We’ve all heard the claims of probiotic yogurts and their benefits for human health, but aside from improving our belly dancing skills, what exactly are probiotic bacteria doing?
An elegant study from the Jeffrey Gordon lab explored the effects of consuming fermented milk products (FMPs) containing probiotic bacteria on the human gut microbiota. They sequenced fecal samples from 7 pairs of monozygotic twins before, during, and after a 7-week period of consuming a FMP containing 5 probiotic strains to investigate if probiotic bacteria alter the composition of the microbiota. They conducted complimentary experiments in gnotobiotic mice harbouring a synthetic microbial community consisting of 15 strains whose genomes are sequenced and are considered functionally equivalent to the human gut microbiota. They then introduced 5 FMP strains and sequenced the model community to observe its dynamics over time. In both humans and mice, they observed that the community remained relatively stable during the period of exposure to FMP bacteria, an interesting finding suggesting that probiotics do not exert their effect by altering the proportions of microbial populations in the gut.
They then turned to RNA-seq to ask whether the bacterial community displayed functional changes. The transcriptional profile of the most dominant and persistent FMP strain revealed up-regulation of genes involved in catabolism of xylooligosaccharides in vivo in both mice and humans. They also found that the model community responded to the introduction of the FMP strains by altering expression of genes involved in metabolic pathways, primarily those associated with carbohydrate metabolism, and noted differences in carbohydrate metabolites in the urine of the mice. Perhaps the metabolic shift of the FMP bacteria and the resident microbiota is a key contributor to the benefits of FMPs on intestinal health.
Not only does this study provide insight as to how probiotics impact the gut microbiota, it also emphasizes that it’s not necessarily what microbes are there, but rather what they are doing that is relevant to our health. Our determination to uncover links between the microbiome and states of health and disease requires a global analysis, similar to this study, including techniques to study microbial communities at the genomic, transcriptomic, and metabolomic level. With this approach we will begin to understand the identity and functionality of our microbial ecosystem in a healthy stable state and further determine how divergence can positively or negatively impact our health.