Cited by 1,138Gut microbiota and healthMicrobial Community Ecology and PhysiologyOral microbiology and periodontitis research

The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.

Moving pictures of the human microbiome

Open access

Caporaso, J Gregory, Lauber, Christian L, Costello, Elizabeth K, Berg-Lyons, Donna, Gonzalez, Antonio, Stombaugh, Jesse, Knights, Dan, Gajer, Pawel, Ravel, Jacques, Fierer, Noah, Gordon, Jeffrey I, Knight, Rob·2011·Genome Biology

DOI 10.1186/gb-2011-12-5-r50PMC PMC3271711

Open this paper in CoChat — free account Open PDF

Abstract

BACKGROUND: Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn’s disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints. RESULTS: We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual’s microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members. CONCLUSIONS: DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.

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

Crossref · 10.1186/gb-2011-12-5-r50

Cites

21 of 21 references verified0 citation errors · 0 not checkable

Statistics

Figure 1 Principal coordinates analysis of unweighted UniFrac distances between samples. (a) Costello et al. [6] samples. (b) M3, F4 time series samples. (c) M3, F4 time series, PC1 versus time (days). Panels (a,b) and (c) show two independent principal coordinates analyses. To compare the Costello et al. 454 data (a) with the time series Illumina data (b), these data were generated in a single principal coordinates analysis of UniFrac distances at 500 sequences per sample. Panel (c) does not contain the 454 data, so makes use of the increased sampling depth possible on Illumina (evenly sampled to 5,000 sequences per sample for UniFrac calculations).CC BY · PubMed Central

Figure 2 Temporal core microbiome. Fraction of species-level operational taxonomic units (OTUs) composing the core microbiota by number of samples in which an OTU must be present to be considered part of the core.CC BY · PubMed Central

Figure 3 Community membership. Community membership summary for all OTUs in (a) M3 gut, (b) F4 gut, (c) M3 tongue, (d) F4 tongue, (e) M3 left palm, (f) F4 left palm, (g) M3 right palm, and (h) F4 right palm. Points are OTUs colored by their median relative abundance computed over all samples where they occur, and pie charts summarize the class-level taxa observed as persistent and transient OTUs.CC BY · PubMed Central

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
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
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
Global 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 9,944
Self-citation
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913
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
Self-citation
Vaginal microbiome of reproductive-age women
Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002611107 · Cited by 4,254
Self-citation
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
Self-citation
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 · cited 2×
“…together, our observations paint a picture of a human microbiome that is highly variable over time (Figures 2 and 3; Additional files 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15), but from which stable patterns of similarities and differences among body habitats and individuals emerge (Figure…”
BackgroundSelf-citation
Development of the Human Infant Intestinal Microbiota
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050177 · Cited by 2,877

