez-Bello, M. G., et al. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-024-01107-0 · Cited by 193
Zhou, X., Shen, X., Johnson, J. S., Spakowicz, D. J., Agnello, M., Zhou, W., Avina, M., Honkala, A. T., Chleilat, F., Chen, S. J., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.02.012 · Cited by 181
Role of gut microbiota in intestinal wound healing and barrier function
Alam, A., & Neish, A. (2018) · Tissue Barriers · doi:10.1080/21688370.2018.1539595 · Cited by 166
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 158
Unravelling the antimicrobial action of antidepressants on gut commensal microbes
Chait, Y. A., Mottawea, W., Tompkins, T. A., & Hammami, R. (2020) · Scientific Reports · doi:10.1038/s41598-020-74934-9 · Cited by 158
The Epigenetic Connection Between the Gut Microbiome in Obesity and Diabetes
Sharma, M., Li, Y., Stoll, M. L., & Tollefsbol, T. O. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2019.01329 · Cited by 156
Li, J., Li, Y., Ivey, K. L., Wang, D. D., Wilkinson, J. E., Franke, A., Lee, K. H., Chan, A., Huttenhower, C., Hu, F. B., et al. (2022) · Gut · doi:10.1136/gutjnl-2020-322473 · Cited by 137
Self-citationCross-species RNA-seq for deciphering host–microbe interactions
Westermann, A. J., & Vogel, J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00326-y · Cited by 143
Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults
Martinson, J. N. V., Pinkham, N. V., Peters, G. W., Cho, H., Heng, J., Rauch, M., Broadaway, S. C., & Walk, S. T. (2019) · The ISME Journal · doi:10.1038/s41396-019-0435-7 · Cited by 130
Enterosignatures define common bacterial guilds in the human gut microbiome
Frioux, C., Ansorge, R., Özkurt, E., Nedjad, C. G., Fritscher, J., Quince, C., Waszak, S. M., & Hildebrand, F. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.05.024 · Cited by 137
Dispersal strategies shape persistence and evolution of human gut bacteria
Hildebrand, F., Gossmann, T. I., Frioux, C., Özkurt, E., Myers, P. N., Ferretti, P., Kuhn, M., Bahram, M., Nielsen, H. B., & Bork, P. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.05.008 · Cited by 130
Basciani, S., Camajani, E., Contini, S., Persichetti, A., Risi, R., Bertoldi, L., Strigari, L., Prossomariti, G., Watanabe, M., Mariani, S., et al. (2020) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgaa336 · Cited by 132
Nishijima, S., Stankevič, E., Aasmets, O., Schmidt, T., Nagata, N., Keller, M. I., Ferretti, P., Juel, H. B., Fullam, A., Robbani, S. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.022 · Cited by 140
Mei, Z., Wang, F., Bhosle, A., Dong, D., Mehta, R. S., Ghazi, A. R., Zhang, Y., Liu, Y., Rinott, E., Ma, S., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03067-7 · Cited by 130
Self-citationTowards a mechanistic understanding of reciprocal drug–microbiome interactions
Zimmermann, M., Patil, K. R., Typas, A., & Maier, L. (2021) · Molecular Systems Biology · doi:10.15252/msb.202010116 · Cited by 124
Shkoporov, A. N., Khokhlova, E. V., Stephens, N., Hueston, C. M., Seymour, S., Hryckowian, A. J., Scholz, D., Ross, R. P., & Hill, C. (2021) · BMC Biology · doi:10.1186/s12915-021-01084-3 · Cited by 115
Moreno‐Indias, I., Lahti, L., Nedyalkova, M., Elbere, I., Roshchupkin, G. V., Adilović, M., Aydemir, Ö., Bakır-Güngör, B., Pau, E. C. D. S., D’Elia, D., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.635781 · Cited by 115
O’Donnell, S. T., Ross, R. P., & Stanton, C. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.03084 · Cited by 118
Association of the gut microbiota with cognitive function in midlife
