Host lifestyle affects human microbiota on daily timescales
Open accessAbstract
BACKGROUND: Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities. RESULTS: Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. Travel from the developed to the developing world in one subject led to a nearly two-fold increase in the Bacteroidetes to Firmicutes ratio, which reversed upon return. Enteric infection in the other subject resulted in the permanent decline of most gut bacterial taxa, which were replaced by genetically similar species. Still, even during periods of overall community stability, the dynamics of select microbial taxa could be associated with specific host behaviors. Most prominently, changes in host fiber intake positively correlated with next-day abundance changes among 15% of gut microbiota members. CONCLUSIONS: Our findings suggest that although human-associated microbial communities are generally stable, they can be quickly and profoundly altered by common human actions and experiences.
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
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?
Short-term, dramatic dietary interventions have demonstrated the ability to alter microbiota diversity quickly in humans.
“Short-term, dramatic dietary interventions have demonstrated the ability to alter microbiota diversity quickly in humans [5].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [5]
Mouse models have indicated that manipulation of macronutrient intake can consistently shift the composition of the gut microbiota within the span of a day.
“Likewise, mouse models have indicated that manipulation of macronutrient intake can consistently shift the composition of the gut microbiota within the span of a day [5,6,18,19].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [5]
One longitudinal study involving daily gut microbiota investigations of two individuals over the course of a year found that changes in fibre intake are positively correlated with a change in abundance of 15% of the microbial community the following day.
“One longitudinal study involving daily gut microbiota investigations of two individuals over the course of a year found that changes in fibre intake are positively correlated with a change in abundance of 15% of the microbial community the following day [5].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [5]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · 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
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891 · see citing works
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 · see citing works
Self-citationGlobal patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,633 · see citing works
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · see citing works
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Statsmodels: Econometric and Statistical Modeling with Python
Seabold, S., & Perktold, J. (2010) · Proceedings of the Python in Science Conferences · doi:10.25080/majora-92bf1922-011 · Cited by 6,673 · see citing works
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works
Spurious regressions in econometrics
Granger, C. W. J., & Newbold, P. (1974) · Journal of Econometrics · doi:10.1016/0304-4076(74)90034-7 · Cited by 6,276 · see citing works
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works
Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804812105 · Cited by 4,413 · see citing works
The Analysis of Time Series: An Introduction
Dickey, D. A., & Chatfield, C. (1991) · Technometrics · doi:10.2307/1268794 · Cited by 3,551 · see citing works
Automatic Time Series Forecasting: The forecast Package for R
Hyndman, R. J., & Khandakar, Y. (2008) · Journal of Statistical Software · doi:10.18637/jss.v027.i03 · Cited by 3,548 · see citing works
The Statistical Analysis of Compositional Data
Aitchison, J. (1982) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/j.2517-6161.1982.tb01195.x · Cited by 3,457 · see citing works
The Statistical Analysis of Compositional Data
Piepel, G. F., & Aitchison, J. (1988) · Technometrics · doi:10.2307/1270335 · Cited by 3,410 · see citing works
Testing for unit roots in autoregressive-moving average models of unknown order
Saïd, S. E., & Dickey, D. A. (1984) · Biometrika · doi:10.1093/biomet/71.3.599 · Cited by 3,258 · see citing works
Bacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231 · see citing works
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
Inferring Correlation Networks from Genomic Survey Data
Friedman, J., & Alm, E. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002687 · Cited by 2,688 · see citing works
Succession of microbial consortia in the developing infant gut microbiome
Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540 · see citing works
Dethlefsen, L., & Relman, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000087107 · Cited by 2,421 · see citing works
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works
A review of saliva: normal composition, flow, and function.
