EAPSI: Refining Analysis Methods for Examining Human Gut Bacteria

Nettles Rachel M, Provo UT

Investigators

Abstract

The human gut microbiome is the community of microbes living in the intestinal tract, including the stomach, the small and large intestines, and the colon. The composition of the gut microbiome affects many aspects of human health, including the incidence of inflammatory diseases of the bowel (e.g. inflammatory bowel disease) and other parts of the body (e.g. rheumatoid arthritis), various cancers, and diabetes. Many researchers use a mouse model in their investigations of the gut microbiome. However, the mouse model, while convenient for research, is not necessarily a reliable model as a predictor of human response to the microbiome. Therefore, it is imperative to be trained in research on the human microbiome itself. This is possible in the laboratory of Professor Gerald Tannock, at the University of Otago, Dunedin, New Zealand. The purpose of this research is to gain valuable expertise in human microbiome research by refining the methodology used by Professor Tannock to analyze the structure of infant gut microbial communities. Studies involving the microbiome often require the use of next-generation, high-throughput sequencing (HTS). Despite the ubiquitous use of sequencing, there is no approved universal method for analyzing this data, as research-directed questions will often call for different bioinformatic approaches. This can cause problems when attempting to compare the results from two studies that used two different methods for analyzing the data. This project will incorporate the latest analytical tools to search for fine detail trends in microbiome data that may be hidden when using default approaches. QIIME is a commonly used software package that focuses on quality screening and analysis of HTS data from amplified marker genes. We will utilize this package to test different approaches of analyzing sequencing data, and will compare outputs in an attempt to reveal previously hidden associations between individual microbiomes. This study will allow us to suggest improved analysis pipelines that may be implemented by other investigators working in the field of gut microbiome research. This award under the East Asia and Pacific Summer Institutes program supports summer research by a U.S. graduate student and is jointly funded by NSF and the Royal Society of New Zealand.