Microbiome Analyses for Toxicological Studies

Curr Protoc Toxicol. 2018 Aug;77(1):e53. doi: 10.1002/cptx.53. Epub 2018 Jul 25.


Microbiomes can be thought of as the integration of biotic and abiotic factors, including the microbial communities and the distinct physio-chemical properties that are present in a habitat. The microbes within a microbiome can influence the chemical environment by degrading medications inside patients or contaminants in the environment, such as hydrocarbons released after the Deepwater Horizon oil spill. Identifying and monitoring the relative abundance of microbes can help to elucidate variations in their response to toxins and should be considered as a variable in statistical analyses. In addition, the presence of pathogenic microbes or toxin-producing species could affect the observed toxicity of an environment. The protocols in this unit begin with the collection of samples, proceeds to sequencing of the bacterial DNA, and ends with an analysis of the bacterial community in light of environmental metadata. © 2018 by John Wiley & Sons, Inc.

Keywords: 16S rRNA sequencing; bioinformatics; microbiome; toxicology.