Humphrey, S. P., & Williamson, R. (2001) · The Journal of prosthetic dentistry (Print) · doi:10.1067/mpr.2001.113778 · Cited by 2,276 · see citing works
The Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058 · see citing works
Diagnostic Checking in Regression Relationships
Zeileis, A., & Hothorn, T. (2015) · WU Research · Cited by 1,904 · see citing works
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice
Devkota, S., Wang, Y., Musch, M. W., Leone, V., Fehlner-Peach, H., Nadimpalli, A., Antonopoulos, D. A., Jabri, B., & Chang, E. B. (2012) · Nature · doi:10.1038/nature11225 · Cited by 1,904 · see citing works
Chatfield, C., & Xing, H. (1990) · Chapman & Hall/CRC eBooks · doi:10.1201/9781351259446 · Cited by 1,816 · see citing works
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2010.118 · Cited by 1,632 · see citing works
Antibiotics in early life alter the murine colonic microbiome and adiposity
Cho, I., Yamanishi, S., Cox, L., Methé, B. A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012) · Nature · doi:10.1038/nature11400 · Cited by 1,613 · see citing works
Temporal Dynamics of the Human Vaginal Microbiota
Gajer, P., Brotman, R. M., Bai, G., Sakamoto, J. M., Schütte, U. M. E., Zhong, X., Koenig, S. S. K., Fu, L., Ma, Z. S., Zhou, X., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003605 · Cited by 1,552 · see citing works
Selective stimulation of bifidobacteria in the human colon by oligofructose and inulin
Gibson, G. R., Beatty, E. R., Wang, X., & Cummings, J. H. (1995) · Gastroenterology · doi:10.1016/0016-5085(95)90192-2 · Cited by 1,529 · see citing works
The Application of Ecological Theory Toward an Understanding of the Human Microbiome
Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M., & Relman, D. A. (2012) · Science · doi:10.1126/science.1224203 · Cited by 1,437 · see citing works
Alternative stable states in ecology
Beisner, B., Haydon, D., & Cuddington, K. (2003) · Frontiers in Ecology and the Environment · doi:10.1890/1540-9295(2003)001[0376:assie]2.0.co;2 · Cited by 1,385 · see citing works
Zoetendal, E. G., Akkermans, A. D. L., & de Vos, W. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3854-3859.1998 · Cited by 1,360 · see citing works
Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009836 · Cited by 1,160 · see citing works
Moving pictures of the human microbiome
Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., et al. (2011) · Genome Biology · doi:10.1186/gb-2011-12-5-r50 · Cited by 1,138 · see citing works
Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050244 · Cited by 1,048 · see citing works
Duncan, S. H., Belenguer, A., Holtrop, G., Johnstone, A. M., Flint, H. J., & Lobley, G. E. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02340-06 · Cited by 941 · see citing works
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
Strimmer, K. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn209 · Cited by 723 · see citing works
Buffie, C. G., Jarchum, I., Equinda, M., Lipuma, L., Gobourne, A., Viale, A., Ubeda, C., Xavier, J., & Pamer, E. G. (2012) · Infection and Immunity · doi:10.1128/iai.05496-11 · Cited by 596 · cited 2× · see citing works
“Background The temporal dynamics of host-associated microbial communities (the microbiota) are of growing interest due to these communities’ relevance for health [1-5].”
BackgroundPhylogenetic Approaches for Describing and Comparing the Diversity of Microbial Communities
Martin, A. P. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.8.3673-3682.2002 · Cited by 519 · see citing works
Proceedings of the 8th Python in Science Conference
(2009) · Proceedings of the Python in Science Conferences · doi:10.25080/rjfg8479 · Cited by 497 · see citing works
Lopez-Siles, M., Khan, T. M., Duncan, S. H., Harmsen, H. J. M., Garcia-Gil, L. J., & Flint, H. J. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.06858-11 · Cited by 433 · see citing works
Acute Gastrointestinal Infection Induces Long-Lived Microbiota-Specific T Cell Responses
Hand, T. W., dos Santos, L. M., Bouladoux, N. J., Molloy, M. J., Pagán, A. J., Pepper, M., Maynard, C. L., Elson, C. O., & Belkaid, Y. (2012) · Science · doi:10.1126/science.1220961 · Cited by 384 · see citing works
Human gut microbiome adopts an alternative state following small bowel transplantation
Hartman, A., Lough, D., Barupal, D. K., Fiehn, O., Fishbein, T., ZASLOFF, M. A., & Eisen, J. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904847106 · Cited by 341 · see citing works
PHYLOGENETIC CLUSTERING AND OVERDISPERSION IN BACTERIAL COMMUNITIES
Horner‐Devine, M. C., & Bohannan, B. J. M. (2006) · Ecology · doi:10.1890/0012-9658(2006)87[100:pcaoib]2.0.co;2 · Cited by 336 · see citing works
Cordero, O. X., Ventouras, L.-A., DeLong, E. F., & Polz, M. F. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213344109 · Cited by 334 · see citing works
Heer, J., Kong, N., & Agrawala, M. (2009) · CHI Conference on Human Factors in Computing Systems · doi:10.1145/1518701.1518897 · Cited by 290 · see citing works
Proceedings of the 19th Python in Science Conference
(2020) · Proceedings of the Python in Science Conferences · doi:10.25080/majora-342d178e-02b · Cited by 284 · see citing works
PyCogent: a toolkit for making sense from sequence
Knight, R. D., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J. G., Easton, B. C., Eaton, M., Hamady, M., Lindsay, H. A., Liu, Z. Z., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-8-r171 · Cited by 194 · see citing works
Walsh, N. P., Montague, J. C., Callow, N., & Rowlands, A. V. (2003) · Archives of Oral Biology · doi:10.1016/j.archoralbio.2003.08.001 · Cited by 192 · see citing works
