Application of integrated in vitro fecal cultivation and 16S rRNA gene sequencing for optimizing beneficial gut microbiota combinations

Abstract

Obesity is a global health concern closely linked to changes in gut microbiota and other metabolic disorders. In this study, we used 16S rRNA gene amplicon sequencing to analyze the gut microbiota composition of normal and obese fecal samples. We further investigated the influence of a beneficial gut microbiota combination, consisting of Phocaeicola vulgatus KBL981, Roseburia intestinalis KBL982, and Akkermansia muciniphila KBL983, strains considered beneficial for obesity management, using in vitro feces cultivation. Results showed a significant difference between the microbiota composition of normal and obesity fecal samples, with the obesity group displaying lower diversity and higher levels of pathogenic Shigella boydii and inflammation-related Bacteroides fragilis. The ideal beneficial gut microbiota mixture (1:1:100) significantly enhanced microbial diversity, balanced the short-chain fatty acid ratio, promoted the growth of beneficial bacteria, and inhibited the growth of harmful obesity-related species. However, oversupplementation of beneficial microbiota reduced the microbial diversity and disrupted the microbial ecosystem. The current study demonstrates that a combined beneficial gut microbiota treatment can help manage obesity-related dysbiosis.