Proteomic study of Akkermansia muciniphila and Bifidobacterium species co-culture under different carbon sources

<i>Akkermansia muciniphila</i> and <i>Bifidobacterium</i> spp. are major probiotic strains that have been shown to improve host metabolism and treat metabolic diseases. Previous studies have proposed formulating these probiotics as a therapeutic product to improve efficacy, but how they affect the growth and protein expression of each other in response to different nutrient environments remains unexplored. Here, we performed label-free quantitative proteomics on <i>A. muciniphila</i> and two <i>Bifidobacterium</i> species, <i>Bifidobacterium longum</i> and <i>Bifidobacterium breve</i>, in the presence of different carbon sources. <i>Akkermansia muciniphila</i> displayed distinct growth profiles when co-cultured with <i>B. breve</i> and <i>B. longum</i> in media containing monosaccharides (glucose and N-acetyl-D-glucosamine) or mucin. <i>Akkermansia muciniphila</i> led to reduced abundance of <i>B. longum</i> in co-culture compared to monoculture, irrespective of whether the media contained monosaccharides or mucin. By contrast, <i>B. breve</i> led to reduced abundance of <i>A. muciniphila</i> in co-culture compared to monoculture in the presence of the monosaccharides but not in the mucin medium. Proteomics analysis revealed that <i>B. breve</i> induced substantial alterations in the protein expression of <i>A. muciniphila</i> when cultured in the media with monosaccharides, but the two species minimally affected each other's protein expression when cultured in the mucin medium. By screening health-relevant dietary fibers, we discovered that arabinoxylan selectively boosts the growth of <i>B. longum</i> in monoculture and co-culture. Notably, in the presence of arabinoxylan, <i>B. longum</i> promotes the growth of <i>A. muciniphila</i> and increases the expression of Amuc_1100 protein, leading to the enhancement of barrier integrity of intestinal epithelial cells. In sum, we demonstrated that glycans shape the growth and proteome profiles of <i>A. muciniphila</i> and <i>B. breve</i> or <i>B. longum</i> co-cultures and highlight that dietary fibers can be utilized to improve the functionality of the probiotic community.