LB 20-205 - Metabarcoding of caribou feces : what can we expect ?

Background/Question/Methods:

Caribou is one of Canada's most iconic and endangered species. In recent years, significant research has been done on habitat use and population dynamics in order to better understand population status and limiting factors. In this study, we contribute to this effort in further developing metabarcoding methods to characterize the animals’ diet along with individual and population-level measures of health. Using fecal pellets, we tested different markers for the plant and fungi components of the diet, the gut microbiome and parasites. We extracted DNA from 92 caribou feces collected during the winter in 7 local populations of boreal caribou from Manitoba and Saskatchewan. From these DNA extracts, we amplified and sequenced different taxonomic markers: the 18S rRNA gene to characterize the diet and detect parasites, the ITS regions of plants and fungi to further explore the diet, and the 16S rRNA gene of prokaryotes to describe the gut microbiome. After bioinformatics processing, a community matrix for each of the functional groups of interest was constructed to highlight differences and similarities among populations.

Results/Conclusions:

Analysis of the 18S did not allowed the detection of the fungal part of the lichen, therefore algal sequences were used as a proxy for lichens, leading to low taxonomic resolution as one single algal species could form several lichen species. Taxonomic resolution was also low for most plant species. Nevertheless, 18S data still allowed the populations to be differentiated based on algal and plant sequence profiles. Preliminary results for the ITSs indicated that these markers provide better taxonomic identification of lichens and plants. Sequencing of the 16S allowed to detect bacterial phyla known to colonize the rumen and underline differences in gut microbiome composition between populations. 18S further identified parasites and revealed a male bias in prevalence. Overall, our results showed the need to use multiple markers to generate relevant information for caribou populations. The 18S includes parasites and diet at broad taxonomic level, ITSs provide more precise diet identification, and 16S allows for the analysis of diet-gut microbiome interactions. The application of metabarcoding methods in the context of caribou ecology is likely to develop rapidly, providing additional insights into the species biology and the impact of range characteristics and anthropogenic disturbances on different populations.