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

Jordy Evan Sulaiman^1*Yuewei Zhan²Shuchen Wang²Ka Lun Lai²James Ho Wa Li²Daniel Ye Yutong^3,4Karl Tsim^3,4Kenneth, King-yip CHENG^5*Yong Lai^2*Henry Lam^2*

• ¹Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong, SAR China
• ²Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong, SAR China
• ³Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, Hong Kong, Hong Kong, SAR China
• ⁴State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, Hong Kong, Hong Kong, SAR China
• ⁵Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, Hong Kong, Hong Kong, SAR China

Akkermansia muciniphila and Bifidobacterium 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 A. muciniphila and two Bifidobacterium species, B. longum and B. breve, in the presence of different carbon sources. A. muciniphila displayed distinct growth profiles when co-cultured with B. breve and B. longum in media containing monosaccharides (glucose and N-acetyl-D-glucosamine) or mucin. A. muciniphila led to reduced abundance of B. longum in co-culture compared to monoculture, irrespective of whether the media contained monosaccharides or mucin. By contrast, B. breve led to reduced abundance of A. muciniphila in co-culture compared to monoculture in the presence of the monosaccharides but not in the mucin medium. Proteomics analysis revealed that B. breve induced substantial alterations in the protein expression of A. muciniphila 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 B. longum in monoculture and co-culture. Notably, in the presence of arabinoxylan, B. longum promotes the growth of A. muciniphila 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 A. muciniphila and B. breve or B. longum co-cultures and highlight that dietary fibers can be utilized to improve the functionality of the probiotic community.