Metabarcoding analyses for intestinal microbiota can be valuable in animal conservation: the example of the critically endangered bat Coleura seychellensis

Bats represent a quarter of all mammals; most species are globally threatened or vulnerable. Choleura seychellensis is the only insectivorous bat endemic to the Seychelles and is on the IUCN list. DNA metabarcoding of fecal samples utilizes the mitochondrial gene of the cytochrome c oxidase subunit 1 (COI) and has emerged as a powerful tool for studying the foraging niche of various species. This innovative technique harnesses the information encoded in an organism's DNA to gain valuable insights into its dietary preferences and ecological interactions. In wild animals, applying COI markers could be crucial because current methods for studying diets have many limitations. This study, conducted in 2022, aimed to describe the diet of C. seychellensis using COI and compared it to the microbial diversity of the intestinal microbiota. The analysis of the COI gene allowed us to identify the insects that made up the diet of C. seychellensis. The highest percentage of insects was attributed to ants belonging to the genus Camponotus, also known as carpenter ants, which are known for damaging wood. The predominant species is Camponotus grandidieri, native to the Seychelles. During the sampling period in March, Camponotus ants are known to engage in nuptial flights and can be preyed upon by bats. Regarding intestinal microbiota, the prevalent phyla were Proteobacteria and Bacteroides, similar to the microbiota of insects. Gathering new information about bat diets through the years and data on the intestinal microbiota can help identify biomarkers for health, providing important insights. Applying metabarcoding analyses for intestinal microbiota and diet can be valuable in animal conservation. This approach has enormous potential, even though it is still in its early stages. To date, no conservation policies or legislation include assessments of the microbiome.