Examining the Effect of Collection Method on the Microbial Communities Detected by Shotgun Metagenomics in Elephant Dung

Abstract

The development of new ways to non-invasively monitor and manage endangered, cryptic or otherwise inaccessible wildlife populations is of critical importance to conservation initiatives. New fecal DNA (fDNA) approaches offer considerable potential to inform these efforts, as the DNA which is present in an animal’s feces contains a wealth of information about that individual’s diet, health, metabolism, and resistance to disease. Specifically, shotgun metagenomic sequencing of DNA from feces represents an exciting new development in molecular analytics, enabling high resolution characterization of microbial communities in samples. In spite of this, no studies have been done to standardize the collection methods of samples from wild animals for shotgun metagenomics or to evaluate whether different collection methods can lead to differences in the microbial communities which are detected in a sample. In this study, I conducted shotgun metagenomic analyses on fecal samples collected from a captive elephant at the Oregon Zoo and developed an efficient bioinformatic pipeline to analyze the microbial communities detected. Each fecal sample was collected from the same elephant using five different, commonly-used collection methods. DNA was then extracted from each of these samples, sequenced on an Illumina MiSeq, and analyzed using the pipeline which I developed. Based on preliminary results, bacteria and archaea were identified to the genus level, and detected community composition varied by collection method. This work emphasizes both the potential and feasibility of shotgun metagenomics for informing conservation efforts and the need to standardize collection methods in shotgun metagenomic studies of wild populations.