The Mammalian Microbiome and Its Importance in Laboratory Animal Research

Abstract

In this issue are assembled 10 fascinating, well-researched papers that describe the emerging field centered on the microbiome of vertebrate animals and how these complex microbial populations play a fundamental role in shaping homeostasis of the host. The content of the papers will deal with bacteria and, because of relative paucity of information on these organisms, will not include discussions on viruses, fungus, protozoa, and parasites that colonize various animals. Dissecting the number and interactions of the 500-1000 bacterial species that can inhabit the intestines of animals is made possible by advanced DNA sequencing methods, which do not depend on whether the organism can be cultured or not. Laboratory animals, particularly rodents, have proven to be an indispensable component in not only understanding how the microbiome aids in digestion and protects the host against pathogens, but also in understanding the relationship of various species of bacteria to development of the immune system. Importantly, this research elucidates purported mechanisms for how the microbiome can profoundly affect initiation and progression of diseases such as type 1 diabetes, metabolic syndromes, obesity, autoimmune arthritis, inflammatory bowel disease, and irritable bowel syndrome. The strengths and limitations of the use of germfree mice colonized with single species of bacteria, a restricted flora, or most recently the use of human-derived microbiota are also discussed.

Keywords: animal; human microbiome; mice; microbiota; models; review.

Figure 1

PubMed Search using terms microbiome or microflora, total hits per year.

Figure 2

Taxonomic classification of bacteria. Descriptions of the gastrointestinal microbiota focus on the levels of phylum and genus (modified from Sheh and Fox 2013).

Figure 3

Concepts for microbial surveillance and standardization in laboratory animals. (a) Traditional and current focus of health monitoring is based on virulence of microorganisms (symbiotic, opportunistic, pathogenic) and aims to exclude or report pathogens (and potential pathogens), depending on the barrier level and specified excluded agents. (b) Microbial relevance (other than pathogenicity) to the host is increasingly recognized, as is the complexity and diversity of the microbiota.