Show all 21 references

Sorted by citations

Items 401–500 of 1,000

Impact of diesel and biodiesel contamination on soil microbial community activity and structure
Mitter, E. K., Germida, J. J., & de Freitas, J. R. (2021) · Scientific Reports · doi:10.1038/s41598-021-89637-y · Cited by 53
Intestinal Microbiota and the Innate Immune System – A Crosstalk in Crohn’s Disease Pathogenesis
Haag, L.-M., & Siegmund, B. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00489 · Cited by 52
[Progress in the knowledge of the intestinal human microbiota].
Robles, V., & Guarner, F. (2013) · PubMed · doi:10.3305/nh.2013.28.3.6601 · Cited by 61
Dietary Habits of 2- to 9-Year-Old American Children Are Associated with Gut Microbiome Composition
Herman, D. R., Rhoades, N., Mercado, J., Argueta, P., Lopez, U., & Flores, G. E. (2020) · Journal of the Academy of Nutrition and Dietetics · doi:10.1016/j.jand.2019.07.024 · Cited by 50
Parallel-META: efficient metagenomic data analysis based on high-performance computation
Su, X., Xu, J., & Ning, K. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-s1-s16 · Cited by 51
Novel therapeutic strategies to counterPseudomonas aeruginosainfections
Fothergill, J. L., Winstanley, C., & James, C. E. (2012) · Expert Review of Anti-infective Therapy · doi:10.1586/eri.11.168 · Cited by 51
Methods in microbiome research: Past, present, and future
Gotschlich, E. C., Colbert, R. A., & Gill, T. (2019) · Best Practice & Research Clinical Rheumatology · doi:10.1016/j.berh.2020.101498 · Cited by 58
The chemistry of gut microbiome in health and diseases
Lau, A., Tan, L. T., Mutalib, N. A., Wong, S. H., Letchumanan, V., & Lee, L. (2021) · Progress In Microbes & Molecular Biology · doi:10.36877/pmmb.a0000175 · Cited by 55
Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Horz, H. (2015) · Life · doi:10.3390/life5021333 · Cited by 53
Pancreas–Microbiota Cross Talk in Health and Disease
Adolph, T. E., Mayr, L., Grabherr, F., Schwärzler, J., & Tilg, H. (2019) · Annual Review of Nutrition · doi:10.1146/annurev-nutr-082018-124306 · Cited by 48
Diversity of nasal microbiota and its interaction with surface microbiota among residents in healthcare institutes
Chen, C., Liou, M., Lee, C., Chang, M.-C., Kuo, H., & Chang, T. (2019) · Scientific Reports · doi:10.1038/s41598-019-42548-5 · Cited by 48
The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study
Figueiredo, G., Gomes, M., Covas, C., Mendo, S., & Caetano, T. (2021) · Microbial Ecology · doi:10.1007/s00248-021-01762-3 · Cited by 49
Gut Microbiome as a Target of Intervention in Inflammatory Bowel Disease Pathogenesis and Therapy
Hetta, ‏. F., Ramadan, Y. N., Alharbi, A. A., Alsharif, S. M., Alkindy, T. T., Alkhamali, A., Albalawi, A. S., & El‐Amin, H. (2024) · Immuno · doi:10.3390/immuno4040026 · Cited by 54
Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities
Parks, D. H., & Beiko, R. G. (2012) · The ISME Journal · doi:10.1038/ismej.2012.88 · Cited by 51
Novel Microbiome-Based Therapeutics for Chronic Rhinosinusitis
Cope, E. K., & Lynch, S. V. (2015) · Current Allergy and Asthma Reports · doi:10.1007/s11882-014-0504-y · Cited by 51
Social-Stress-Responsive Microbiota Induces Stimulation of Self-Reactive Effector T Helper Cells
Werbner, M., Barsheshet, Y., Werbner, N., Zigdon, M., Averbuch, I., Oren, Z., Brant, B., Elliott, E., Gelberg, S., Titelbaum, M., et al. (2019) · mSystems · doi:10.1128/msystems.00292-18 · Cited by 49
Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota
Aljahdali, N. H., Sanad, Y. M., Han, J., & Foley, S. L. (2020) · BMC Microbiology · doi:10.1186/s12866-020-02008-x · Cited by 52
Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping
Welch, J. L. M., Utter, D. R., Rossetti, B. J., Welch, D. B. M., Eren, A. M., & Borisy, G. G. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00568 · Cited by 47
Human microbiome restoration and safety
Daliri, E. B., Tango, C. N., Lee, B. H., & Oh, D. (2018) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2018.05.002 · Cited by 50
The gut microbiome of freshwater Unionidae mussels is determined by host species and is selectively retained from filtered seston
Weingarten, E. A., Atkinson, C. L., & Jackson, C. R. (2019) · PLoS ONE · doi:10.1371/journal.pone.0224796 · Cited by 51
A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome
Zaoli, S., & Grilli, J. (2021) · Science Advances · doi:10.1126/sciadv.abj2882 · Cited by 45
