Impact of Probiotics on Gut Microbiome Bifidobacterium Relative Abundance: First Do No Harm

Background: Several reports have raised safety concerns regarding the use of probiotics. To address these concerns, this study examined the relative abundance (proportion of the microbiome made up of a particular taxa) and normalized read counts (number of times a particular microbe was identified) of Bifidobacteria in the gut microbiome of healthy subjects participating in an ongoing study on the microbiome. Bifidobacteria is a critically important constituent of the human microbiome and plays roles in digestion, gut immunity, and cancer prevention. Methods: Fecal samples were analyzed using next-generation sequencing to evaluate composition and relative abundance of bacterial phyla through species level in each subject`s microbiome. The primary outcomes of this subgroup analysis were relative abundance and normalized read count of genus Bifidobacteria in subjects who took unregulated probiotics, regulated probiotics, or no probiotics. Results: The relative abundance and normalized read count of Bifidobacteria were significantly lower in the microbiome of subjects who took unregulated probiotics (n=15) than in the microbiomes of both those who took regulated probiotics (n=12, P=0.0002) and no probiotics (n=13, P=0.0483) (0.18 vs. 9.59 vs. 5.66 relative abundance). Discussion: Subjects taking unregulated probiotics had a significantly lower relative abundance of Bifidobacteria, which could potentially have a detrimental impact on health. Next-generation sequencing could be a useful tool to guide decisions on the appropriate use of probiotics based on dysbiosis.