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One of the proposed strategies by which the gastrointestinal microbiota can be modulated is via consumption of live microorganisms, often referred to as probiotics. However, most microorganisms are transients, and colonization does not normally occur due to colonization resistance and other ecological factors. To understand the factors that influence the ability of probiotics to persist in the gastrointestinal tract, it is necessary to consider the microbial interactions within the gastrointestinal ecosystem applying principles of community and invasion ecology. The overall goal of this study, therefore, was to test persistence of the probiotic strain Bifidobacterium longum subp. longum AH1206 in a cohort of human subjects, and determine the microbiome features associated with persistence of this organism. The study was conducted as a double blinded, crossover, placebo controlled trial with 23 healthy adults. In contrast to most studies on probiotics, AH1206 persisted in a subset of subjects for 200 days without a measurable impact on the resident microbiota. Long-term persistence was associated with low abundance of B. longum and specific carbohydrate utilization genes of this species in the pre-treatment microbiome, suggesting that inter-individual differences in the availability of resources constitute a niche opportunity for colonization. The findings further suggest that bacterial species absent in the gut microbiome of some individuals can be reestablished, opening opportunities for precision microbiome reconstitution and the personalization of treatments with probiotics or other live biotherapeutics.
