Defining the human microbiome
Open accessAbstract
Rapidly developing sequencing methods and analytical techniques are enhancing our ability to understand the human microbiome, and, indeed, how the microbiome and its constituents are defined. This review highlights recent research that expands our ability to understand the human microbiome on different spatial and temporal scales, including daily time series datasets spanning months. Furthermore, emerging concepts related to defining operational taxonomic units, diversity indices, core versus transient microbiomes, and the possibility of enterotypes are discussed. Additional advances in sequencing technology and in our understanding of the microbiome will provide exciting prospects for exploiting the microbiota for personalized medicine.
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In humans, the microbiota of infants was similar to the vaginal microbiota of their mother after natural birth but mimicked the skin microbiota when caesarean section was performed.
“In humans, studies have shown that the microbiota of infants was similar to the vaginal microbiota of their mother after natural birth but mimicked the skin microbiota when caesarean section was performed (Cho and Blaser, 2012; Ursell et al., 2012).”
From The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission (2022) · cites this paper as Ursell et al., 2012
The human microbiota is the collective term for the trillions of microorganisms that live in and on us.
“The human microbiota is the collective term for the trillions of microorganisms that live in and on us (Ursell et al., 2012)”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Ursell et al., 2012
Microorganisms in the gastrointestinal tract play a role in nutrient uptake, vitamin synthesis, energy harvest, inflammatory modulation, and host immune response.
“The microorganisms in the gastrointestinal tract play a significant role in nutrient uptake, vitamin synthesis, energy harvest, inflammatory modulation, and host immune response, collectively contributing to human health.”
From The athletic gut microbiota (2020) · cites this paper as [4]
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- Authors
- Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R.
- Affiliations
- University of Colorado Boulder (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Knight, Rob
- Venue
- Nutrition Reviews
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-08
- Volume
- 70
- Pages
- S38-S44
- ISSN
- 0029-6643 (ISSN-L)
- PMC
- PMC3426293
- OpenAlex
- W2156591001
- Cited by
- 1,255
- References
- 76
- Citations by year
- 2026: 69 · 2025: 129 · 2024: 212 · 2023: 158 · 2022: 164 · 2021: 126 · 2020: 120 · 2019: 77 · 2018: 68 · 2017: 60 · 2016: 30 · 2015: 18 · 2014: 10 · 2013: 11 · 2012: 2
- FWCI
- 1.20
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nutrition Reviews (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (R01HG004872, HG4872)
- National Institute of General Medical Sciences (T32GM008759, T32GM142607)
- 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, microbiota, operational taxonomic units, diversity indices, core microbiome, enterotypes, spatial and temporal scales, personalized medicine, sequencing technologies
- MeSH terms
- Bacteria, Humans, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, Gastrointestinal Tract, Biodiversity, Metagenome
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