Reassessment of Some Fruit and Vegetable Pectin Levels
BAKER, R. A. (1997) · Journal of Food Science · doi:10.1111/j.1365-2621.1997.tb03973.x · Cited by 91 · see citing works
Treatment Outcomes of Dental Flossing in Twins: Molecular Analysis of the Interproximal Microflora
Corby, P. M. A., Biesbrock, A. R., Bartizek, R. D., Corby, A. L., Monteverde, R., Ceschin, R. C., & Bretz, W. A. (2008) · Journal of Periodontology · doi:10.1902/jop.2008.070585 · Cited by 50 · see citing works
Tan, M. T., Qu, Y., Mascha, E. J., & Schubert, A. (1999) · Statistics in Medicine · doi:10.1002/(sici)1097-0258(19990815)18:15 · Cited by 26 · see citing works
TheRPackagebildfor the Analysis of Binary Longitudinal Data
Gonçalves, M. H., Cabral, M. S., & Azzalini, A. (2012) · Journal of Statistical Software · doi:10.18637/jss.v046.i09 · Cited by 12 · see citing works
Flagged first, then by citations
1 of the 58 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
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
You are what you eat: Diet, health and the gut microbiota
Zmora, N., Suez, J., & Elinav, E. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0061-2 · Cited by 1,792 · see citing works
Dysbiosis and the immune system
Levy, M., Kolodziejczyk, A. A., Thaiss, C. A., & Elinav, E. (2017) · Nature Reviews Immunology · doi:10.1038/nri.2017.7 · Cited by 1,769 · see citing works
Signals from the gut microbiota to distant organs in physiology and disease
Schroeder, B. O., & Bäckhed, F. (2016) · Nature Medicine · doi:10.1038/nm.4185 · Cited by 1,409 · see citing works
Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043 · see citing works
The resilience of the intestinal microbiota influences health and disease
Sommer, F., Anderson, J. M., Bharti, R., Raes, J., & Rosenstiel, P. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.58 · Cited by 1,058 · see citing works
Personalized medicine: motivation, challenges, and progress
Goetz, L. H., & Schork, N. J. (2018) · Fertility and Sterility · doi:10.1016/j.fertnstert.2018.05.006 · Cited by 976 · see citing works
Leone, V., Gibbons, S. M., Martinez, K., Hutchison, A. L., Huang, E. Y., Cham, C. M., Pierre, J. F., Heneghan, A. F., Nadimpalli, A., Hubert, N., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.03.006 · Cited by 908 · see citing works
“Detecting significant oscillatory patterns in 16S rRNA amplicon sequencing data is complicated due to lack of absolute OTU abundance information and limited tools to describe nonlinear relationships in relative abundance data (Friedman and Alm, 2012; David et al., 2014).”
Microbiota: a key orchestrator of cancer therapy
Roy, S., & Trinchieri, G. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.13 · Cited by 883 · see citing works
Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration
Leeming, E. R., Johnson, A. J., Spector, T. D., & Le Roy, C. I. (2019) · Nutrients · doi:10.3390/nu11122862 · Cited by 817 · see citing works
“Likewise, mouse models have indicated that manipulation of macronutrient intake can consistently shift the composition of the gut microbiota within the span of a day [5,6,18,19].”
BackgroundInfluentialMicrobiota and Host Nutrition across Plant and Animal Kingdoms
Hacquard, S., Garrido-Oter, R., González, A., Spaepen, S., Ackermann, G., Lebeis, S., McHardy, A. C., Dangl, J. L., Knight, R., Ley, R., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.009 · Cited by 779 · see citing works
Daily sampling reveals personalized diet-microbiome associations in humans
Johnson, A. J., Vangay, P., Al-Ghalith, G. A., Hillmann, B. M., Ward, T. L., Shields-Cutler, R. R., Kim, A. D., Shmagel, A. K., Syed, A. N., Walter, J., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.05.005 · Cited by 742 · see citing works
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
Shkoporov, A. N., Clooney, A. G., Sutton, T. D. S., Ryan, F. J., Daly, K. M., Nolan, J. A., McDonnell, S. A., Khokhlova, E. V., Draper, L. A., Forde, A., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.09.009 · Cited by 737 · see citing works
Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
Comeau, A., Douglas, G. M., & Langille, M. G. I. (2017) · mSystems · doi:10.1128/msystems.00127-16 · Cited by 674 · see citing works
Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria
Xu, L., Naylor, D., Dong, Z., Simmons, T., Pierroz, G., Hixson, K. K., Kim, Y., Zink, E., Engbrecht, K. M., Wang, Y., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717308115 · Cited by 655 · see citing works
The role of the microbiome in cancer development and therapy
Bhatt, A. P., Redinbo, M. R., & Bultman, S. J. (2017) · CA A Cancer Journal for Clinicians · doi:10.3322/caac.21398 · Cited by 653 · see citing works
“A plethora of other factors affects the microbiome, including international travel, infections, and pharmaceuticals.(27) Subsequent to such changes, or after an infection is resolved, most, but not all, commensal microbiota return to their baseline levels.”
BackgroundBrooks, A., Kohl, K. D., Brucker, R. M., van Opstal, E. J., & Bordenstein, S. R. (2016) · PLoS Biology · doi:10.1371/journal.pbio.2000225 · Cited by 629 · see citing works
Sochocka, M., Donskow-Łysoniewska, K., Diniz, B. S., Kurpas, D., Brzozowska, E., & Leszek, J. (2019) · Molecular Neurobiology · doi:10.1007/s12035-018-1188-4 · Cited by 584 · see citing works
“[25] suggest that although human-associated microbial communities are stable, they can be quickly and profoundly altered by common human actions and experiences.”
