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The Good, the Bad, and the Unknown: Microbial Symbioses of the American Alligator.

Vertebrates coexist with microorganisms in diverse symbiotic associations that range from beneficial to detrimental to the host. Most research has aimed at deciphering the nature of the composite microbial assemblage's genome, or microbiome, from the gastrointestinal (GI) tract and skin of mammals (i.e., humans). In mammals, the GI tract's microbiome aids digestion, enhances uptake of nutrients, and prevents the establishment of pathogenic microorganisms. However, because the GI tract microbiome of the American alligator (Alligator mississippiensis) is distinct from that of all other vertebrates studied to date, being comprised of Fusobacteria in the lower GI tract with lesser abundances of Firmicutes, Proteobacteria, and Bacteroidetes, the function of these assemblages is largely unknown. This review provides a synthesis of our current understanding of the composition of alligators' microbiomes, highlights the potential role of microbiome members in alligators' health (the good), and presents a brief summary of microorganisms detrimental to alligators' health (the bad) including Salmonella spp. and others. Microbial assemblages of the GI tract have co-evolved with their vertebrate host over geologic time, which means that evolutionary hypotheses can be tested using information about the microbiome. For reptiles and amphibians, the number of taxa studied at present is limited, thereby restricting evolutionary insights. Nevertheless, we present a compilation of our current understanding of reptiles' and amphibians' microbiomes, and highlight future avenues of research (the unknown). As in humans, composition of microbiome assemblages provides a promising tool for assessing hosts' health or disease. By further exploring present-day associations between symbiotic microorganisms in the microbiomes of reptiles and amphibians, we can better identify good (beneficial) and bad (detrimental) microorganisms, and unravel the evolutionary history of the acquisition of microbiomes by these poorly-studied vertebrates.