Microbiome Analyses for Toxicological Studies

Authors: BENJAMINO, J - University Of Connecticut; LIDIA, B - University Of Connecticut; GRAF, J - University Of Connecticut

Submitted to: Current Protocols in Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2018
Publication Date: 8/17/2018
Citation: Benjamino, J., Lidia, B., Graf, J. 2018. Microbiome Analyses for Toxicological Studies. Current Protocols in Molecular Biology. 77(1):e53. https://doi.org/10.1002/cptx.53.
DOI: https://doi.org/10.1002/cptx.53

Interpretive Summary: The microbiome is the community of microorganisms living in a particular environment and plays a critical role in health and disease of animals. Understanding the microbiome in healthy and diseased fish and their surrounding environment is important not just for understanding the dynamics of infectious diseases but for developing new intervention strategies. In this manuscript, the entire process of microbiome analyses including sample collection, DNA isolation, 16S rRNA gene amplification, sequencing and data analysis is described. Detailed protocols for working with water and fecal samples are provided. Line-by-line commands for the data analysis are listed and explained. This manuscript should make microbiome analysis more accessible to researchers interested in improving animal health.

Technical Abstract: Significance Statement Microbiomes are microbial communities that are present in habitats with distinct physio-chemical properties (Whipps, Lewis, & Cooke, 1988). These microbes can influence the chemical environment by degrading medications inside patients (Haiser et al., 2013) or contaminants in the environment, such as hydrocarbons released after the Deepwater Horizon oil spill (Gutierrez et al., 2013). 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 the 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. Abstract Studying the microbiome of many systems can provide information about the health and well-being of an organism and the environment. The microbiome of an environment can be used as a proxy for determining the effect of toxic agents on the environment. For example, pathogenic bacteria can be identified or a dysbiosis of the normal microbiota can indicate the presence of a toxin or disruption of the environment. Using 16S rRNA gene sequencing, the bacterial community of a sample can be identified and monitored. After sample collection, the bacterial DNA is isolated and the 16S rRNA gene is amplified and sequenced. The resulting bacterial information can be used to detect a disruption in the environment caused by pathogens, antibiotics, or other toxic compounds.