BackgroundSample storage conditions significantly influence faecal microbiome profiles
Choo, J. M., Leong, L. E. X., & Rogers, G. B. (2015) · Scientific Reports · doi:10.1038/srep16350 · Cited by 506 · see citing works
Artificial Intelligence and Personalized Medicine
Schork, N. J. (2019) · Cancer treatment and research · doi:10.1007/978-3-030-16391-4_11 · Cited by 518 · see citing works
The Human Microbiome and Obesity: Moving beyond Associations
Maruvada, P., Leone, V., Kaplan, L. M., & Chang, E. B. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.10.005 · Cited by 468 · see citing works
Use of Metatranscriptomics in Microbiome Research
Bashiardes, S., Zilberman-Schapira, G., & Elinav, E. (2016) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s34610 · Cited by 470 · see citing works
The role of the microbiome for human health: From basic science to clinical applications
Mohajeri, M. H., Brummer, R. J. M., Rastall, R. A., Weersma, R. K., Harmsen, H. J. M., Faas, M., & Eggersdorfer, M. (2018) · European Journal of Nutrition · doi:10.1007/s00394-018-1703-4 · Cited by 440 · see citing works
“Infections, lifestyle and dietary changes cause microbiome instability, producing major perturbations of the gut microbiome as nicely shown in a high-resolution longitudinal study in two individuals [67].”
BackgroundAdaptive Evolution within Gut Microbiomes of Healthy People
Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434 · see citing works
The Gut Microbiota in Immune-Mediated Inflammatory Diseases
Forbes, J. D., Domselaar, G. V., & Bernstein, C. N. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01081 · Cited by 430 · see citing works
A wellness study of 108 individuals using personal, dense, dynamic data clouds
Price, N. D., Magis, A. T., Earls, J. C., Glusman, G., Levy, R., Lausted, C., McDonald, D. T., Kusebauch, U., Moss, C. L., Zhou, Y., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3870 · Cited by 427 · see citing works
Layer‐by‐Layer Encapsulation of Probiotics for Delivery to the Microbiome
Anselmo, A. C., McHugh, K. J., Webster, J., Langer, R., & Jaklenec, A. (2016) · Advanced Materials · doi:10.1002/adma.201603270 · Cited by 427 · see citing works
Resilience of the Oral Microbiota in Health: Mechanisms That Prevent Dysbiosis
Rosier, B. T., Marsh, P. D., & Mira, A. (2018) · Journal of Dental Research · doi:10.1177/0022034517742139 · Cited by 448 · see citing works
Marcos-Zambrano, L. J., Karađuzović-Hadžiabdić, K., Lončar-Turukalo, T., Przymus, P., Trajkovik, V., Aasmets, O., Berland, M., Gruca, A., Telalović, J. H., Hron, K., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.634511 · Cited by 429 · see citing works
Metagenomics meets time series analysis: unraveling microbial community dynamics
Faust, K., Lahti, L., Gonze, D., de Vos, W. M., & Raes, J. (2015) · Current Opinion in Microbiology · doi:10.1016/j.mib.2015.04.004 · Cited by 407 · see citing works
Ménage à trois in the human gut: interactions between host, bacteria and phages
Mirzaei, M. K., & Maurice, C. F. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.30 · Cited by 404 · see citing works
Zhao, W., Wang, Y., Liu, S., Huang, J., Zhai, Z., He, C., Ding, J., Wang, J., Wang, H., Fan, W., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0117441 · Cited by 403 · see citing works
The Microbiome and Human Biology
Knight, R., Callewaert, C., Marotz, C., Hyde, E. R., Debelius, J. W., McDonald, D., & Sogin, M. L. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022438 · Cited by 373 · see citing works
Gut microbiota and cardiovascular disease: opportunities and challenges
Kazemian, N., Mahmoudi, M., Halperin, F. A., Wu, J. C., & Pakpour, S. (2020) · Microbiome · doi:10.1186/s40168-020-00821-0 · Cited by 392 · see citing works
Microbial nutrient niches in the gut
Pereira, F. C., & Berry, D. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13659 · Cited by 365 · see citing works
“For example, the intake of fibre-rich foods in humans correlates positively with next-day abundances of Bifidobacteria, Roseburia spp., and Eubacterium rectale (David et al., 2014a).”
BackgroundDo Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?
Alberdi, A., Aizpurua, O., Bohmann, K., Mendoza, M. L. Z., & Gilbert, M. T. P. (2016) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2016.06.008 · Cited by 351 · see citing works
Network analysis methods for studying microbial communities: A mini review
Matchado, M. S., Lauber, M., Reitmeier, S., Kacprowski, T., Baumbach, J., Haller, D., & List, M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.05.001 · Cited by 352 · see citing works
“…microbiome studies including local similarity analysis (LSA) [78], Time-decay analysis [79], Augmented Dickey Fuller test [80], Cross correlation [80], Time-varying network inference [81], Hurst exponent [82], Bistability analysis [83], as well as Extended LSA (eLSA) [84], which offers support…”
MethodHugerth, L. W., & Andersson, A. F. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01561 · Cited by 359 · see citing works
“…of a natural microbial community is sampling a time-series with appropriate intervals and length, and using techniques such as Local Similarity Analysis (Ruan et al., 2006; Steele et al., 2011) or auto-and cross-correlation (Fuhrman et al., 2006; Gilbert et al., 2012; David et al., 2014).”
