Development of a Genetic Modification Tool for Human Gut Bacteria Uncovers Factors in Gut Colonization and Inflammation Control

Researchers have developed a genetic manipulation tool for the human gut bacterium Mediterraneibacter gnavus, which has been associated with various diseases including inflammatory bowel disease and allergies. Furthermore, analysis using this tool revealed that the capsular polysaccharide covering the surface of this bacterium is crucial for gut colonization and possesses functions that suppress inflammation.

Over 40 trillion bacteria inhabit the human gut. These communities, known as the gut microbiome, are closely intertwined with our health and diseases. Mediterraneibacter gnavus (formerly Ruminococcus gnavus, hereafter M. gnavus) is a resident bacterium belonging to the Lachnospiraceae family found in the intestinal tract of healthy individuals. However, it is known to be highly abundant in patients with inflammatory bowel diseases (ulcerative colitis and Crohn's disease), drawing attention to its link to pathology. Until now, genetic modification of this bacterium had been difficult, severely limiting research into the molecular mechanisms of factors related to its pathogenicity and colonization.

In this study, multiple molecular genetic tools were developed specifically for M. gnavus, including gene introduction plasmids, fluorescent labeling, and gene deletion methods, making its genetic modification possible. Furthermore, these tools were shown to be applicable not only to M. gnavus but also to other gut bacteria of the Lachnospiraceae family frequently detected in the gut. Functional analysis of M. gnavus using these technologies revealed that the capsular polysaccharide produced by the bacterium is essential for colonization of the intestinal tract. Capsular polysaccharides are carbohydrates that cover the bacterial cell and are thought to inhibit recognition by host immunity. Moreover, mutant strains lacking the capsular polysaccharide showed high inflammatory activity, and strains isolated from Crohn's disease patients showed a tendency to lack the gene clusters involved in capsular polysaccharide production. These findings suggest that capsular polysaccharides are related to the pathogenicity of this bacterium and could be applied as biomarkers by examining their association with disease activity, such as severity and intensity of inflammation.

This research enables gene function analysis for gut bacteria that were previously difficult to genetically modify, and is expected to contribute to elucidating the causes of inflammatory diseases and developing next-generation probiotics (functional gut bacteria that improve the intestinal environment and contribute to health maintenance).

The research was led by Assistant Professor Nozomu Obana of the Faculty of Medicine, University of Tsukuba, and Specially Appointed Professor Shinji Fukuda of the Institute for Advanced Biosciences, Keio University. The team focused on sortase enzymes involved in presenting proteins on the cell surface of M. gnavus and created bacterial strains with six of the eight sortase genes disrupted. They found that srtB4 is essential for presenting capsular polysaccharides. Experiments co-administering wild-type and deficient strains to germ-free mice confirmed that the capsule-deficient strain was rapidly eliminated from the intestinal tract and showed strong inflammatory activity, proving that the capsular polysaccharide is responsible for both colonization and inflammation suppression.