Microbial cross-feeding promotes multiple stable states and species coexistence, but also susceptibility to cheaters.

Mutualism, interspecific cooperation that yields reciprocal benefits, can promote species coexistence, enhancing biodiversity. As a specific form of mutualism, cross-feeding, where each of two mutualists produces a resource the other one needs, has been broadly studied. However, few theoretical studies have examined competition between cross-feeding mutualists and cheaters, who do not synthesize resources themselves. In this paper we study a model with two mutualists, a cheater, two micronutrients that are synthesized and exchanged by the mutualists, and one macronutrient that is only from external supply. We investigate the coexistence of the species in the framework of resource competition theory. In particular, we examine the effect of the mutualists' synthesis rates on their coexistence. In the absence of cheaters, multiple stable states occur if the synthesis rates are high, and higher synthesis rates increase the possibility that mutualists coexist. However, when the cheater is present, higher synthesis rates promote invasion by the cheater: If the cheater is superior on all three resources, it will either persist with at most one mutualist or even trigger extinction of all three species; if the cheater is only superior on the macronutrient, both mutualists may still coexist with the cheater. Our results provide a framework for further study on more complex mutualistic networks and real microbial communities.

Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae.

The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R2 = 0.92 for the training set and R2 = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.

Modulation of the gut microbiome with nisin.

Nisin is a broad spectrum bacteriocin used extensively as a food preservative that was identified in Lactococcus lactis nearly a century ago. We show that orally-ingested nisin survives transit through the porcine gastrointestinal tract intact (as evidenced by activity and molecular weight determination) where it impacts both the composition and functioning of the microbiota. Specifically, nisin treatment caused a reversible decrease in Gram positive bacteria, resulting in a reshaping of the Firmicutes and a corresponding relative increase in Gram negative Proteobacteria. These changes were mirrored by the modification in relative abundance of pathways involved in acetate, butyrate (decreased) and propionate (increased) synthesis which correlated with overall reductions in short chain fatty acid levels in stool. These reversible changes that occur as a result of nisin ingestion demonstrate the potential of bacteriocins like nisin to shape mammalian microbiomes and impact on the functionality of the community.