Date of Completion


Embargo Period



Sarah Hird, Jonathan Klassen, Johann Gogarten

Field of Study

Molecular and Cell Biology


Master of Science

Open Access

Open Access


As scientists discover more information about the communities of bacteria that live on and inside hosts, "the microbiome", a new avenue for understanding the health of humans and animals has opened. There are many analysis pipelines for microbiome data processing, and choice of analytical tools can affect the biological results of the analysis. The current analysis climate does not point toward a single most effective protocol, which hinders comparisons across studies. An important step in microbiome data processing is the assignment of reads into groups of similar organisms. The traditional unit for grouping organisms is the species; however resolving sequences at the species level is not always possible. For this reason, the term “operational taxonomic unit” (OTU) has been used as a proxy for species. Mothur is one popular software package that uses OTUs, as defined by a percent sequence similarity that is set by the user; 97% sequence similarity is frequently cited as the most similar to traditional species. DADA2 is a newer pipeline that classifies unique sequences as “amplicon sequence variants” or ASVs. ASVs assume biological sequences are present in the sample and can resolve differences in sequence variants at as low a single nucleotide. We compared OTUs and ASVs from a dataset of bird gastrointestinal tracts from Equatorial Guinea. One hundred and forty two samples were taken from 92 birds (73 species) and the V4 region of the 16S rRNA gene was used as the microbial fingerprint (515f and 806R primers).

Major Advisor

Sarah Hird