Date of Award

Fall 9-5-2025

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Bioinformatics & Computational Biology

First Advisor

Catherine Putonti

Abstract

The mammalian gastrointestinal (GI) tract harbors a dense and dynamic community of microbes known as the gut microbiota, which plays vital roles in digestion, immunity, and overall health. Among these, probiotic bacteria such as Lactobacillus strains have garnered attention for their ability to influence microbial community structure and host physiology. This study investigated the effects of five Lactobacillus strains, Lactobacillus casei R1A482, Lactobacillus casei O3, Lactobacillus rhamnosus GG, Lactobacillus gasseri ATCC 33323, and Lactobacillus paragasseri UMB1065, on the gut microbiome of Swiss Webster mice over a six-week feeding period. To reduce stress, mice were fed Lactobacillus strains using gelatin pellets instead of traditional ga-vage methods, and stool samples were collected weekly. 16S rRNA amplicon sequencing and whole-genome shotgun metagenomics were used to assess microbial and bacteriophage commu-nity changes in response to treatment. Results showed that gut microbial composition changed slightly over time in response to some treatments. While strains such as L. casei O3, L. rhamno-sus GG, L. gasseri ATCC 33323, and L. paragasseri UMB1065 were associated with modest shifts in microbial structure, others like L. casei R1A482 had little measurable effect. Dynamic patterns of phage activity were also observed in mice treated with L. gasseri ATCC 33323 and L. rhamnosus GG, to see the effect of gut bacterial composition changes on gut phage life cycle dy-namics. However, a direct causal relationship between probiotic supplementation and phage in-duction could not be confirmed.

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