Deep Dive Into Our Science
To predictably harness microbiomes to benefit human health,
we must fundamentally understand the physiologies of these bacteria.
Unfortunately, most human gut bacteria have never been studied using molecular genetic tools. In addition, most gut bacteria are too distantly related to well-studied model bacteria such as Escherichia coli for genes to be accurately annotated via homology. The result? Major gaps in our understanding of gene function in human gut bacteria.
At GutWorks, we have crafted a systematic strategy to close these gaps.
High-throughput genetics is an attractive approach for characterizing the biological functions of the genes in the human microbiome. Foremost, bacterial genetics can be applied en masse to large populations of genetically modified bacteria, permitting parallel assessment of nearly all genes in a bacterium across a multitude of in vitro conditions. The Deutschbauer Lab recently applied one such approach—random barcode transposon site sequencing (RB-TnSeq)—to 32 bacteria to identify phenotypes for >11,000 genes of previously unknown function.
In vitro conditions are valuable for identifying genes involved in substrate transformations and antibiotic resistance. But if we want to understand the natural ecology of gut commensal bacteria, we must apply these large-scale genetic approaches in vivo. Note that in vivo data become more interpretable through comparisons with the in vitro data, and more phenotypes can be detected with a combined strategy.
GutWorks seeks to apply a similar high-throughput strategy to the human gut microbiome, but we need to overcome four major obstacles along the way:
Transforming non-model bacteria remains challenging and is a largely trial-and-error effort
Developing a new genetic system for a non-model bacterium is time consuming, expensive, and prone to failure
Adopting (and adapting) multiple technologies and laboratory workflows complicates the comparison of data across teams
In vivo mouse experiments should ideally be carried out in ex-germ-free mice colonized by mutants of interest, requiring a gnotobiotic mouse facility.