Culture-Based Methods Provide Critical Phenotypic Ecological Characteristics of Bacteria and their Bacteriophage Undiscernible via Genomics Open Access

Abstract

Despite a massive amount of research, the population dynamic, ecological, and evolutionary mechanisms that determine the distribution and abundance of microbes in the human gut microbiome have yet to be determined. Using fecal microbiota transplantation (FMT) doses as a proxy for the human gut microbiome, we have employed molecular and culture-based methods to investigate such mechanisms for Escherichia coli in the gut. Genetic analysis suggests there is little genetic variation among isolates of E. coli and among the their lytic phages. Nevertheless, there is phenotypic variation. While all E. coli isolates tested are susceptible to the FMT-sourced phages, there is substantial quantitative variation across the bacteria in their susceptibility to the phage and in the capacity of the phage to infect the different isolates of the bacteria. Taken at large, the results of this study question whether the purely correlative and bioinformatic analysis conventionally used to study microbiomes is able to elucidate the mechanisms that determine the structure of these microbial communities.

Table of Contents

Introduction 1

Results 2

Discussion 8

Materials and Methods 8

Supplementary Data 13

Appendix 17

References 19 

About this Honors Thesis

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School	Emory College
Department	Biology
Degree	B.S.
Submission	Honors Thesis
Language	English
Research Field	Biology, Bioinformatics Biology, Microbiology Biology, Ecology
Keyword	Phenotype Bacteriophage Variation FMT
Committee Chair / Thesis Advisor	Bruce R. Levin, Emory University
Committee Members	Michael Woodworth, Emory University Nic Vega, Emory University

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