Publication Date


Document Type


Committee Members

Barbara Hull (Committee Member), Shulin Ju (Committee Member), Oleg Paliy (Advisor)

Degree Name

Master of Science (MS)


The microbiota of the human gastrointestinal tract is the focus of current research due to their role in human health and disease. Modern methods characterize the communities of gut microbiota through the use of culture independent techniques. Technologies such as microarrays and next generation sequencing (NGS) determine microbial profiles by analyzing the pool of 16S ribosomal small subunit RNA genes in the community. These techniques operate through the measurement of genomic content rather than through direct analysis of cells. This approach predisposes the methods to discrepancies and bias. In contrast, the use of fluorescence in situ hybridization (FISH) to analyze the gut microbiota allows for the visualization of the cells as well as determination of relative abundances of target taxa. This work describes the application of FISH to visualize the relative abundances of several different members of human gut microbiota between select samples. The results showed that the abundance data obtained from FISH are similar to data collected with microarray and NGS techniques. FISH data demonstrated that there is an enrichment of class Bacilli and genus Prevotella in the gastrointestinal tract of Egyptian children, while children from the U.S. show a higher level of genus Bacteroides. This study also showed that the abundances of class Bacteroidia and genus Bifidobacterium fluctuate in adults undergoing a diet intervention program replacing typical diets with high-protein or high-fat diets. In conclusion, this work illustrates the capabilities of FISH to visualize the members of human gut microbiota and quantify relative abundances of target taxa that are a part of a larger community.

Page Count


Department or Program

Microbiology and Immunology

Year Degree Awarded