MethodWhy does the microbiome affect behaviour?
Johnson, K. V.-A., & Foster, K. R. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0014-3 · Cited by 333 · see citing works
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 351 · see citing works
Understanding 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 329 · see citing works
“The overall diversity and community architecture of healthy adult microbiomes do not change dramatically in the absence of significant perturbation [26, 40, 41].”
BackgroundSewage Reflects the Microbiomes of Human Populations
Newton, R. J., McLellan, S. L., Dila, D. K., Vineis, J. H., Morrison, H. G., Eren, A. M., & Sogin, M. L. (2015) · mBio · doi:10.1128/mbio.02574-14 · Cited by 299 · see citing works
“Lifestyle differences can reproducibly alter the human gut microbiome (27), and microbial community composition is a known indicator of obesity (28–30), with up to 90% predictive accuracy for individuals (31).”
BackgroundRole of dietary fiber in the recovery of the human gut microbiome and its metabolome
Tanes, C., Bittinger, K. L., Gao, Y., Friedman, E. S., Nessel, L. A., Paladhi, U. R., Chau, L., Panfen, E., Fischbach, M. A., Braun, J. G., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.12.012 · Cited by 306 · see citing works
“Dietary fiber from fruits and vegetables has large effects on the structure and function of the murine microbiota, with some effects being reproducible in humans (David et al., 2014; Kovatcheva-Datchary et al., 2015).”
BackgroundBalance Trees Reveal Microbial Niche Differentiation
Morton, J. T., Sanders, J., Quinn, R. A., McDonald, D., Gonzalez, A., Vázquez-Baeza, Y., Navas-Molina, J. A., Song, S. J., Metcalf, J. L., Hyde, E. R., et al. (2017) · mSystems · doi:10.1128/msystems.00162-16 · Cited by 254 · see citing works
“This suggests that there is substantial functional redundancy across OTUs, which has been observed previously in time series studies in the context of infection (27); in other words, in these microbial communities, many players might be sporadically distributed across similar niches.”
Mobile genes in the human microbiome are structured from global to individual scales
Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., et al. (2016) · Nature · doi:10.1038/nature18927 · Cited by 288 · see citing works
“If this is true, then diet and drugs could modify the functions of the microbiome, even if the long-term species composition is stable 29,30 .”
Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi
Auchtung, T. A., Fofanova, T. Y., Stewart, C. J., Nash, A. K., Wong, M. C., Gesell, J. R., Auchtung, J. M., Ajami, N. J., & Petrosino, J. F. (2018) · mSphere · doi:10.1128/msphere.00092-18 · Cited by 290 · see citing works
“levels in the GI tract (30), there was no evidence that that was the situation for any fungi”
BackgroundMicrobiota succession throughout life from the cradle to the grave
Martino, C., Dilmore, A. H., Burcham, Z. M., Metcalf, J. L., Jeste, D., & Knight, R. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00768-z · Cited by 275 · see citing works
Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis
Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2019) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090817-062503 · Cited by 284 · see citing works
“Even highly abundant organisms vary widely in relative abundance from day to day in samples from the mouth (14, 94).”
BackgroundEnvironmental 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 278 · see citing works
Role of microbial communities in the pathogenesis of periodontal diseases and caries
Mira, Á., Simón‐Soro, Á., & Curtis, M. A. (2017) · Journal Of Clinical Periodontology · doi:10.1111/jcpe.12671 · Cited by 283 · see citing works
“Lifestyle was also found to be the driver of variability in other studies (David et al. 2014).”
ResultГригорьева, И. Н. (2020) · Journal of Personalized Medicine · doi:10.3390/jpm11010013 · Cited by 288 · see citing works
“Yet, each person still maintained a personalized microbiome [140].”
BackgroundStability of the human faecal microbiome in a cohort of adult men
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., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0096-0 · Cited by 273 · see citing works
The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get
Yang, J., & Yu, J. Q. (2018) · Protein & Cell · doi:10.1007/s13238-018-0543-6 · Cited by 280 · see citing works
“More than that, several studies have revealed that the human gut microbiome is relatively stable in adults over time except in the case of special events such as diet intervention, infectious diarrhea or international immigration (David et al., 2014a; Faith et al., 2013).”
BackgroundUniversality of human microbial dynamics
Bashan, A., Gibson, T. E., Friedman, J., Carey, V. J., Weiss, S. T., Hohmann, E. L., & Liu, Y.-Y. (2016) · Nature · doi:10.1038/nature18301 · Cited by 270 · see citing works
“11 .”
ConStrains identifies microbial strains in metagenomic datasets
Luo, C., Knight, R. D., Siljander, H., Knip, M., Xavier, R. J., & Gevers, D. (2015) · Nature Biotechnology · doi:10.1038/nbt.3319 · Cited by 267 · see citing works
“29.”
