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Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species
Open accessAbstract
Next-generation sequencing has greatly contributed to an improved ecological understanding of the human gut microbiota. Nevertheless, questions remain regarding the characteristics of this ecosystem and the ecological processes that shape it, and controversy has arisen regarding the stability of the bacterial populations and the existence of a temporal core. In this study, we have characterized the fecal microbial communities of three human individuals over a one-year period by 454 pyrosequencing of 16S rRNA tags in order to investigate the temporal characteristics of the bacterial communities. The findings revealed a temporal core of 33 to 40 species-level Operational Taxonomic Units (OTUs) within subjects. Although these OTUs accounted only for around 12% of the total OTUs detected, they added up to >75% of the total sequences obtained for each individual. In order to determine the capacity of the sequencing and bioinformatic approaches applied during this study to accurately determine the proportion of a core microbiota, we analyzed the fecal microbiota of nine mice with a defined three-member community. This experiment revealed that the sequencing approach inflated the amount of rare OTUs, which introduced a significant degree of artificial variation across samples, and hence reduced the apparent fraction of shared OTUs. However, when assessing the data quantitatively by focusing on dominant lineages, the sequencing approaches deliver an accurate representation of the community. In conclusion, this study revealed that the human fecal microbiota is dominated by around 40 species that maintain persistent populations over the duration of one year. The findings allow conclusions about the ecological factors that shape the community and support the concept of a homeostatic ecosystem controlled largely by deterministic processes. Our analysis of a three-member community revealed that methodological artifacts of OTU-based approaches complicate core calculations, and these limitations have to be considered in the interpretation of microbiome studies.
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“The core gut microbiota in adulthood is relatively stable, but environmental factors have been identified that can shape the gut microbial community (23,35,36).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [35]
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Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 40,207
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
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481
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
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
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
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
Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease
Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., DuGar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., et al. (2011) · Nature · doi:10.1038/nature09922 · Cited by 5,597
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
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. L., Garrity, G. M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,873
MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT
Savage, D. C. (1977) · Annual Review of Microbiology · doi:10.1146/annurev.mi.31.100177.000543 · Cited by 2,436
Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity
Henao-Mejia, J., Elinav, E., Jin, C., Hao, L., Mehal, W. Z., Strowig, T., Thaiss, C. A., Kau, A. L., Eisenbarth, S. C., Jurczak, M. J., et al. (2012) · Nature · doi:10.1038/nature10809 · Cited by 2,435
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
The merging of community ecology and phylogenetic biology
Cavender‐Bares, J., Kozak, K. H., Fine, P. V. A., & Kembel, S. W. (2009) · Ecology Letters · doi:10.1111/j.1461-0248.2009.01314.x · Cited by 2,321
The role of the gut microbiota in nutrition and health
Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.156 · Cited by 2,283
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112
Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5
Vijay-Kumar, M., Aitken, J. D., Carvalho, F. A., Cullender, T. C., Mwangi, S., Srinivasan, S., Sitaraman, S. V., Knight, R., Ley, R. E., & Gewirtz, A. T. (2010) · Science · doi:10.1126/science.1179721 · Cited by 2,068