Philornis downsi (Diptera: Muscidae), an Avian Nest Parasite Invasive to the Galapagos Islands, in Mainland Ecuador
Bulgarella, M., Quiroga, M. A., Vera, G. A. B., Dregni, J., Cunninghame, F., Munoz, D. A. M., Monje, L. D., Causton, C. E., & Heimpel, G. E. (2015) · Annals of the Entomological Society of America · doi:10.1093/aesa/sav026 · Cited by 47
Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization
Cai, Y., Gu, H., & Kenney, T. (2017) · Microbiome · doi:10.1186/s40168-017-0323-1 · Cited by 46
The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome
Kiely, C. J., Pavli, P., & O'Brien, C. L. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1448742 · Cited by 49
Population Dynamics in a Changing Environment: Random versus Periodic Switching
Taitelbaum, A., West, R., Assaf, M., & Mobilia, M. (2020) · Physical Review Letters · doi:10.1103/physrevlett.125.048105 · Cited by 47
Oral Microbiota Transplant: A Potential New Therapy for Oral Diseases
Nascimento, M. M. (2017) · Journal of the California Dental Association · doi:10.1080/19424396.2017.12222506 · Cited by 47
Visualizing time-related data in biology, a review
Secrier, M., & Schneider, R. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt021 · Cited by 46
Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions
López, C. D., Vidaki, A., & Kayser, M. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102627 · Cited by 49
Effects of hyperosmotic stress on the intestinal microbiota, transcriptome, and immune function of mandarin fish (Siniperca chuatsi)
Ouyang, H., Deng, N., Xu, J., Huang, J., Han, C., Liu, D., Liu, S., Yan, B., Han, L., Li, S., et al. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2022.738901 · Cited by 43
Modeling microbial community structure and functional diversity across time and space
Larsen, P. E., Gibbons, S. M., & Gilbert, J. A. (2012) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2012.02588.x · Cited by 47
Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Contreras, A. V., Cocom-Chan, B., Hernández‐Montes, G., Portillo-Bobadilla, T., & Reséndis-Antonio, O. (2016) · Frontiers in Physiology · doi:10.3389/fphys.2016.00606 · Cited by 49
Toward an Intensive Longitudinal Understanding of Activated Sludge Bacterial Assembly and Dynamics
Jiang, X., Ye, L., Ju, F., Wang, Y., & Zhang, T. (2018) · Environmental Science & Technology · doi:10.1021/acs.est.7b05579 · Cited by 45
Societal collapse or transformation, and resilience
Pearson, L. J., & Pearson, C. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207552109 · Cited by 45
The Role of Fatty Acid Metabolites in Vaginal Health and Disease: Application to Candidiasis
Baldewijns, S., Sillen, M., Palmans, I., Vandecruys, P., Van Dijck, P., & Demuyser, L. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.705779 · Cited by 44
Synergistic anti-inflammatory effect of gut microbiota and lithocholic acid on liver fibrosis
Shao, J., Ge, T., Tang, C., Wang, G., Pang, L., & Chen, Z. (2022) · Inflammation Research · doi:10.1007/s00011-022-01629-4 · Cited by 47
Lactiplantibacillus plantarum ZJ316 Reduces Helicobacter pylori Adhesion and Inflammation by Inhibiting the Expression of Adhesin and Urease Genes
Wu, S., Xu, Y. Y., Chen, Z., Chen, Y., Wei, F., Xia, C., Zhou, Q., Li, P., & Gu, Q. (2023) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202300241 · Cited by 44
Phylogenetics and the Human Microbiome
Matsen, F. A., IV (2014) · Systematic Biology · doi:10.1093/sysbio/syu053 · Cited by 47
Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere
Newton, R., & Shade, A. L. (2016) · Aquatic Microbial Ecology · doi:10.3354/ame01801 · Cited by 44
Host genetics and microbiome associations through the lens of genome wide association studies
Weissbrod, O., Rothschild, D., Barkan, E., & Segal, E. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2018.05.003 · Cited by 45
Detecting interaction networks in the human microbiome with conditional Granger causality
Mainali, K. P., Bewick, S. A., Vecchio-Pagán, B., Karig, D., & Fagan, W. F. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007037 · Cited by 43
Diversity and Biogeography of Human Oral Saliva Microbial Communities Revealed by the Earth Microbiome Project
Wang, J., Feng, J., Zhu, Y., Li, D., Wang, J., & Chi, W. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.931065 · Cited by 46
Replenishing our defensive microbes
