Which and how many bacteria, archaea, fungi, viruses, or protozoa (collectively, the microbiome) might inhabit the tissues or surfaces of an animal host is impacted by myriad factors, including the animal host’s biology, ecology, lifestage, health status, and diet. Much of my lab focuses on understanding the players and the dynamics in the microbial universe that is the digestive tract of various animal species.
The digestive tract of animals is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of the gut. Each microorganism brings with it an array of capabilities for digesting or producing different chemical compounds. In many cases, the animal host is reliant on these microbial functions to digest its diet and maintain a hesitant truce with the more exuberant members of the gut community. Each organ in the digestive tract creates a unique environment, with variations in temperature, oxygen content, pH, salinity, muscle contractions, animal cells, and animal enzymes. These conditions, and their effect on the animal’s diet as it moves through the gut, combine as selective factors for which and how many microorganisms thrive in any location. This effect on the microbial communities requires us to use spatial resolution in our studies – or sampling multiple locations along the gut. Yet, this is invasive and logistically difficult to do in live animals, and it prevents us from using temporal resolution – or sampling over time to understand the dynamics of that host-associated microbial community.
Related Reviews
- Garcia-Mazcorro, J.F., Ishaq, S.L., Rodriguez-Herrera, M.V., Garcia-Hernandez, C.A., Kawas, J.R., Nagaraja, T.G. 2019. Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits. Animal: 1-9. Impact 2.026. Article.
- St-Pierre, B., Cersosimo, L.M., Ishaq, S.L., Wright, A-D.G. 2015. Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animals. Frontiers in Microbiology 6:776. Impact 4.165. Article.
- Ishaq S.L., Wright A-D.G. 2015. Terrestrial Vertebrate Animal Metagenomics, Wild Ruminants. In: Highlander, SK, Rodriguez-Valera, F, White, BA. (Ed.) Encyclopedia of Metagenomics: SpringerReference. Springer-Verlag Berlin Heidelberg. Article.
- Ishaq, S.L., Wright, A-D.G. 2015. Wild Ruminants. In: Rumen Microbiology – Evolution to Revolution. AK Puniya, R Singh, DN Kamra (eds). Springer India. Pp. 37-45. Article.