Meyer, K., Lulla, A., Debroy, K., Shikany, J. M., Yaffe, K., Meirelles, O., & Launer, L. J. (2022) · JAMA Network Open · doi:10.1001/jamanetworkopen.2021.43941 · Cited by 110
Role of Microbiota-Derived Metabolites in Alcoholic and Non-Alcoholic Fatty Liver Diseases
Park, J. W., Kim, S. E., Lee, N. Y., Kim, J. H., Jung, J.-H., Jang, M.-K., Park, S.-H., Lee, M.-S., Kim, D.-J., Kim, H.-S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010426 · Cited by 110
Understanding human health through metatranscriptomics
Ojala, T., Kankuri, E. M., & Kankainen, M. (2023) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2023.02.002 · Cited by 113
Functional and evolutionary significance of unknown genes from uncultivated taxa
del Río, Á. R., Giner‐Lamia, J., Cantalapiedra, C. P., Botas, J., Deng, Z., Hernández-Plaza, A., Palmer, M. M., Santamaría‐Hernando, S., Rodríguez‐Herva, J. J., Ruscheweyh, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06955-z · Cited by 110
Pathogenic functions of host microbiota
Rath, S., Rud, T., Karch, A., Pieper, D. H., & Vital, M. (2018) · Microbiome · doi:10.1186/s40168-018-0542-0 · Cited by 98
Maskarinec, G., Hullar, M. A. J., Monroe, K. R., Shepherd, J., Hunt, J., Randolph, T. W., Wilkens, L. R., Boushey, C. J., Marchand, L. L., Lim, U., et al. (2019) · Journal of Nutrition · doi:10.1093/jn/nxz065 · Cited by 98
Yeoh, Y. K., Sun, Y., Ip, L., Wang, L., Chan, F. K. L., Miao, Y., & Ng, S. C. (2022) · Scientific Reports · doi:10.1038/s41598-022-12721-4 · Cited by 102
Volatility as a Concept to Understand the Impact of Stress on the Microbiome
Bastiaanssen, T. F. S., Gururajan, A., van de Wouw, M., Moloney, G. M., Ritz, N. L., Long-Smith, C. M., Wiley, N., Murphy, A., Lyte, J. M., Fouhy, F., et al. (2020) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2020.105047 · Cited by 93
McGovern, A. S., Hamlin, A. S., & Winter, G. (2019) · Australian & New Zealand Journal of Psychiatry · doi:10.1177/0004867419877954 · Cited by 98
Microbiome epidemiology and association studies in human health
VanEvery, H., Franzosa, E. A., Nguyen, L. H., & Huttenhower, C. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00529-x · Cited by 86
Self-citationMuñoz, R. R. S., Mantz, S., Martínez, I., Li, F., Schmaltz, R. J., Pudlo, N. A., Urs, K., Martens, E. C., Walter, J., & Ramer‐Tait, A. E. (2022) · The ISME Journal · doi:10.1038/s41396-022-01208-9 · Cited by 88
A great-ape view of the gut microbiome
Nishida, A. H., & Ochman, H. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0085-z · Cited by 84
Manghi, P., Bhosle, A., Wang, K., Marconi, R., Selma‐Royo, M., Ricci, L., Asnicar, F., Golzato, D., Ma, W., Hang, D., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01858-9 · Cited by 84
Self-citationHanson, B. T., Kits, K. D., Löffler, J., Burrichter, A. G., Fiedler, A. W., Denger, K., Frommeyer, B., Herbold, C. W., Rattei, T., Karcher, N., et al. (2021) · The ISME Journal · doi:10.1038/s41396-021-00968-0 · Cited by 70
Zhao, N., Cao, J., Xu, J., Liu, B., Liu, B., Chen, D., Xia, B., Chen, L., Zhang, W., Zhang, Y., et al. (2021) · Advanced Science · doi:10.1002/advs.202102593 · Cited by 76
Association Between the Sulfur Microbial Diet and Risk of Colorectal Cancer
Wang, Y., Nguyen, L. H., Mehta, R. S., Song, M., Huttenhower, C., & Chan, A. T. (2021) · JAMA Network Open · doi:10.1001/jamanetworkopen.2021.34308 · Cited by 81
Self-citationOjala, T., Häkkinen, A.-E., Kankuri, E. M., & Kankainen, M. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.05.004 · Cited by 81
Rajakovich, L. J., Fu, B., Bollenbach, M., & Balskus, E. P. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101498118 · Cited by 79
