Honors Theses and Capstones

Date of Award

Spring 2025

Project Type

Senior Honors Thesis

College or School

COLSA

Department

Molecular, Cellular, and Biomedical Sciences

Program or Major

Biomedical Science: Medical and Veterinary Sciences

Degree Name

Bachelor of Science

First Advisor

David Needle

Abstract

This study is of an exploratory nature and focuses on characterizing the eukaryotic microbiota present in the respiratory tissues of six wild canids and one domestic canine. The contents of this document largely pertain to dry lab analyses of 18S barcodes in bioinformatics programs – primarily QIIME2 running in the GitBash command line, service for which was hosted by the UNH Ron Bioinformatics training server. All procedures listed within the section below were performed by second parties at the UNH Hubbard Center for Genomics Studies (HCGS), the New Hampshire Veterinary Diagnostics Lab (NHVDL), and the UNH Microbial Ecology and Emerging Diseases (MEED) Research Group.

Biopsies were performed on one deceased domestic canine (Canis familaris) and six deceased foxes originating from central and southern New Hampshire. The six fox samples constituted two species: two gray foxes (Urocyon cinereoargenteus) and four red foxes (Vulpes vulpes). Biopsies were performed by the UNH MEED lab staff, and bulk respiratory tissue samples collected from all canids were stored on ice in the NHVDL biobank before being thawed prior to DNA extraction. 18S metabarcoding was performed on the samples using the 18S V4 primer, and all wet lab procedures regarding DNA extraction, PCR amplification, library preparation, and sequencing were performed by HCGS.

The findings of this study indicate that opportunistic species of Malassezia fungi could potentially appear in the respiratory microbiomes of wild canids in cases where their occurrence is facilitated by the presence of other pathogens whose activities could contribute to a suppression of host immune responses. Additionally, the co-occurrence of two tick-borne parasite species – Hepatozoon canis and Babesia microti – are discussed in relation to their potential for increasing host mortality when considering interactions between their pathologic features. Findings from analyses of read-percentage per-taxa-per-sample suggest an inverse relationship between their respective parasitic loads which could indicate intra-host competition between both parasite species.

Comments

All relevant code for bioinformatics analyses is uploaded to the following github repo, made public for viewing: https://github.com/cb1476/18s-Data-Processing-Pipeline

Download

Share

COinS