Probiotics are beneficial bacteria that can improve digestion, support the immune system, and influence metabolism. Now, researchers have found that a probiotic called BV9 initially competes with a native gut microbe in a diet rich in inulin—a type of dietary fiber found in plants. However, the two bacteria evenutally coexist.

The findings, published in Cell Systems, suggest that diet shapes probiotic colonization, offering strategies to improve colonization, modulate the microbiota, and control harmful microbes.

Probiotics work by joining the gut microbiota, but their success depends on surviving stomach acid and competing with existing microbes. However, how probiotics interact with gut bacteria and how these interactions affect long-term health remains poorly understood.

So, researchers led by Zhe Han at Hainan University in China set out to study how the probiotic BV9 colonizes the guts of mice fed different diets.

Dietary influence

The ability of BV9 to settle in the gut depended on the diet of the mice, the team found. BV9 colonized more effectively the guts of mice fed a high-fiber, high-inulin diet than mice fed a high-fat diet or normal diet. In mice on a high-inulin diet, the successful colonization of BV9 led to changes in the gut microbiota, with the probiotic bacterium becoming dominant and altering both the types of bacteria present and their metabolic functions. 

In mice on a high-inulin diet, BV9 competed with a native gut bacterium called Parabacteroides distasonis, while in high-fat or normal diets, BV9 had little effect on this microbe. 

Over time, BV9 reduced the abundance of P. distasonis in mice on a high-inulin diet. However, the two bacteria eventually coexisted. This coexistence involved genetic changes in both species, particularly in DNA regions that affect gene regulation and influence metabolism. 

Microbial competition

Further analyses revealed that BV9 mainly uses inulin through a fructose-based metabolic pathway, while P. distasonis shifted to a glucose-based pathway as the two microbes coexisted. This adaptation allows both bacteria to use inulin as a food source, the researchers found.

The findings highlight that probiotic colonization is nutrient-dependent and can be shaped through dietary interventions, suggesting strategies for improving probiotics or even suppressing harmful bacteria, the authors say.

Although more research is needed to better understand how probiotics adapt and interact in the gut, they add, “this study fills a critical gap in our understanding of niche competition in colonization.”