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
Quantifying the roles of immigration and chance in shaping prokaryote community structure
Sloan, W. T., Lunn, M., Woodcock, S., Head, I. M., Nee, S., & Curtis, T. P. (2005) · Environmental Microbiology · doi:10.1111/j.1462-2920.2005.00956.x · Cited by 1,903
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
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
Microbes in Gastrointestinal Health and Disease
Neish, A. S. (2008) · Gastroenterology · doi:10.1053/j.gastro.2008.10.080 · Cited by 1,423
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
Kunin, V., Engelbrektson, A., Ochman, H., & Hugenholtz, P. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02051.x · Cited by 1,280
Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00493.x · Cited by 1,255
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
Long-term impacts of antibiotic exposure on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2010) · Microbiology · doi:10.1099/mic.0.040618-0 · Cited by 1,067
Willing, B. P., Dicksved, J., Halfvarson, J., Andersson, A. F., Lucio, M., Zheng, Z., Järnerot, G., Tysk, C., Jansson, J. K., & Engstrand, L. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.08.049 · Cited by 1,032
Towards the human intestinal microbiota phylogenetic core
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J., Ugarte, E., Muñoz‐Tamayo, R., Paslier, D. L. E., Nalin, R., et al. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01982.x · Cited by 927
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907
The human gut microbiome: ecology and recent evolutionary changes
Walter, J., & Ley, R. (2011) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090110-102830 · Cited by 720
Self-citationPhylogenetic analysis of community assembly and structure over space and time
Emerson, B. C., & Gillespie, R. G. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.07.005 · Cited by 709
Tannock, G. W., Munro, K., Harmsen, H. J. M., Welling, G. W., Smart, J., & Gopal, P. K. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.6.2578-2588.2000 · Cited by 671
Martínez, I., Kim, J., Duffy, P. R., Schlegel, V. L., & Walter, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015046 · Cited by 645
Self-citationGut microbiome composition is linked to whole grain-induced immunological improvements
Martínez, I., Lattimer, J. M., Hubach, K. L., Case, J. A., Yang, J., Weber, C. G., Louk, J. A., Rose, D. J., Kyureghian, G., Peterson, D. A., et al. (2013) · The ISME Journal · doi:10.1038/ismej.2012.104 · Cited by 614
Self-citationNEUTRAL THEORY AND THE EVOLUTION OF ECOLOGICAL EQUIVALENCE
Hubbell, S. P. (2006) · Ecology · doi:10.1890/0012-9658(2006)87[1387:ntateo]2.0.co;2 · Cited by 603
Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities
Ochman, H., Worobey, M., Kuo, C., Ndjango, J.-B. N., Peeters, M., Hahn, B. H., & Hugenholtz, P. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000546 · Cited by 511
Assembly of the human intestinal microbiota
Dethlefsen, L., Eckburg, P. B., Bik, E. M., & Relman, D. A. (2006) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.06.013 · Cited by 509
From Structure to Function: the Ecology of Host-Associated Microbial Communities
Robinson, C. J., Bohannan, B. J. M., & Young, V. B. (2010) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00014-10 · Cited by 473
Role of the intestinal microbiome in health and disease: from correlation to causation
de Vos, W. M., & de Vos, E. A. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00505.x · Cited by 440
Mechanisms controlling pathogen colonization of the gut
Stecher, B., & Hardt, W. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.10.003 · Cited by 431
Martínez, I., Wallace, G., Zhang, C., Legge, R. M., Benson, A. K., Carr, T. P., Moriyama, E. N., & Walter, J. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00380-09 · Cited by 360
Self-citationMcFall‐Ngai, M. (2007) · Nature · doi:10.1038/445153a · Cited by 345
Walter, J., Britton, R. A., & Roos, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000099107 · Cited by 341
Self-citationJalanka-Tuovinen, J., Salonen, A., Nikkilä, J., Immonen, O., Kekkonen, R., Lahti, L., Palva, A., & de Vos, W. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023035 · Cited by 340
