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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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![Figure 1 Experimental design. 33 (two subjects) and 32 (one subject) samples were collected in a 56-week time period from human subjects that participated in two dietary trials testing the effect of resistant starches and GOS on the fecal microbiota [31], [32]. Fecal samples were collected weekly throughout both trials (17 in Trial 1 and 16 in trial 2), and the two trials were interspaced by a 24-week period without sampling.](/paper-figures/f1888a89c00745b8bdb735aa8b083df3/long-term-temporal-analysis-of-the-human-fecal-microbiota-revealed-a-stable-core-figure-1.jpg)
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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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Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease
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Gut biogeography of the bacterial microbiota
Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro3552 · Cited by 2,535
How informative is the mouse for human gut microbiota research?
Nguyen, T. L. A., Vieira-Silva, S., Liston, A., & Raes, J. (2015) · Disease Models & Mechanisms · doi:10.1242/dmm.017400 · Cited by 1,334
“Some xenobiotics, such as antibiotics, can also strongly affect the gut microbiota composition and function (Maurice et al., 2013).”
BackgroundPerez-Muñoz, M. E., Arrieta, M.-C., Ramer-Tait, A. E., & Walter, J. (2017) · Microbiome · doi:10.1186/s40168-017-0268-4 · Cited by 1,096
Self-citationFassarella, M., Blaak, E. E., Penders, J., Nauta, A., Smidt, H., & Zoetendal, E. G. (2020) · Gut · doi:10.1136/gutjnl-2020-321747 · Cited by 818
Defining and quantifying the core microbiome: Challenges and prospects
Neu, A. T., Allen, E. E., & Roy, K. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2104429118 · Cited by 653
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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