Understanding modern and ancient human gut microbiome assemblies [Nodes Seminar]

The gut microbiota of healthy individuals is commonly dominated by the Bacteroidota phylum. Within this phylum, members of the Bacteroidaceae and Prevotellaceae family tend to exclusively predominate the microbiomes of populations with industrialized and traditional lifestyles, respectively. These predominance patterns are mainly attributed to distinct diets and are associated with ambiguous health outcomes. Prevotellaceae predominance in the microbiota has been associated with healthy lifestyles and improved health outcomes, whereas Bacteroidaceae predominance is associated with diets high in processed foods and animal fat. Interrogating experimentally how such microbiota compositional patterns are shaped beyond association studies is critical for elucidating microbiome health biomarkers.
How these different microbiota configurations are shaped and how they interact with pathogens and different dietary patterns, remains largely unexplored experimentally. Through synthetic community design, anaerobic microbiology, gnotobiotics, and metagenomics analysis, we elucidate the principles that govern major microbiota signatures in human populations. We focus on niche interactions between members of the Bacteroidaceae and Prevotellaceae families and systematically assess how dietary components influence interactions between these two bacterial families. Together, our studies provide new insights into the long-standing question of what drives major human microbiota configurations. Given these signatures, our work explores how infections and environmental signals drive the evolution of the major inhabitants of the human gut leaving lasting and functional signatures on the gut microbiota.