Graduation Year


Graduation Month


Document Type


Degree Name

Bachelor of Science

School or Department

Wildlife Biology


Wildlife Biology – Terrestrial

Faculty Mentor

Professor Mark Hebblewhite

Faculty Mentor Department

Wildlife Biology

Faculty Reader(s)

Professor William E. Holben


metagenomics, biomarker, elk, non-invasive, wildlife, 16S

Subject Categories

Bioinformatics | Environmental Microbiology and Microbial Ecology | Genetics | Genomics | Molecular Biology | Molecular Genetics | Other Animal Sciences | Other Genetics and Genomics | Other Nutrition


The composition of the intestinal bacterial community (intestinal microbiome) of mammals is associated with changes in diet, stress, disease and physical condition of the animal. The relationship between health and the microbiome has been extensively demonstrated in studies of humans and mice; this provides strong support for its potential utility in wildlife. When managing elk (Cervus canadensis), federal and state agencies currently must rely on invasive sampling and coarse demographic data on which to base their decisions. By developing microbiome-based biomarkers that vary as a function of elk body condition and disease (i.e. microbial biomarkers), we hope to provide managers with the ability to monitor direct impacts from environmental stressors on individual animals and the herd. This approach, once established, represents a low cost, non-invasive sampling method based simply on fecal pellet collection in the field and intestinal microbiome analysis in the lab. Montana Fish, Wildlife and Parks collected the scat and linked body condition metrics from four GPS collared populations in Montana in winter 2014, using helicopter teams and invasive sampling methods. We analyzed 111 individual wild elk fecal microbiomes using Illumina MiSeq sequencing of partial 16S-rRNA gene amplicons. Using the QIIME pipeline and a floating search feature selection algorithm (SFFS) with linear discriminate analysis (LDA) and leave-one-out cross validation (CV) we were able to elucidate informative patterns in bacterial taxa presence and abundance by comparing them to various measured body conditions and geographic locations of elk sampled. Microbial biomarkers provide potential for managers to routinely obtain fine scale non-invasive health metrics from scat samples obtained in the field for species of concern.


Message from author, November 2015:

I have temporarily removed this research while publishing an expanded/revised version elsewhere. If you are interested in this document or its methods please contact me directly:

Honors College Research Project




© Copyright 2015 Samuel B. Pannoni