Comparison of fresh fecal samples from two populations (NAM and USA) (Part 2 of 2)

The relationships between gut microbiota and animal health are an
important consideration that are increasingly influential in the
management of wild and ex situ endangered species, such as the cheetah
(Acinonyx jubatus). To better understand these relationships, fresh fecal
samples are currently required as a non-invasive alternative for the gut
microbiome. Unfortunately, fresh samples are challenging to collect,
especially in the wild. This study had two main aims: 1) to determine the
optimal collection time point for cheetah feces after deposit in their
native environment of Namibia as a guide for wild cheetah fecal microbiome
studies; and 2) to characterize the cheetah fecal microbiota between two
ex situ cheetah populations from two locations (Front Royal, VA, USA and
Otjiwarongo, Namibia), which also consume different diets (commercial diet
+ carcass supplements and carcass only, respectively). Fresh fecal samples
were collected from 16 cheetahs (Virginia, n = 8; Namibia n = 8) and
analyzed for bacterial community diversity and composition using 16S rRNA
gene amplicon sequencing. First, we found no difference in bacterial
richness, diversity, or community composition from fresh fecal material
compared to subsequent samples of decomposing fecals over a four-day
sampling period in Namibia. Second, fresh cheetah samples in semi-wild
conditions in Namibia had higher number of bacterial taxa, more
phylogenetically diverse bacteria and contained compositionally distinct
microbiomes (Bray-Curtis dissimilarity, Jaccard, and unweighted UniFrac
measures) from cheetahs in zoo-managed conditions in the USA. We also
found few differences in predictive functions of the fecal microbiota
between the populations, where only one disease-related pathway was higher
in the USA samples. Overall, our findings suggest that in dry season
conditions (no recorded rainfall) in Namibia, fecals may be usable for up
to three days after defecation for microbial ecology studies. We provide
observational data on how to identify fecals within four days of being
voided (see supplemental photos). There are major demographic and dietary
differences between ex situ Namibian and USA populations, and we suggest
further investigation into the influence of diet and population on the gut
microbiota and health of cheetahs.