Universality of human microbial dynamics
Open accessAbstract
Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies--the Human Microbiome Project and the Student Microbiome Project--we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.
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Alterations in bacterial communities may be more important than changes in single bacterial species, and due consideration must be paid to functional community networks in the design and implementation of targeted therapies.
“Thus, alterations in bacterial communities may be more important than changes in single bacterial species, and due consideration must be paid to functional community networks in the design and implementation of targeted therapies[218,219].”
From Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health (2017) · cites this paper as [218]
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- Authors
- Bashan, A., Gibson, T. E., Friedman, J., Carey, V. J., Weiss, S. T., Hohmann, E. L., & Liu, Y.-Y.
- Affiliations
- Brigham and Women's Hospital (US)
- Massachusetts Institute of Technology (US)
- Harvard University (US)
- Corresponding author
- Liu, Yang-Yu
- ORCID
- Venue
- Nature
- Published
- 2016-06-08
- Volume
- 534
- Issue
- 7606
- Pages
- 259-262
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4902290
- OpenAlex
- W2409622550
- Cited by
- 270
- References
- 38
- Citations by year
- 2026: 14 · 2025: 25 · 2024: 26 · 2023: 24 · 2022: 21 · 2021: 27 · 2020: 19 · 2019: 24 · 2018: 35 · 2017: 36 · 2016: 19
- FWCI
- 19.76
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (R01HL091528)
- 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, microbial community dynamics, gut microbiota, oral microbiota, skin microbiome, Clostridium difficile infection, fecal microbiota transplantation, interindividual variability, population dynamics model, microbiota-based therapy, Human Microbiome Project, microbial growth rate, species interactions, metagenomics
- MeSH terms
- Gastrointestinal Microbiome, Fecal Microbiota Transplantation, Clostridium Infections, Computer Simulation, Cross-Sectional Studies, Environment, Humans, Intestines, Mouth, Organ Specificity, Skin, Species Specificity, Clostridioides difficile, Ecosystem, Metagenomics, Microbiota, Healthy Volunteers, Datasets as Topic
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