Microbes living in the human gut have a profound impact on health, with their community composition affecting nutrition, metabolism, gastrointestinal function, and more. A detailed understanding of how these communities form, persist, and determine health outcomes through processes like immune signaling and nutrient absorption could help unlock the full potential of microbiome-dependent therapies. Unfortunately, the complexity of human gut microbe communities makes them difficult to study, slowing progress towards answering fundamental questions about their genetics, physiology, and regulation.

Past research has applied genetic approaches to interrogate these questions in a select few model organisms, such as E.coli, within the context of the adult gut microbiome. But scientists still lack effective genetic tools for studying the vast majority of microbiome members.

One group of beneficial human gut bacteria that remains untapped is Bifidobacteria, which are associated with infant breastfeeding and represent a major component of the developing human gut microbiome. A deeper understanding of Bifidobacteria activity in the digestive tract could offer therapeutic interventions for early-life disorders associated with microbiome imbalances and disruptions. 

So far, it’s proven cumbersome to develop genetic tools robust enough to parse the complicated host- and strain-specific interactions at play with different Bifidobacteria species. Researchers in Kerwyn Casey Huang’s lab at Stanford University sought to overcome these historic challenges, and worked with Environmental Genomics & Systems Biology (EGSB) senior scientist Adam Deutschbauer and research scientist Hans Carlson to leverage their expertise using randomly barcoded transposon sequencing (RB-TNseq) and high-throughput (high-volume) chemical genomics.

Deutschbauer was on the team that first developed RB-TnSeq in 2015 as part of a collaboration between the ENIGMA Science Focus Area and the DOE Joint Genome Institute. RB-TnSeq is a technique that centers on modifying transposons—mobile genetic elements that can insert into a genome at random locations—to carry unique DNA barcodes. The barcoded transposons are then introduced into a bacterial population, where they insert themselves randomly into genomes and create a library of tagged mutant bacteria strains. Researchers can then track the barcodes to compare how different mutants fare under varying experimental conditions, allowing them to zero in on genes that are important for growth and resilience in specific environments.

A recent study, published in Cell, documented the team’s success in using RB-TnSeq to generate a genetic library for Bifidobacterium breve, a representative species of Bifidobacteria. Using these newly-developed tools, the authors surveyed the importance of different genes in supporting Bifidobacterium breve survival. Through a series of experiments conducted in living mice and chickens, the researchers tracked how individual mutant strains coped when their hosts were fed different diets or subjected to environmental stressors. This approach revealed several genes that drive key functional adaptations in Bifidobacteria biology and influence their persistence in the developing intestinal tract.

The team’s detailed overview of the genetic basis for Bifidobacterium breve fitness, along with the other genome-scale resources they developed, will support ongoing biological investigations in Bifidobacteria and other bacteria that reside in the human gut. Ultimately, the study provides a template strategy for the rapid characterization of non-model microbes, and could offer foundational tools for developing Bifidobacteria-based probiotics or prebiotics with therapeutic benefits.