Ursell, L. K., Treuren, W. V., Metcalf, J. L., Pirrung, M., Gewirtz, A. T., & Knight, R. D. (2013) · BioEssays · doi:10.1002/bies.201300018 · Cited by 42
Self-citation
Dynamic efficiency of the human intestinal microbiota
Candela, M., Biagi, E., Turroni, S., Maccaferri, S., Figini, P., & Brigidi, P. (2013) · Critical Reviews in Microbiology · doi:10.3109/1040841x.2013.813900 · Cited by 45
Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations
Kuntal, B. K., Gadgil, C. J., & Mande, S. S. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00288 · Cited by 43
Dietary Patterns Impact Temporal Dynamics of Fecal Microbiota Composition in Children With Autism Spectrum Disorder
Berding, K., & Donovan, S. M. (2020) · Frontiers in Nutrition · doi:10.3389/fnut.2019.00193 · Cited by 45
Microbiotyping the Sinonasal Microbiome
Bassiouni, A., Paramasivan, S., Shiffer, A., Dillon, M. R., Cope, E. K., Cooksley, C. M., Ramezanpour, M., Moraitis, S., Ali, M. J., Bleier, B. S., et al. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00137 · Cited by 44
Self-citation
Implications of the Human Microbiome Project for Epidemiology
Foxman, B., & Rosenthal, M. (2013) · American Journal of Epidemiology · doi:10.1093/aje/kws449 · Cited by 43
Gut microbiota, cannabinoid system and neuroimmune interactions: New perspectives in multiple sclerosis
Mestre, L., Carrillo-Salinas, F. J., Mecha, M., Feliú, A., & Guaza, C. (2018) · Biochemical Pharmacology · doi:10.1016/j.bcp.2018.08.037 · Cited by 43
Effects of phlorotannin and polysaccharide fractions of brown seaweed Silvetia compressa on human gut microbiota composition using an in vitro colonic model
Vázquez-Rodríguez, B., Santos‐Zea, L., Heredia‐Olea, E., Acevedo-Pacheco, L., Santacruz, A., Gutierrez-Uribe, J. A., & Cruz‐Suárez, L. E. (2021) · Journal of Functional Foods · doi:10.1016/j.jff.2021.104596 · Cited by 41
Dietary Supplementation with Vitamin D, Fish Oil or Resveratrol Modulates the Gut Microbiome in Inflammatory Bowel Disease
Wellington, V. N. A., Sundaram, V. L., Singh, S., & Sundaram, U. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010206 · Cited by 43
Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease
Kubinski, R., Djamen-Kepaou, J.-Y., Zhanabaev, T., Hernández-García, Á., Bauer, S., Hildebrand, F., Korcsmáros, T., Karam, S., Jantchou, P., Kafi, K., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.784397 · Cited by 40
Expanding the boundaries of local similarity analysis
Durno, W. E., Hanson, N. W., Konwar, K. M., & Hallam, S. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-s1-s3 · Cited by 41
An in vitro study to assess the impact of tetracycline on the human intestinal microbiome
Jung, J. Y., Ahn, Y., Khare, S., Gokulan, K., Piñeiro, S. A., & Cerniglia, C. E. (2017) · Anaerobe · doi:10.1016/j.anaerobe.2017.12.011 · Cited by 41
Temporal 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
Methodological Considerations in Longitudinal Analyses of Microbiome Data: A Comprehensive Review
Lyu, R., Qu, Y., Divaris, K., & Wu, D. (2023) · Genes · doi:10.3390/genes15010051 · Cited by 41
A designed synthetic microbiota provides insight to community function in Clostridioides difficile resistance
Tian, S., Kim, M. S., Zhao, J., Heber, K., Hao, F., Koslicki, D., Tian, S., Singh, V., Patterson, A. D., & Bisanz, J. E. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.02.007 · Cited by 44
The intestinal microbiome in human disease and how it relates to arthritis and spondyloarthritis
Costello, M., Robinson, P. C., Benham, H., & Brown, M. A. (2015) · Best Practice & Research Clinical Rheumatology · doi:10.1016/j.berh.2015.08.001 · Cited by 44
Host-emitted amino acid cues regulate bacterial chemokinesis to enhance colonization
Robinson, C. D., Sweeney, E. G., Ngo, J. S., Ma, E., Perkins, A., Smith, T. J., Fernandez, N. L., Waters, C. M., Remington, S. J., Bohannan, B. J. M., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.003 · Cited by 38
The Gut Microbiome and Substance Use Disorder
Russell, J. T., Zhou, Y., Weinstock, G. M., & Bubier, J. A. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.725500 · Cited by 40
Fecal Microbiota Transplants for Inflammatory Bowel Disease Treatment: Synthetic- and Engineered Communities-Based Microbiota Transplants Are the Future
Khan, R., Roy, N., Ali, H., & Naeem, M. (2022) · Gastroenterology Research and Practice · doi:10.1155/2022/9999925 · Cited by 41
Microbial–immune cross‐talk and regulation of the immune system
