Chapter 12: Human Microbiome Analysis
Open accessAbstract
Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.
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Humans contain trillions of microbes, comparable in number to human cells, that interact with the host at many sites during development.
“there are trillions of microbes as numerous as human cells, that interact with the host constantly at numerous sites”
From The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy (2018) · cites this paper as Morgan and Huttenhower, 2012
Microbiota contribute to many host functions, including immunity.
“they play such a large role in numerous host functions including immunity”
From The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy (2018) · cites this paper as Morgan and Huttenhower, 2012
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- Authors
- Morgan, X. C., & Huttenhower, C.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Corresponding author
- Huttenhower, Curtis
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-12-27
- Volume
- 8
- Issue
- 12
- Pages
- e1002808
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC3531975
- OpenAlex
- W2102813808
- Cited by
- 496
- References
- 179
- Citations by year
- 2026: 9 · 2025: 25 · 2024: 25 · 2023: 41 · 2022: 38 · 2021: 59 · 2020: 64 · 2019: 48 · 2018: 50 · 2017: 48 · 2016: 34 · 2015: 29 · 2014: 18 · 2013: 8
- FWCI
- 7.06
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R01HG005969)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human microbiome, microbiota, metagenomics, metatranscriptomics, shotgun sequencing, microbial community diversity, functional genomics, inflammatory bowel disease, antibiotic resistance, microbial ecology
- MeSH terms
- Bacteria, Genes, Bacterial, Humans, RNA, Ribosomal, 16S, Host-Pathogen Interactions, Metagenome, Metagenomics
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