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
Bikel, S., Valdez-Lara, A., Cornejo-Granados, F., Rico, K., Canizales-Quinteros, S., Soberón, X., Del Pozo-Yauner, L., & Ochoa-Leyva, A. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.06.001 · Cited by 263 · see citing works
“R806, targeting the V4 region, was highly recommended by several human microbiome studies [20,28,36,37] and a well-established”
BackgroundYing, S., Zeng, D.-N., Chi, L., Tan, Y., Galzote, C., Cardona, C., Lax, S. M., Gilbert, J. A., & Quan, Z. (2015) · PLoS ONE · doi:10.1371/journal.pone.0141842 · Cited by 252 · see citing works
“Recent evidence suggests that when an individual changes their city of residence for more than a month (Boston, USA to Bangkok, Thailand), it can have a significant impact on the structure and composition of their saliva and stool microbiota [10].”
BackgroundTransmission of human-associated microbiota along family and social networks
Brito, I., Gurry, T., Zhao, S., Huang, K. H., Young, S., Shea, T. P., Naisilisili, W., Jenkins, A., Jupiter, S. D., Gevers, D., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0409-6 · Cited by 239 · see citing works
Painold, A., Mörkl, S., Kashofer, K., Halwachs, B., Dalkner, N., Bengesser, S., Birner, A., Fellendorf, F. T., Platzer, M., Queissner, R., et al. (2018) · Bipolar Disorders · doi:10.1111/bdi.12682 · Cited by 255 · see citing works
Bharwani, A., Mian, M. F., Surette, M. G., Bienenstock, J., & Forsythe, P. (2017) · BMC Medicine · doi:10.1186/s12916-016-0771-7 · Cited by 236 · see citing works
“Certain factors impart transient changes in the community, while others, for instance, antibiotic usage, leave behind a more persistent signature [67, 68].”
BackgroundSteadyCom: Predicting microbial abundances while ensuring community stability
Chan, S. H. J., Simons, M., & Maranas, C. D. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005539 · Cited by 233 · see citing works
The Microbiome in Psychology and Cognitive Neuroscience
Sarkar, A., Harty, S., Lehto, S. M., Moeller, A. H., Dinan, T. G., Dunbar, R., Cryan, J. F., & Burnet, P. W. J. (2018) · Trends in Cognitive Sciences · doi:10.1016/j.tics.2018.04.006 · Cited by 231 · see citing works
Transmission of the gut microbiota: spreading of health
Browne, H. P., Neville, B. A., Forster, S. C., & Lawley, T. D. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.50 · Cited by 228 · see citing works
Seganfredo, F. B., Blume, C. A., Moehlecke, M., Giongo, A., Casagrande, D. S., Spolidoro, J. V. N., Padoin, A. V., Schaan, B. D., & Mottin, C. C. (2017) · Obesity Reviews · doi:10.1111/obr.12541 · Cited by 228 · see citing works
“However, lifestyle modifications, dietary changes and supplements rapidly and broadly impact microbiota dynamics, which might occur on a day-to-day timescale (68).”
BackgroundFungal-Bacterial Interactions in Health and Disease
Krüger, W., Vielreicher, S., Kapitan, M., Jacobsen, I. D., & Niemiec, M. J. (2019) · Pathogens · doi:10.3390/pathogens8020070 · Cited by 228 · see citing works
Hall, M. W., Singh, N., Ng, K. F., Lam, D. K., Goldberg, M. B., Tenenbaum, H. C., Neufeld, J. D., G. Beiko, R., & Senadheera, D. B. (2017) · npj Biofilms and Microbiomes · doi:10.1038/s41522-016-0011-0 · Cited by 226 · see citing works
The gut microbiota and gastrointestinal surgery
Guyton, K. L., & Alverdy, J. C. (2016) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2016.139 · Cited by 225 · see citing works
Probabilistic Invasion Underlies Natural Gut Microbiome Stability
Obadia, B., Güvener, Z. T., Zhang, V., Ceja-Navarro, J. A., Brodie, E., Ja, W. W., & Ludington, W. B. (2017) · Current Biology · doi:10.1016/j.cub.2017.05.034 · Cited by 216 · see citing works
The Microbiome in Populations with a Low and High Prevalence of Caries
Johansson, I., Witkowska, E., Kaveh, B., Holgerson, P. L., & Tanner, A. C. R. (2015) · Journal of Dental Research · doi:10.1177/0022034515609554 · Cited by 227 · see citing works
“The oral microbiota is stable and in harmony with the host, unless disturbed by medication, disease, low pH (Marsh 2003), or significant changes in diet (David et al. 2014).”
BackgroundVandeputte, D., Commer, L. D., Tito, R. Y., Kathagen, G., Sabino, J., Vermeire, S., Faust, K., & Raes, J. (2021) · Nature Communications · doi:10.1038/s41467-021-27098-7 · Cited by 218 · see citing works
Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins
Moreno-Gallego, J. L., Chou, S., Rienzi, S. C. D., Goodrich, J. K., Spector, T. D., Bell, J. T., Youngblut, N. D., Hewson, I., Reyes, A., & Ley, R. E. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.019 · Cited by 211 · see citing works
“It is well established that diet is a strong driver of daily microbiome fluctuation (Claesson et al., 2012; David et al., 2014; De Filippo et al., 2010; Wu et al., 2011), so the effect of diet on the virome is likely mediated by the microbiome.”
