Date of Completion

Spring 5-1-2024

Thesis Advisor(s)

Sarah Hird

Honors Major

Molecular and Cell Biology

Disciplines

Biodiversity | Bioinformatics | Environmental Microbiology and Microbial Ecology | Genomics | Microbiology

Abstract

The microbial communities that are present in and on vertebrates are collectively called the microbiome. The composition of a microbiome is dependent upon the host, the environment, and evolution. There has been extensive research on the bacterial composition of host-associated microbiomes, however, there has been much less work on the archaeal composition of host-associated microbiomes. Archaea have previously been assumed to primarily exist in extreme environments, but this may not be true and has been influenced by their generally low abundance and methodological difficulties in detection. It is possible they are consistent members of diverse host-associated microbiomes.

Archaea-specific PCR primers were used to study the archaeal component of the fecal microbiome of 24 Anna’s hummingbirds (Calypte anna). The purpose of this investigation was to compare Archaea-specific primers to “universal” primers that amplify both archaea and bacteria in the detection of archaea in the Anna’s hummingbird and to effectively complete a microbiome analysis. The sequencing data were used to identify and quantify the archaea present in the samples. The most prevalent order of archaea was Nitrososphaerales, which was present in all 24 samples using the Archaea-specific primers. The universal primers only detected archaea in one sample, where twelve reads assigned to the order Methanobacteriales were detected. Overall, we found that by using Archaea-specific primers, there was an increase in archaeal reads and taxonomic diversity in comparison to the use of universal primers that mainly detected bacteria only.

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