Cahenzli, J., Balmer, M. L., & McCoy, K. D. (2012) · Immunology · doi:10.1111/j.1365-2567.2012.03624.x · Cited by 44
Using convolutional neural networks to explore the microbiome
Reiman, D. J., Metwally, A. A., & Dai, Y. D. (2017) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/embc.2017.8037799 · Cited by 40
Probiotics
Mizock, B. A. (2015) · Disease-a-Month · doi:10.1016/j.disamonth.2015.03.011 · Cited by 42
Emerging Role of the Gut Microbiome in Irritable Bowel Syndrome
Singh, P., & Lembo, A. J. (2021) · Gastroenterology Clinics of North America · doi:10.1016/j.gtc.2021.03.003 · Cited by 39
The Microbiome as a Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota
Murphy, K., Le, S. M., Wilson, A. E., & Warner, D. A. (2023) · Integrative and Comparative Biology · doi:10.1093/icb/icad031 · Cited by 40
High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion
Zhang, Z., Li, D., Refaey, M. M., & Xu, W. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01531 · Cited by 42
Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels
Zysset‐Burri, D. C., Keller, I., Berger, L., Neyer, P. J., Steuer, C., Wolf, S., & Zinkernagel, M. S. (2019) · Scientific Reports · doi:10.1038/s41598-019-51698-5 · Cited by 38
Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model
Taylor, M. N., & Vega, N. M. (2021) · mSystems · doi:10.1128/msystems.00608-20 · Cited by 37
Assessing time dependent changes in microbial composition of biological crime scene traces using microbial RNA markers
Salzmann, A. P., Arora, N., Russo, G., Kreutzer, S., Snipen, L. G., & Haas, C. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102537 · Cited by 39
Mussel Mass Mortality and the Microbiome: Evidence for Shifts in the Bacterial Microbiome of a Declining Freshwater Bivalve
Richard, J. C., Campbell, L. J., Leis, E. M., Agbalog, R. E., Dunn, C. D., Waller, D. L., Knowles, S., Putnam, J., & Goldberg, T. L. (2021) · Microorganisms · doi:10.3390/microorganisms9091976 · Cited by 38
Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations
Marsh, K. J., Raulo, A. M., Brouard, M., Troitsky, T. S., English, H. M., Allen, B. E., Raval, R., Venkatesan, S., Pedersen, A. B., Webster, J. P., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.809735 · Cited by 39
A core microbiome associated with the peritoneal tumors of pseudomyxoma peritonei
Gilbreath, J. J., Semino‐Mora, C., Friedline, C. J., Liu, H., Bodi, K. L., McAvoy, T. J., Francis, J., Nieroda, C. A., Sardi, A., Dubois, A., et al. (2013) · Orphanet Journal of Rare Diseases · doi:10.1186/1750-1172-8-105 · Cited by 38
Antagonistics of Lactobacillus plantarum ZDY2013 against Helicobacter pylori SS1 and its infection in vitro in human gastric epithelial AGS cells
Zhao, K., Xie, Q., Xu, D., Guo, Y., Tao, X., Wei, H., & Wan, C. (2018) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2018.04.003 · Cited by 37
Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics
Cardona, C., Lax, S. M., Larsen, P. E., Stephens, B., Hampton‐Marcell, J., Edwardson, C. F., Henry, C., Bonn, B. V., & Gilbert, J. A. (2018) · mSystems · doi:10.1128/msystems.00052-18 · Cited by 37
Xenobiotics and the Human Gut Microbiome: Metatranscriptomics Reveal the Active Players
Ursell, L. K., & Knight, R. D. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.02.013 · Cited by 37
Self-citation
Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection
Grier, A., Gill, A. L., Kessler, H. A., Corbett, A. M., Bandyopadhyay, S., Java, J., Holden‐Wiltse, J., Falsey, A. R., Topham, D. J., Mariani, T. J., et al. (2020) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiaa577 · Cited by 39
Predicting microbiomes through a deep latent space
García-Jiménez, B., Muñoz, J., Cabello, S., Medina, J., & Wilkinson, M. D. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa971 · Cited by 38
Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research
Shamarina, D., Stoyantcheva, I., Mason, C. E., Bibby, K. J., & Elhaik, E. (2017) · Microbiome · doi:10.1186/s40168-017-0349-4 · Cited by 36
New insight into the gut microbiome through metagenomics
Nielsen, J., & Ji, B. (2015) · Advances in Genomics and Genetics · doi:10.2147/agg.s57215 · Cited by 36
Temporal Variability of Oral Microbiota over 10 Months and the Implications for Future Epidemiologic Studies