BackgroundHost Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota
Wiles, T. J., Jemielita, M., Baker, R. P., Schlomann, B. H., Logan, S. L., Ganz, J., Melançon, E., Eisen, J. S., Guillemin, K. J., & Parthasarathy, R. (2016) · PLoS Biology · doi:10.1371/journal.pbio.1002517 · Cited by 206 · see citing works
“It is interesting to note that recent metagenomic analyses of human intestinal microbiota have uncovered signatures of sudden shifts in species composition, the origins of which remain unknown [15,46], perhaps indicating stochastic dynamics are widespread in natural intestinal systems.”
BackgroundSalmonella versus the Microbiome
Rogers, A. W. L., Tsolis, R. M., & Bäumler, A. J. (2020) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00027-19 · Cited by 202 · see citing works
“Disruption of the microbiota with antibiotics can clear a niche (54) and pro-”
BackgroundMeasuring the biodiversity of microbial communities by flow cytometry
Props, R., Monsieurs, P., Mysara, M., Clement, L., & Boon, N. (2016) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12607 · Cited by 205 · see citing works
“…between microbial biodiversity and ecosystem function (Konopka, Lindemann & Fredrickson 2015), to monitor community stability (Prest et al. 2013; David et al. 2014) or to identify early warning signals that indicate critical ecosystem transitions (e.g. eutrophication) (Wang et al. 2012).”
BackgroundMicrobiomes of Site-Specific Dental Plaques from Children with Different Caries Status
Richards, V. P., Alvarez, A. J., Luce, A. R., Bedenbaugh, M., Mitchell, M. L., Burne, R. A., & Nascimento, M. M. (2017) · Infection and Immunity · doi:10.1128/iai.00106-17 · Cited by 201 · see citing works
“Previous studies have shown that microbiomes of different parts of the human body can remain stable for months and even years (25, 26), but they can also be highly variable over short periods of time (27, 28).”
BackgroundTools 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
“One of the hallmarks of the human microbiome is its dynamic nature that can be transformed and altered over time [114, 115], but this may potentially be in direct contrast to the observation of a core microbiota that resists perturbation [116–118].”
ResultLinks between the microbiome and bone
Hernandez, C. J., Guss, J. D., Luna, M., & Goldring, S. R. (2016) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.2887 · Cited by 200 · see citing works
“Factors that have been shown to alter the steady state of the gut flora include aging,((16)) diet,((19)) environment,((21)) physiologic state, and chronic treatment with oral antibiotics.”
BackgroundThe subgingival periodontal microbiota of the aging mouth
Feres, M., Teles, F., Teles, R. P., Figueiredo, L. C., & Faveri, M. (2016) · Periodontology 2000 · doi:10.1111/prd.12136 · Cited by 202 · see citing works
“(18) is that the stability of the oral FERES et al.”
BackgroundMethodResultInfluentialHost genetic variation and its microbiome interactions within the Human Microbiome Project
Kolde, R., Franzosa, E. A., Rahnavard, G., Hall, A. B., Vlamakis, H., Stevens, C., Daly, M. J., Xavier, R. J., & Huttenhower, C. (2018) · Genome Medicine · doi:10.1186/s13073-018-0515-8 · Cited by 182 · see citing works
Martínez, I., Maldonado-Gomez, M. X., Gomes-Neto, J. C., Kittana, H., Ding, H., Schmaltz, R., Joglekar, P., Cardona, R. J., Marsteller, N. L., Kembel, S. W., et al. (2018) · eLife · doi:10.7554/elife.36521 · Cited by 199 · see citing works
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 189 · see citing works
Modelling approaches for studying the microbiome
Kumar, M., Ji, B., Zengler, K., & Nielsen, J. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0491-9 · Cited by 190 · see citing works
Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study
Burcham, Z. M., Garneau, N. L., Comstock, S. S., Tucker, R. M., Knight, R., Metcalf, J. L., Scientists, G. O. T. L. C., Miranda, A., Reinhart, B., Meyers, D., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-59016-0 · Cited by 183 · see citing works
Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis
He, Y., Wu, W. H., Wu, S., Zheng, H., Li, P., Sheng, H.-F., Chen, M.-X., Chen, Z., Ji, G., Zheng, Z., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0557-6 · Cited by 187 · see citing works
Gut Dysbiosis and Muscle Aging: Searching for Novel Targets against Sarcopenia
Picca, A., Fanelli, F., Calvani, R., Mulè, G., Pesce, V., Sisto, A., Pantanelli, C., Bernabei, R., Landi, F., & Marzetti, E. (2018) · Mediators of Inflammation · doi:10.1155/2018/7026198 · Cited by 181 · see citing works
“Even for short-term changes in consumption (4 days), animal-based and plant-based diets alter microbial community structure in a specific manner [72].”
BackgroundTemporal and technical variability of human gut metagenomes
Voigt, A. Y., Costea, P. I., Kultima, J. R., Li, S. S., Zeller, G., Sunagawa, S., & Bork, P. (2015) · Genome biology · doi:10.1186/s13059-015-0639-8 · Cited by 177 · see citing works
“(weeks to one year; for example, [8,12,23,24]) and only rarely over long periods (5 and 12 years [9,11]).”
