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

Fontaine, Jacob (Spring 2022)

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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 

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