Interactions between dietary fibre and the gut microbiota
Thomson, C. L., García, A. L., & Edwards, C. A. (2021) · Proceedings of The Nutrition Society · doi:10.1017/s0029665121002834 · Cited by 80
Liu, M., Devlin, J. C., Hu, J., Volkova, A., Battaglia, T., Ho, M. L., Asplin, J. R., Byrd, A. L., Loke, P., Li, H., et al. (2021) · eLife · doi:10.7554/elife.63642 · Cited by 73
Viral biogeography of the mammalian gut and parenchymal organs
Shkoporov, A. N., Stockdale, S. R., Lavelle, A., Kondova, I. I., Hueston, C. M., Upadrasta, A., Khokhlova, E. V., van der Kamp, I., Ouwerling, B., Draper, L. A., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01178-w · Cited by 71
Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies
Daliri, E. B., Ofosu, F. K., Chelliah, R., Lee, B. H., & Oh, D. (2021) · Biomolecules · doi:10.3390/biom11020300 · Cited by 77
Circulating microbiome in patients with portal hypertension
Gedgaudas, R., Bajaj, J. S., Skiecevičienė, J., Varkalaitė, G., Jurkeviciute, G., Gelman, S., Valantienė, I., Zykus, R., Pranculis, A., Bang, C., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2029674 · Cited by 66
Byrd, A. L., Liu, M., Fujimura, K. E., Lyalina, S., Nagarkar, D. R., Charbit, B., Bergstedt, J., Patin, E., Harrison, O. J., Quintana-Murci, L., et al. (2021) · Journal of Experimental Medicine · doi:10.1084/jem.20200606 · Cited by 63
“05), consistent with previous findings (Flores et al., 2014; Mehta et al., 2018) and ecological theory (McCann, 2000; Schindler et al.”
BackgroundResultInfluentialTimescales of gut microbiome dynamics
Schlomann, B. H., & Parthasarathy, R. (2019) · Current Opinion in Microbiology · doi:10.1016/j.mib.2019.09.011 · Cited by 69
Shotgun metagenomics of dust microbiome from flight deck and cabin in civil aviation aircraft
Sun, Y., Fu, X., Li, Y., Yuan, Q., Ou, Z., Lindgren, T., Deng, Y., & Norbäck, D. (2020) · Indoor Air · doi:10.1111/ina.12707 · Cited by 65
Bastiaanssen, T. F. S., Quinn, T. P., & Loughman, A. (2023) · Nature Mental Health · doi:10.1038/s44220-023-00148-3 · Cited by 71
Mancabelli, L., Milani, C., Biase, R. D., Bocchio, F., Fontana, F., Lugli, G. A., Alessandri, G., Tarracchini, C., Viappiani, A., Conto, F. D., et al. (2024) · mSystems · doi:10.1128/msystems.01294-23 · Cited by 64
Structure of the Mucosal and Stool Microbiome in Lynch Syndrome
Yan, Y., Drew, D. A., Markowitz, A. J., Lloyd‐Price, J., Abu-Ali, G., Nguyen, L. H., Tran, C., Chung, D. C., Gilpin, K. K., Meixell, D. A., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.03.005 · Cited by 65
Self-citationEffects of the long-term storage of human fecal microbiota samples collected in RNAlater
Tap, J., Cools-Portier, S., Pavan, S., Druesne, A., Öhman, L., Törnblom, H., Simrén, M., & Derrien, M. (2019) · Scientific Reports · doi:10.1038/s41598-018-36953-5 · Cited by 63
Jia, J., Cheng, M., Xue, X., Guan, Y., & Wang, Z. (2020) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2020.110182 · Cited by 59
Porcari, S., CICCARESE, C., Heidrich, V., Rondinella, D., Quaranta, G., Severino, A., Arduini, D., Buti, S., Fornarini, G., Primi, F., et al. (2026) · Nature Medicine · doi:10.1038/s41591-025-04189-2 · Cited by 62
High-resolution ISR amplicon sequencing reveals personalized oral microbiome
Mukherjee, C., Beall, C. J., Griffen, A. L., & Leys, E. J. (2018) · Microbiome · doi:10.1186/s40168-018-0535-z · Cited by 58
The Intestinal Microbiota May Be a Potential Theranostic Tool for Personalized Medicine
Domenico, M. D., Ballini, A., Boccellino, M., Scacco, S., Lovero, R., Charitos, I. A., & Santacroce, L. (2022) · Journal of Personalized Medicine · doi:10.3390/jpm12040523 · Cited by 54
Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome
Li, Y., Wang, D. D., Satija, A., Ivey, K. L., Li, J., Wilkinson, J. E., Li, R., Baden, M. Y., Chan, A. T., Huttenhower, C., et al. (2021) · Journal of Nutrition · doi:10.1093/jn/nxab175 · Cited by 55
Self-citationDevaux, C. A., & Raoult, D. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01379 · Cited by 53
Differding, M. K., Doyon, M., Bouchard, L., Perron, P., Guérin, R., Asselin, C., Massé, E., Hivert, M., & Mueller, N. T. (2020) · Pediatric Obesity · doi:10.1111/ijpo.12642 · Cited by 49
Ilett, E. E., Jørgensen, M., Noguera-Julián, M., Daugaard, G., Murray, D. D., Helleberg, M., Paredes, R., Lundgren, J. D., Sengeløv, H., & MacPherson, C. R. (2019) · Scientific Reports · doi:10.1038/s41598-019-49956-7 · Cited by 48
Daele, E. V., Knol, J., & Belzer, C. (2019) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2019.1680601 · Cited by 49
The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health
Eetemadi, A., Rai, N., Pereira, B. M. P., Kim, M., Schmitz, H. H., & Tagkopoulos, I. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00393 · Cited by 51
The oral-gut microbiome axis in inflammatory bowel disease: from inside to insight
Wang, A., Zhai, Z., Ding, Y., Wei, J., Wei, Z., & Cao, H. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1430001 · Cited by 51
Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly
Ivey, K. L., Chan, A. T., Izard, J., Cassidy, A., Rogers, G. B., & Rimm, E. B. (2019) · mBio · doi:10.1128/mbio.01205-19 · Cited by 43
Self-citationA transomic cohort as a reference point for promoting a healthy human gut microbiome
Jie, Z., Liang, S., Ding, Q., Li, F., Tang, S., Wang, D., Lin, Y., Chen, P., Cai, K., Qiu, X., et al. (2021) · Medicine in Microecology · doi:10.1016/j.medmic.2021.100039 · Cited by 43
Long-term dynamics of the human oral microbiome during clinical disease progression
Duran-Pinedo, A. E., Solbiati, J., Teles, F., Teles, R. P., Zang, Y., & Frias‐Lopez, J. (2021) · BMC Biology · doi:10.1186/s12915-021-01169-z · Cited by 44
Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women
Ke, S., Guimond, A., Tworoger, S. S., Huang, T., Chan, A. T., Liu, Y., & Kubzansky, L. D. (2023) · Psychological Medicine · doi:10.1017/s0033291723000612 · Cited by 47
Self-citationTemporal Variability and Stability of the Fecal Microbiome: The Multiethnic Cohort Study
Fu, B. C., Randolph, T. W., Lim, U., Monroe, K. R., Cheng, I. C., Wilkens, L. R., Marchand, L. L., Lampe, J. W., & Hullar, M. A. J. (2018) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-18-0348 · Cited by 43
The Microbiome as a Circadian Coordinator of Metabolism
Alvarez, Y., Glotfelty, L., Blank, N., Dohnalová, L., & Thaiss, C. A. (2020) · Endocrinology · doi:10.1210/endocr/bqaa059 · Cited by 39
Li, Y., Wang, F., Li, J., Ivey, K. L., Wilkinson, J. E., Wang, D. D., Li, R., Liu, G., Eliassen, A. H., Chan, A. T., et al. (2022) · BMC Microbiology · doi:10.1186/s12866-022-02495-0 · Cited by 41
Self-citationHu, Y., Li, J., Wang, B., Zhu, L., Li, Y., Ivey, K. L., Lee, K. H., Eliassen, A. H., Chan, A. T., Huttenhower, C., et al. (2023) · Gut · doi:10.1136/gutjnl-2023-330410 · Cited by 42
Self-citationBae, M., Le, C., Mehta, R. S., Dong, X., Pieper, L. M., Ramirez, L., Alexander, M., Kiamehr, S., Turnbaugh, P. J., Huttenhower, C., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.10.002 · Cited by 42
Self-citationPopulation dynamics of the human gut microbiome: change is the only constant
Priya, S., & Blekhman, R. (2019) · Genome biology · doi:10.1186/s13059-019-1775-3 · Cited by 40
Stress, inflammation, microbiome and depression
