Assessing gut microbiomes of the dusky shrew (Sorex monticola) in southeast Alaska

NSF fellow: Price Holman, Rutgers University

Mentor: Dr. Stephen Greiman

The dusky shrew (Sorex monticola) is an insectivorous small mammal found throughout western North America, including on numerous islands of the Alexander Archipelago of southeast Alaska. The Alexander Archipelago contains about 1,100 islands, providing an interesting opportunity to examine the impact of island biogeography on the shrew gut microbial community. Shrews feed on a high protein diet, consisting of a wide variety of invertebrates, which have led to a unique gut microbiome when compared to other small sympatric mammals that have more herbivorous diets. This project aimed to understand the factors that are most impactful on the gut microbiome of S. monticola. Increased distance from the mainland, small island size, and logging intensity were predicted to have a negative effect on gut microbiome diversity, while near-shore, large or undisturbed islands were predicted to have a positive effect. Shrews were captured from 2005-2007 by pitfall trap and their gastrointestinal tracts were removed, frozen in liquid nitrogen, and archived at the Museum of Southwestern Biology. From the lower portion of thirty-seven of these frozen GI tracts, DNA was extracted and submitted for long read 16S amplicon sequencing. Long read sequencing is extremely beneficial as it provides enough genetic information (1500bp) to classify organisms to species level. 177,362 sequence reads were assembled into 1500bp fragments from a total collection of 354,724 reads. We eliminated sequencing errors as well as classified our sequence reads via the dada2 package with SILVA bacterial database. 2204 unique Amplicon sequence variants were obtained and analyzed using the web program Calypso. The results of statistical analysis showed a significant difference in beta microbiome diversity based on locality (island). Additionally, there was a significant difference based on logging intensity (e.g. severe, moderate, or rare). In terms of alpha diversity, however, there were no significant differences across all variables. This study begins to lay a foundation for understanding how land use change and island biogeography affects biodiversity.