Title

Developing Non-invasive Microbial Biomarkers to Inform Elk (C. canadensis) Health in Wild Montana Populations

Presentation Type

Poster

Abstract

Background: The composition of the fecal microbiome of mammals is associated with changes in diet, stress, disease and physical condition of an animal. When managing wildlife, Federal and State agencies currently must rely on invasive sampling and coarse observational demographic data to make their decisions. By developing microbiome-based biomarkers that vary as a function of animal body condition and disease, we hope to provide managers with the ability to monitor direct impacts from environmental stressors on individual animals and the herd. This approach represents a low cost, non-invasive sampling method based simply on fecal pellet collection in the field and intestinal microbiome analysis in the lab. Methods: We analyzed 111 individual wild elk (Cervus canadensis) using Illumina MiSeq sequencing of partial 16S-rRNA gene amplicons from the fecal microbiome. Montana Fish, Wildlife and Parks collected the scat and linked body condition metrics from three GPS collared populations in Montana in winter using helicopter teams and invasive sampling methods. Using the QIIME program and a floating search feature selection with leave-one-out cross validation (CV) we were able to elucidate informative bacterial taxa and general bacterial composition profiles and compare them to known body conditions. Results: This experiment succeeded in initial development and confirmation of microbial biomarkers in elk with individuals from the Sapphire population clustering significantly using CV by pregnancy (CV 92.31%), sex (CV 96.15%) and body fat percentage (CV 96.15%) in females using linear discriminate analysis (LDA). Conclusion: As our microbial biomarker approach matures, we hope to apply it broadly toward the management of wildlife species non-invasively. Non-invasive biomarkers can support endangered species research and conservation when animal populations are fragile and cannot sustain traditional invasive sampling or when more cost effective information is desired.

Category

Life Sciences

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Apr 17th, 11:00 AM Apr 17th, 12:00 PM

Developing Non-invasive Microbial Biomarkers to Inform Elk (C. canadensis) Health in Wild Montana Populations

South UC Ballroom

Background: The composition of the fecal microbiome of mammals is associated with changes in diet, stress, disease and physical condition of an animal. When managing wildlife, Federal and State agencies currently must rely on invasive sampling and coarse observational demographic data to make their decisions. By developing microbiome-based biomarkers that vary as a function of animal body condition and disease, we hope to provide managers with the ability to monitor direct impacts from environmental stressors on individual animals and the herd. This approach represents a low cost, non-invasive sampling method based simply on fecal pellet collection in the field and intestinal microbiome analysis in the lab. Methods: We analyzed 111 individual wild elk (Cervus canadensis) using Illumina MiSeq sequencing of partial 16S-rRNA gene amplicons from the fecal microbiome. Montana Fish, Wildlife and Parks collected the scat and linked body condition metrics from three GPS collared populations in Montana in winter using helicopter teams and invasive sampling methods. Using the QIIME program and a floating search feature selection with leave-one-out cross validation (CV) we were able to elucidate informative bacterial taxa and general bacterial composition profiles and compare them to known body conditions. Results: This experiment succeeded in initial development and confirmation of microbial biomarkers in elk with individuals from the Sapphire population clustering significantly using CV by pregnancy (CV 92.31%), sex (CV 96.15%) and body fat percentage (CV 96.15%) in females using linear discriminate analysis (LDA). Conclusion: As our microbial biomarker approach matures, we hope to apply it broadly toward the management of wildlife species non-invasively. Non-invasive biomarkers can support endangered species research and conservation when animal populations are fragile and cannot sustain traditional invasive sampling or when more cost effective information is desired.