Determinants of raffinose family oligosaccharide use inBacteroidesspecies

Abstract

Bacteroidesspecies are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, howBacteroidesutilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by ⍺-1,6 bonds to a sucrose (glucose ⍺-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization inBacteroides thetaiotaomicron. Here, we identify two different types of mutations that increaseBT1871mRNA levels and improveB. thetaiotaomicrongrowth on RFOs. First, a novel spontaneous duplication ofBT1872andBT1871places these genes under control of a ribosomal promoter, driving highBT1871transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increaseBT1871transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization inB. thetaiotaomicron. Examining the genomes of otherBacteroidesspecies, we found homologs of BT1871 in subset and show that representative strains of species containing a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.ImportanceThe gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the gut microbiota since they remain undigested by the host. Here, we study how the model gut commensal,Bacteroides thetaiotaomicronutilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.