Uncovering the molecular strategies that allow human gut symbionts to degrade insoluble dietary and host glycans

The human intestine harbours enormous numbers (100 trillion) of resident gut micro-organisms that have important consequences for many aspects of health. The energy sources that support the growth of this complex community derive largely from carbohydrates (glycans) that are not degraded by host enzymes, in particular from dietary plant polysaccharides and host-secreted mucin. Much of the non-digestible carbohydrate that enters the large intestine is in the form of insoluble material such as starch particles, plant cell wall fragments and secreted mucus. Rather few bacterial species have the ability to degrade these insoluble substrates. Those that do must be considered 'keystone species', responsible for releasing energy to the rest of the microbial community, and also, via the uptake of microbially-produced short fatty acid products across the gut wall, providing around 10% of the host's energy supply from the diet. Understanding of microbial glycan utilization is therefore fundamental to understanding the impact of diet upon health, and for developing approaches to manipulate the gut microbiota for health benefit. Almost all of the detailed work so far on glycan metabolism by the human gut microbiota has focussed on gram-negative Bacteroides and there is very little information on the equally numerous gram-positive bacteria belonging to the Firmicutes phylum. Recent evidence indicates however that it is certain Firmicutes, especially Ruminococcus spp., that play 'keystone' roles in initiating the degradation of insoluble substrates, whereas human colonic Bacteroides spp. tend to favour soluble carbohydrates. This proposal will therefore investigate for the first time the molecular mechanisms that enable human colonic species of Ruminococcus to degrade particulate resistant starch (R. bromii), cereal bran rich in plant cell wall polysaccharides (R. champanellensis) and insoluble mucin (R. gnavus). The work will exploit the available genome sequences to enable functional studies on extracellular enzymes, enzyme complexes and substrate attachment mechanisms. Preliminary work already shows that organization at the level of the genome and enzyme systems (including likely extracellular enzyme complexes) is completely different from that in Bacteroides spp. A second main element of the proposal will examine interactions of these primary degraders with other species that are likely to compete for solubilized products of insoluble substrates (including Bacteroides spp.), or to modify metabolism by utilizing fermentation products (acetogenic bacteria). These interactions will be explored in vitro and also in vivo by using gnotobiotic animal models (colonised by single, or combinations of, Ruminococcus strains). The project will substantially advance our understanding of the interdependency of different groups within the human gut microbiota and the impact of variations in gut microbiota composition, and will help to test and predict the fermentability of different types of plant material in the gut. Results from this work will help us understand how to keep a beneficial relationship with our gut bacteria and should lead to the development of novel strategies to maintain a 'healthy' gut microbiota and to re-adjust the microbial community following disturbance ('dysbiosis') eg. caused by antibiotics or disease states.