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Curr Protoc Toxicol. 2018 Nov;78(1):e54. doi: 10.1002/cptx.54. Epub 2018 Sep 19.

Structural and Functional Analysis of the Gut Microbiome for Toxicologists.

Author information

1
Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania.
2
Metabolomics, The Pennsylvania State University, University Park, Pennsylvania.

Abstract

Characterizing the reciprocal interactions between toxicants, the gut microbiota, and the host, holds great promise for improving our mechanistic understanding of toxic endpoints. Advances in culture-independent sequencing analysis (e.g., 16S rRNA gene amplicon sequencing) combined with quantitative metabolite profiling (i.e., metabolomics) have provided new ways of studying the gut microbiome and have begun to illuminate how toxicants influence the structure and function of the gut microbiome. Developing a standardized protocol is important for establishing robust, reproducible, and importantly, comparative data. This protocol can be used as a foundation for examining the gut microbiome via sequencing-based analysis and metabolomics. Two main units follow: (1) analysis of the gut microbiome via sequencing-based approaches; and (2) functional analysis of the gut microbiome via metabolomics.

KEYWORDS:

bioinformatics; metabolomics; microbiome; toxicology

PMID:
30230220
DOI:
10.1002/cptx.54

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