Vogtmann, E., Hua, X., Zhou, L. F., Wan, Y., Suman, S., Zhu, B., Dagnall, C. L., Hutchinson, A. A., Jones, K. M., Hicks, B. D., et al. (2018) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-17-1004 · Cited by 36
Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations
Vet, S., de Buyl, S., Faust, K., Danckaert, J., Gonze, D., & Gelens, L. (2018) · PLoS ONE · doi:10.1371/journal.pone.0197462 · Cited by 35
Akkermansia and Microbial Degradation of Mucus in Cats and Dogs: Implications to the Growing Worldwide Epidemic of Pet Obesity
García-Mazcorro, J. F., Minamoto, Y., Kawas, J. R., Suchodolski, J. S., & de Vos, W. M. (2020) · Veterinary Sciences · doi:10.3390/vetsci7020044 · Cited by 35
Gut microbiota and artificial intelligence approaches: A scoping review
Iadanza, E., Fabbri, R., Bašić-Čičak, D., Amedei, A., & Telalović, J. H. (2020) · Health and Technology · doi:10.1007/s12553-020-00486-7 · Cited by 40
Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy
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
The respiratory microbiota during health and disease: a paediatric perspective
Koppena, I. J. N., Boscha, A. A. T. M., Sandersa, E. A. M., van Houtenb, M. A., & Bogaert, D. (2015) · Pneumonia · doi:10.15172/pneu.2015.6/656 · Cited by 37
First insights into the living groundwater mycobiome of the terrestrial biogeosphere
Nawaz, A., Purahong, W., Lehmann, R. G., Herrmann, M., Totsche, K. U., Küsel, K., Wubet, T., & Buscot, F. (2018) · Water Research · doi:10.1016/j.watres.2018.07.067 · Cited by 38
Gut microbiota in patients with prostate cancer: a systematic review and meta-analysis
Huang, H., Liu, Y., Zhi, W., Chen, C., Wang, C., Li, H., & Yang, X. (2024) · BMC Cancer · doi:10.1186/s12885-024-12018-x · Cited by 39
Imbalance in gut microbial interactions as a marker of health and disease
López, R. C., Bonachela, J. A., Dominguez-Bello, M. G., Manhart, M., Levin, S. A., Blaser, M. J., & Muñoz, M. A. (2026) · Science · doi:10.1126/science.ady1729 · Cited by 40
A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome
Darcy, J. L., Washburne, A., Robeson, M. S., Prest, T. L., Schmidt, S. K., & Lozupone, C. (2020) · The ISME Journal · doi:10.1038/s41396-020-0613-7 · Cited by 34
Recurrent Clostridium difficile infection and the microbiome
Almeida, R., Gerbaba, T. K., & Petrof, E. O. (2015) · Journal of Gastroenterology · doi:10.1007/s00535-015-1099-3 · Cited by 34
Papel de la microbiota intestinal en el desarrollo de la esclerosis múltiple
Castillo-Álvarez, F., & Marzo-Sola, M. E. (2015) · Neurología · doi:10.1016/j.nrl.2015.07.005 · Cited by 34
Molecular ecological tools to decipher the role of our microbial mass in obesity
Hermes, G. D. A., Zoetendal, E. G., & Smidt, H. (2014) · Beneficial Microbes · doi:10.3920/bm2014.0016 · Cited by 34
The human metagenome: our other genome?
Brüls, T., & Weissenbach, J. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr353 · Cited by 34
Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure
Zeamer, A. L., Salive, M.-C., An, X., Beaudoin, F. L., House, S. L., Stevens, J. S., Zeng, D., Neylan, T. C., Clifford, G. D., Linnstaedt, S. D., et al. (2023) · Translational Psychiatry · doi:10.1038/s41398-023-02643-8 · Cited by 34
The role of gut microbiota in human metabolism and inflammatory diseases: a focus on elderly individuals
Khaledi, M., Poureslamfar, B., Alsaab, H. O., Tafaghodi, S., Hjazi, A. M., Singh, R., Alawadi, A. H., Alsaalamy, A. H., Qasim, Q. A., & Sameni, F. (2024) · Annals of Microbiology · doi:10.1186/s13213-023-01744-5 · Cited by 50
Personalized microbiome dynamics – Cytometric fingerprints for routine diagnostics
Koch, C., & Müller, S. (2017) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2017.06.005 · Cited by 31
Clinician Guide to Microbiome Testing
Staley, C. M., Kaiser, T., & Khoruts, A. (2018) · Digestive Diseases and Sciences · doi:10.1007/s10620-018-5299-6 · Cited by 39
An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data
Li, C., Chng, K. R., Kwah, J. S., Av‐Shalom, T. V., Tucker‐Kellogg, L., & Nagarajan, N. (2019) · Microbiome · doi:10.1186/s40168-019-0729-z · Cited by 32
Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms
VanInsberghe, D., Elsherbini, J., Varian, B. J., Poutahidis, T., Erdman, S. E., & Polz, M. F. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0668-2 · Cited by 31
Alterations of Gut Microbiota by Overnutrition Impact Gluconeogenic Gene Expression and Insulin Signaling
He, L. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22042121 · Cited by 35

