Abstracts Category : Other

Quantitative Analysis of Microbial Species in a MetagenomeBased onTheir Signature Sequences

by Pooja Yadav

ABSTRACTXu, Zhaohui, AdvisorMcKay, RobertRoy,SankardasShotgun metagenomics has provided a relatively new andpowerful approach to study the environmental samples tocharacterize the microbial communities in contrast to pure culturesby conventional techniques. To determine the microbial diversityand to understand the role of microbesin the ecosystem,quantitative studies are important whose values are comparableacross differentstudies and samples. We have developed astatistical approach to microbial profiling which encompassesquantitative characterization and comparison of relative abundanceof the microbes ina metagenome sample based on their signaturesequences (unique k-mers). We demonstrated theutility of thisapproach by characterizing and quantifying the relative abundanceof the microbes in4 different simulated metagenome samples(Comp_25, Comp_50, Comp_75, and Comp_100). Thesuffix of simulatedmetagenome name represents the gene content percentage of reporterspecies in the simulated metagenomes.The analysis of simulatedmetagenomes for data volume 6e9 and 6e10 furnish theinformationabout the abundance of species by identifying the uniquek-mers (signature sequences) of thesix reporter species B.licheniformis, L. brevis, L. fermentum, L. plantarum, P. ananatis,and P.vagans. Our developed approach has efficiently identified theabundance of 4 reporter speciesi.e. B. licheniformis, L. brevis, L.fermentum, P. ananatis whereas 2 species L. plantarum and P.vaganswere overestimated in the simulated metagenomes. So, application ofadvanced statistics,refinement of the algorithm, and an increase indata volume would be our next steps to improvethe accuracy of ourapproach to estimate the ratio of species of ametagenome.Advisors/Committee Members: Xu, Zhaohui (Advisor).