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Do probiotics alter gut microbiome composition?

Probiotic ads tout the number of live bacteria they contain, typically numbering in the billions. But our guts already contain trillions of bacteria. Do probiotics actually change the makeup of our microbiomes?

Study under review: Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials


The human gut is home to trillions of microbes that work synergistically[1] with the digestive system to synthesize nutrients from compounds we are not capable of digesting, enhance immune function, and even regulate brain behavior (see Study Deep Dives #6 and #16). Unsurprisingly, various diseases such as rheumatoid arthritis[2], irritable bowel syndrome[3], obesity[4], and diabetes[5] have all been associated with specific changes to the microbiome when compared to healthy people.

What defines the microbiome of “healthy” people? Humans harbor more than 1,000 species[6] of bacteria in the gut, with most belonging to the Bacteroidetes and Firmicutes phyla, and there is considerable variation[7] among apparently healthy individuals, owed in no small part to differences in lifestyle, environment, and diet. This marked complexity makes it difficult to separate meaningful patterns from unimportant noise.

Nonetheless, several themes[8] have emerged from population-level analyses, some of which are depicted in Figure 1. These analyses suggest that a healthy gut microbiome is one that provides an abundance of metabolic pathways (i.e. does a bunch of biochemistry that benefits the host), has a diversity and evenness of microbial groups (lots of different bacteria with no single group overpowering another), and demonstrates the ability to resist harm and return to a healthy state after insult. Indeed, at least one study[9] has shown the microbiome of healthy adults is relatively stable (unchanged) over a five-year period.

Figure 1: Possible factors that make the gut microbiome "healthy"

Reference: Lloyd-Price et al. Genome Med. 2016 Apr.

If a healthy microbiome is diverse and stable over time, then what impact does consuming probiotics have? There is evidence[10] suggesting that probiotic therapy is effective at returning a dysregulated microbiome to a healthy one, but evidence of an effect in already healthy humans is weak. The current systematic review sought to evaluate whether consuming probiotic supplements influenced the composition of healthy people’s gut microbiome composition.
A healthy microbiome is diverse, stable, and capable of numerous metabolic functions. A change away from these general traits is associated with various disease states, and probiotic supplementation appears to help with a return towards normality. However, the effect of probiotics in an already healthy gut is not well-characterized. The current study sought to fill this knowledge gap.

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