Chapter 12: Human Microbiome Analysis

By Xochitl C. Morgan, Curtis Huttenhower. PLoS Comput. Biol., 2012

470 citations recorded by the source corpus.

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.

Subfields: Ecology, Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/54335cae8c3ff09215fbf47cdff74622a208462c

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Citations in the corpus

The amphibian microbiome: natural range of variation, pathogenic dysbiosis, and role in conservation (2017, background): “Sources Faith (1992), Moreira and López-Garcı́a (2011), Lozupone et al. (2011), Kuczynski et al. (2011), Morgan and Huttenhower (2012), Ursell et al. (2012), Swenson (2014a, b) Alpha diversity within-sample taxonomic diversity, acts as a summary statistic of a single population Beta diversity…”
Relating the metatranscriptome and metagenome of the human gut (2014, background): “Antonie van Leeuwenhoek 66(1-3):271–294.”
The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy. (2018, background): “Therefore, it is not surprising that they play such a large role in numerous host functions including immunity (Sender et al., 2016; Morgan and Huttenhower, 2012).”