Scanlan, P. D., Shanahan, F., O'Mahony, C., & Marchesi, J. R. (2006) · Journal of Clinical Microbiology · doi:10.1128/jcm.00312-06 · Cited by 330
Davis, L. M. G., Martínez, I., Walter, J., Goin, C., & Hutkins, R. W. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025200 · Cited by 329
Self-citationThe Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri
Frese, S. A., Benson, A. K., Tannock, G. W., Loach, D. M., Kim, J., Zhang, M., Oh, P. L., Heng, N. C. K., Patil, P. B., Juge, N., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001314 · Cited by 312
Self-citationMolecular analysis of the composition of the bifidobacterial and lactobacillus microflora of humans
McCartney, A. L., Wenzhi, W., & Tannock, G. W. (1996) · Applied and Environmental Microbiology · doi:10.1128/aem.62.12.4608-4613.1996 · Cited by 294
Long‐term monitoring of the human intestinal microbiota composition
Rajilić-Stojanović, M. D., Heilig, H. G. H. J., Tims, S., Zoetendal, E. G., & de Vos, W. M. (2012) · Environmental Microbiology · doi:10.1111/1462-2920.12023 · Cited by 286
The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection
Schlüter, J., & Foster, K. R. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001424 · Cited by 237
Davis, L. M. G., Martínez, I., Walter, J., & Hutkins, R. W. (2010) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2010.10.007 · Cited by 223
Self-citationVanhoutte, T., Huys, G. R. B., Brandt, E. D., & Swings, J. (2004) · FEMS Microbiology Ecology · doi:10.1016/j.femsec.2004.03.001 · Cited by 215
Degnan, P. H., Pusey, A. E., Lonsdorf, E. V., Goodall, J. R., Wroblewski, E. E., Wilson, M. L., Rudicell, R. S., Hahn, B. H., & Ochman, H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110994109 · Cited by 200
Stabilization of the murine gut microbiome following weaning
Schloss, P. D., Schubert, A. M., Zackular, J. P., Iverson, K. D., Young, V. B., & Petrosino, J. F. (2012) · Gut Microbes · doi:10.4161/gmic.21008 · Cited by 154
Jeraldo, P., Sipos, M., Chia, N., Brulc, J. M., Dhillon, A. S., Konkel, M. E., Larson, C. L., Nelson, K. E., Qu, A., Schook, L. B., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1206721109 · Cited by 149
Savage, D. C. (1972) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/25.12.1372 · Cited by 103
From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome
Fierer, N., Ferrenberg, S. M., Flores, G. E., González, A., Kueneman, J. G., Legg, T. M., Lynch, R. C., McDonald, D. T., Mihaljevic, J. R., O’Neill, S., et al. (2012) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110411-160307 · Cited by 89
A rendezvous with our microbes
Gordon, J. I., & Klaenhammer, T. R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1101958108 · Cited by 58
Predominant Gram-Positive Bacteria in Human Feces: Numbers, Variety, and Persistence
Gossling, J., & Slack, J. M. (1974) · Infection and Immunity · doi:10.1128/iai.9.4.719-729.1974 · Cited by 48
Bayesian estimation of bacterial community composition from 454 sequencing data
Cheng, L., Walker, A. W., & Corander, J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks227 · Cited by 30
Johnson, J. L. (1980) · Applied and Environmental Microbiology · doi:10.1128/aem.39.2.407-413.1980 · Cited by 15
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Metadata
- Authors
- Martínez, I., Muller, C. E., & Walter, J.
- Affiliations
- University of Nebraska–Lincoln (US)
- Corresponding author
- Walter, Jens
- ORCID
- Walter, Jens
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-07-16
- Volume
- 8
- Issue
- 7
- Pages
- e69621
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3712949
- OpenAlex
- W1997884922
- Cited by
- 181
- References
- 62
- Citations by year
- 2026: 2 · 2025: 9 · 2024: 9 · 2023: 10 · 2022: 14 · 2021: 20 · 2020: 17 · 2019: 8 · 2018: 14 · 2017: 20 · 2016: 17 · 2015: 26 · 2014: 11 · 2013: 4
- FWCI
- 8.67
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Lincoln (University of Nebraska) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- 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 gut microbiome, fecal microbiota, temporal stability, core microbiome, operational taxonomic units, sequencing artifacts, rare OTUs, 16S rRNA, deterministic community assembly
- MeSH terms
- Adult, Bacteria, Feces, Female, Humans, RNA, Ribosomal, 16S, Young Adult
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