First insights into the fecal bacterial microbiota of the black–tailed prairie dog (Cynomys ludovicianus) in Janos, Mexico

Abstract

Intestinal bacteria are an important indicator of the health of their host. Incorporating periodic assessment of the taxonomic composition of these microorganisms into management and conservation plans can be a valuable tool to detect changes that may jeopardize the survival of threatened populations. Here we describe the diversity and abundance of fecal bacteria for the black–tailed prairie dog (Cynomys ludovicianus), a threatened species, in the Janos Biosphere Reserve, Chihuahua, Mexico. We analyzed fecal samples through next generation massive sequencing and amplified the V3–V4 region of the 16S rRNA gene using Illumina technology. The results were analyzed with QIIME based on the EzBioCloud reference. We identified 12 phyla, 22 classes, 33 orders, 54 families and 263 genera. The phyla Firmicutes and Bacteroidetes were the most abundant groups and are associated with healthy intestinal communities and high efficiency in the energy diet. Most of the bacterial genera reported here for C. ludovicianus are not pathogenic and are normally found in mammalian feces. Some of the other bacteria are associated with soil, water and plants, possibly in relation to the habitat of the black– tailed prairie dog. This is the first study to report the fecal bacteria of C. ludovicianus in Mexico and it provides a baseline for determining this species’ health for use in long–term conservation strategies.