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.

Original languageEnglish (US)
Article numbere54
JournalCurrent Protocols in Toxicology
Volume78
Issue number1
DOIs
StatePublished - Nov 1 2018

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Functional analysis
Structural analysis
Metabolomics
Poisons
Metabolites
Cell culture
Genes
rRNA Genes
Gastrointestinal Microbiome

All Science Journal Classification (ASJC) codes

  • Toxicology

Cite this

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title = "Structural and Functional Analysis of the Gut Microbiome for Toxicologists",
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.",
author = "Nichols, {Robert G.} and Jingwei Cai and Murray, {Iain Alexander} and Imhoi Koo and Smith, {Philip B.} and Perdew, {Gary H.} and Patterson, {Andrew David}",
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AU - Nichols, Robert G.

AU - Cai, Jingwei

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AU - Smith, Philip B.

AU - Perdew, Gary H.

AU - Patterson, Andrew David

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