Authors: Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., Gordon, J. I., & Knight, R.
Affiliations: University of Colorado Boulder (US)
Cooperative Institute for Research in Environmental Sciences (US)
Stanford Medicine (US)
University of Maryland, Baltimore (US)
Washington University in St. Louis (US)
Howard Hughes Medical Institute (US)
Corresponding author: Knight, Rob
ORCID: Caporaso, J Gregory
Lauber, Christian L
Costello, Elizabeth K
Stombaugh, Jesse
Knights, Dan
Ravel, Jacques
Fierer, Noah
Gordon, Jeffrey I
Knight, Rob
Venue: Genome Biology
Publisher: Springer Science and Business Media LLC
Published: 2011-05-30
Volume: 12
Issue: 5
Pages: R50-R50
ISSN: 1465-6906 (ISSN-L)
1474-760X
DOI: 10.1186/gb-2011-12-5-r50
PMC: PMC3271711
OpenAlex: W2126218947
Cited by: 1,138
References: 21
Citations by year: 2026: 25 · 2025: 50 · 2024: 69 · 2023: 80 · 2022: 68 · 2021: 88 · 2020: 102 · 2019: 93 · 2018: 83 · 2017: 84 · 2016: 78 · 2015: 79 · 2014: 78 · 2013: 82 · 2012: 61
FWCI: 30.93
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/2.0/ (tdm)
creativecommons.org/licenses/by/2.0/ (vor)
Locations: Genome biology (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion)
Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
Funders: Howard Hughes Medical Institute
Bill and Melinda Gates Foundation
Crohn's and Colitis Foundation of America
Amazon Web Services
Crohn's and Colitis Foundation
National Institutes of Health (5u01ai070921-07, DK078669)
National Human Genome Research Institute (R01HG004872, HG004872, HG004872-02S1)
National Institute of Allergy and Infectious Diseases (AI070921, AI083264, UH2AI083264)
National Institute of Diabetes and Digestive and Kidney Diseases (DK078669, P01DK078669)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Keywords: human microbiome, temporal variation, core microbiome, microbial community dynamics, body site differences, interindividual variability, microbiome sequencing
MeSH terms: Bacteria, Computer Simulation, Humans, Obesity, Organ Specificity, RNA, Ribosomal, 16S, Seasons, Time Factors, Inflammatory Bowel Diseases, Genomics, Gastrointestinal Tract, Metagenome, High-Throughput Nucleotide Sequencing

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

Moving pictures of the human microbiome

Abstract

Overview

Integrity signals

Figures

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks