Cited by 496Gut microbiota and healthGenomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

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Chapter 12: Human Microbiome Analysis

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Morgan, Xochitl C., Huttenhower, Curtis·2012·PLoS Computational Biology

DOI 10.1371/journal.pcbi.1002808PMC PMC3531975

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Abstract

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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Authors: Morgan, X. C., & Huttenhower, C.
Affiliations: Harvard University (US)
Broad Institute (US)
Corresponding author: Huttenhower, Curtis
ORCID: Morgan, Xochitl C.
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
DOI: 10.1371/journal.pcbi.1002808
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
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
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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