BackgroundTransient invaders can induce shifts between alternative stable states of microbial communities
Amor, D. R., Ratzke, C., & Gore, J. (2020) · Science Advances · doi:10.1126/sciadv.aay8676 · Cited by 184 · see citing works
The oral microbiota – a mechanistic role for systemic diseases
Jia, G., Zhi, A., Lai, P. F. H., Wang, G., Xia, Y., Xiong, Z., Zhang, H., Che, N., & Ai, L. (2018) · BDJ · doi:10.1038/sj.bdj.2018.217 · Cited by 183 · see citing works
A psychology of the human brain-gut-microbiome axis
Allen, A. P., Dinan, T. G., Clarke, G., & Cryan, J. F. (2017) · Social and Personality Psychology Compass · doi:10.1111/spc3.12309 · Cited by 174 · see citing works
“Case evidence has demonstrated profound changes in the microbiota following intercontinental travel, which are reversible upon return (David et al., 2014).”
BackgroundMicrobial Contribution to the Human Metabolome: Implications for Health and Disease
Treuren, W. V., & Dodd, D. (2019) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-020117-043559 · Cited by 176 · see citing works
Hospitalization type and subsequent severe sepsis
Prescott, H. C., Dickson, R. P., Rogers, M. A. M., Langa, K. M., & Iwashyna, T. J. (2015) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201503-0483oc · Cited by 181 · see citing works
Microbial communities as dynamical systems
Gonze, D., Coyte, K. Z., Lahti, L., & Faust, K. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2018.07.004 · Cited by 172 · see citing works
“In panel (c), the trajectory of the gut community of individual B is shown [5], with a Salmonella infection.”
BackgroundAlterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties
Guss, J. D., Horsfield, M. W., Fontenele, F. F., Sandoval, T. N., Luna, M., Apoorva, F., Lima, S. F., Bicalho, R. C., Singh, A. K., Ley, R. E., et al. (2017) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.3114 · Cited by 174 · see citing works
“The gut microbiome is initially obtained at birth((11)) and subsequently shaped by factors such as environment((12)) and diet.((13,14)) Exposure to the gut microbiome is necessary for the proper education and development of the innate and adaptive immune systems.”
BackgroundAnhê, F. F., Varin, T. V., Barz, M. L., Desjardins, Y., Levy, E. H., Roy, D., & Marette, A. (2015) · Current Obesity Reports · doi:10.1007/s13679-015-0172-9 · Cited by 178 · see citing works
Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology
Guo, L., McLean, J. S., Yang, Y., Eckert, R., Kaplan, C. W., Kyme, P., Sheikh, O., Varnum, B., Lux, R., Shi, W., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1506207112 · Cited by 172 · see citing works
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 172 · see citing works
Mapping the ecological networks of microbial communities
Xiao, Y., Angulo, M. T., Friedman, J., Waldor, M. K., Weiss, S. T., & Liu, Y. (2017) · Nature Communications · doi:10.1038/s41467-017-02090-2 · Cited by 169 · see citing works
“First of all, it has been shown that the composition of the human gut microbiome remains stable for months and possibly even years until a major perturbation occurs through either antibiotic administration or drastic dietary changes 52 – 55 .”
The Gut Microbiome in Hypertension
Avery, E. G., Bartolomaeus, H., Maifeld, A., Markó, L., Wiig, H., Wilck, N., Rosshart, S. P., Forslund, S. K., & Müller, D. N. (2021) · Circulation Research · doi:10.1161/circresaha.121.318065 · Cited by 174 · see citing works
- Authors
- David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E., & Alm, E. J.
- Affiliations
- Harvard University (US)
- Qiagen (Denmark) (DK)
- Massachusetts Institute of Technology (US)
- École Polytechnique Fédérale de Lausanne (CH)
- Broad Institute (US)
- Corresponding author
- Alm, Eric J
- Venue
- Genome biology
- Published
- 2014-07-25
- Volume
- 15
- Issue
- 7
- Pages
- R89-R89
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4405912
- OpenAlex
- W2103088074
- Cited by
- 950
- References
- 58
- Citations by year
- 2026: 27 · 2025: 60 · 2024: 74 · 2023: 80 · 2022: 117 · 2021: 95 · 2020: 105 · 2019: 85 · 2018: 85 · 2017: 98 · 2016: 65 · 2015: 52 · 2014: 5
- FWCI
- 30.09
- Type
- journal article
- Language
- en
- Update notices
- correction (2016-05-31)
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Foundation (0821391)
- 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 microbiota, gut microbiota, salivary microbiota, host lifestyle, microbiota dynamics, daily fluctuations, microbial community stability, Firmicutes/Bacteroidetes ratio, gastrointestinal infections, dietary fiber intake, host behavior
- MeSH terms
- Bacteria, Bacterial Infections, Developing Countries, Feces, Humans, Life Style, Longitudinal Studies, Male, Phylogeny, Saliva, Genetic Variation, Sequence Analysis, DNA, Developed Countries, 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