Medina-Rodriguez, E. M., Cruz, A. A., Abreu, J. C. D., & Beurel, E. (2023) · Pharmacology Biochemistry and Behavior · doi:10.1016/j.pbb.2023.173561 · Cited by 41
Wu-Woods, N. J., Barlow, J. T., Trigodet, F., Shaw, D. G., Romano, A. E., Jabrì, B., Eren, A. M., & Ismagilov, R. F. (2023) · Nature Methods · doi:10.1038/s41592-023-02025-4 · Cited by 42
The Impact of the Gut Microbiome, Environment, and Diet in Early-Onset Colorectal Cancer Development
Dai, R., Kelly, B. N., Ike, A., Berger, D. L., Chan, A. T., Drew, D. A., Ljungman, D., Mutiibwa, D., Ricciardi, R., Tumusiime, G., et al. (2024) · Cancers · doi:10.3390/cancers16030676 · Cited by 38
Self-citationEarly development of the skin microbiome: therapeutic opportunities
Casterline, B. W., & Paller, A. S. (2020) · Pediatric Research · doi:10.1038/s41390-020-01146-2 · Cited by 39
Alterations of gut microbiota composition in post-finasteride patients: a pilot study
Borgo, F., Macandog, A. D. G., Diviccaro, S., Falvo, E., Giatti, S., Cavaletti, G., & Melcangi, R. C. (2020) · Journal of Endocrinological Investigation · doi:10.1007/s40618-020-01424-0 · Cited by 36
Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease
Sharpton, S. R., Yong, G. J. M., Terrault, N. A., & Lynch, S. V. (2018) · Hepatology Communications · doi:10.1002/hep4.1284 · Cited by 37
Schierová, D., Roubalová, R., Kolář, M., Stehlíková, Z., Rob, F., Jackova, Z., Coufal, Š., Thon, T., Mihula, M., Modrák, M., et al. (2021) · Cells · doi:10.3390/cells10113188 · Cited by 36
Zaccaria, E., Klaassen, T., Alleleyn, A. M. E., Boekhorst, J., Smokvina, T., Kleerebezem, M., & Troost, F. J. (2023) · Microbiome · doi:10.1186/s40168-023-01491-4 · Cited by 34
Metadata
- Authors
- Mehta, R. S., Abu-Ali, G. S., Drew, D. A., Lloyd-Price, J., Subramanian, A., Lochhead, P., Joshi, A. D., Ivey, K. L., Khalili, H., Brown, G. T., DuLong, C., Song, M., Nguyen, L. H., Mallick, H., Rimm, E. B., Izard, J., Huttenhower, C., & Chan, A. T.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Brigham and Women's Hospital (US)
- University of Nebraska–Lincoln (US)
- Corresponding author
- Huttenhower, Curtis
- Chan, Andrew T.
- ORCID
- Venue
- Nature Microbiology
- Published
- 2018-01-15
- Volume
- 3
- Issue
- 3
- Pages
- 347-355
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC6016839
- OpenAlex
- W2783226215
- Cited by
- 273
- References
- 48
- Citations by year
- 2026: 16 · 2025: 29 · 2024: 43 · 2023: 36 · 2022: 31 · 2021: 43 · 2020: 43 · 2019: 17 · 2018: 15
- FWCI
- 10.30
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Lincoln (University of Nebraska) (submittedVersion)
- Funders
- Massachusetts General Hospital
- Crohn's and Colitis Foundation (454674, 563526)
- National Heart, Lung, and Blood Institute (R01HL035464)
- National Cancer Institute (R01CA202704, L30 CA209764, U01CA152904, UM1CA167552)
- National Institute of Diabetes and Digestive and Kidney Diseases (K01DK110267, K24DK098311, P30DK043351)
- National Institute of Dental and Craniofacial Research (U54DE023798)
- 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
- fecal microbiota, within-person variability, between-person variation, metatranscriptomics, metagenomics, Health Professionals Follow-up Study, adult male, biomarkers
- MeSH terms
- Gastrointestinal Microbiome, Adult, Aged, Bacteria, Feces, Follow-Up Studies, Health Personnel, Humans, Male, Middle Aged, Prospective Studies, Cohort Studies, Gene Expression, Gene Expression Profiling, Metagenomics, High-Throughput Nucleotide Sequencing, 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 ›
Are you an author, or do you see a problem with this page? Request a review
