Carbohydrates and the oxidative branch of the pentose phosphate pathway modify Bacteroides thetaiotaomicron phage resistance by phase-variable S-layers.

The human gut microbiota consists of hundreds of bacterial species, some of which persist in the presence of lytic phage that infect them. Bacteroides employ numerous phase-variable strategies to survive in the presence of phage, including capsular polysaccharides (CPS) and S-layer lipoproteins. We previously reported that a Bacteroides thetaiotaomicron strain lacking CPS exhibits almost complete resistance to multiple phages when forced to express the S-layer protein BT1927. However, this strain was only resistant after certain growth conditions, suggesting nutritional variables alter infection and resistance. We grew this strain on various simple sugars and polysaccharides, finding that some substrates (fructose, glucose) promote strong resistance to a single phage (ARB25), while others like N-acetylgalactosamine (GalNAc) and mucin O-glycans increase susceptibility. Mixing fructose and GalNAc indicates the effects of GalNAc are dominant. Despite increasing ARB25 susceptibility, GalNAc did not reduce BT1927 transcript or protein levels. Instead, GalNAc reduced the amount of BT1927 displayed on the cell surface and increased outer membrane vesiculation. Mutants in any of the three steps of the oxidative branch of the pentose phosphate pathway-grown in fructose-behaved similarly to wild-type cells grown in GalNAc, illuminating this pathway in the regulation of sugar-mediated phage resistance. Despite promoting strong resistance, cells grown in glucose/fructose sometimes displayed sub-populations that appeared to completely lack surface BT1927, suggesting another checkpoint exists to control whether this phage defense is deployed. Finally, we show the mucin sugar GalNAc increases susceptibility to several other phage, which has implications for B. thetaiotaomicron persistence in niches like the mucus layer.IMPORTANCEThe persistence of viruses that infect bacteria (bacteriophages or phages) in the human gut microbiome and their effects on bacterial physiology and host health are active areas of investigation. Our study investigates how various sugars and polysaccharides alter the susceptibility of the model gut symbiont Bacteroides thetaiotaomicron to lytic phages that are capable of infecting it. Our finding that the mucin sugar, N-acetylgalactosamine, and mucin O-glycans that contain this sugar reduce B. thetaiotaomicron resistance to multiple phages has implications for how this symbiont persists in different gut microhabitats, such as the mucus layer, and which defense mechanisms it can deploy to survive in these niches.