The human gastrointestinal tract harbors a diverse ecosystem of commensal microbes that play an integral role in human health. Alterations to microbial composition, including those driven through diet or medication, are associated with a plethora of diseases, including inflammatory bowel disease, diabetes and obesity. However, limited knowledge of the functional requirements of individual bacterial species has limited the transition from associative taxonomic profiling to causative validation. This has also limited our ability to study microbial interactions and the formation of an optimal microbiome community structure, to inform therapeutic development.
Applying culturing techniques, we aimed to improve functional microbiome analysis methods to enhance the mechanistic understandings of the processes determining microbiome community structure. Initial phenotypic and whole genome analysis of 89 gastrointestinal isolates was performed to assess the varying nutrient requirements of common gastrointestinal isolates, highlighting isolate level growth variation and carbohydrate dependencies. This analysis demonstrates a diverse array of nutrient requirements and highlights the need for detailed, strain level investigation of therapeutic candidates. Future application of these studies at the community level with multi-omic analysis of temporal datasets will be required to assess the role of nutrient availability in community establishment.