The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract

Abstract

The human gut symbiont Ruminococcus gnavus displays strain-specific repertoires of glycoside hydrolases (GHs) contributing to its spatial location in the gut. Sequence similarity network analysis identified strain-specific differences in blood-group endo-β-1,4-galactosidase belonging to the GH98 family. We determined the substrate and linkage specificities of GH98 from R. gnavus ATCC 29149, RgGH98, against a range of defined oligosaccharides and glycoconjugates including mucin. We showed by HPAEC-PAD and LC-FD-MS/MS that RgGH98 is specific for blood group A tetrasaccharide type II (BgA II). Isothermal titration calorimetry (ITC) and saturation transfer difference (STD) NMR confirmed RgGH98 affinity for blood group A over blood group B and H antigens. The molecular basis of RgGH98 strict specificity was further investigated using a combination of glycan microarrays, site-directed mutagenesis, and X-ray crystallography. The crystal structures of RgGH98 in complex with BgA trisaccharide (BgAtri) and of RgGH98 E411A with BgA II revealed a dedicated hydrogen network of residues, which were shown by site-directed mutagenesis to be critical to the recognition of the BgA epitope. We demonstrated experimentally that RgGH98 is part of an operon of 10 genes that is overexpresssed in vitro when R. gnavus ATCC 29149 is grown on mucin as sole carbon source as shown by RNAseq analysis and RT-qPCR confirmed RgGH98 expression on BgA II growth. Using MALDI-ToF MS, we showed that RgGH98 releases BgAtri from mucin and that pretreatment of mucin with RgGH98 confered R. gnavus E1 the ability to grow, by enabling the E1 strain to metabolise BgAtri and access the underlying mucin glycan chain. These data further support that the GH repertoire of R. gnavus strains enable them to colonise different nutritional niches in the human gut and has potential applications in diagnostic and therapeutics against infection.

Microbiota-induced regulatory T cells associate with FUT2-dependent susceptibility to rotavirus gastroenteritis

“…It does not mean that these associations do not exist, but they may be obscured by the large diversity of the human gut microbiota and by the possibility that FUT2 or HBGAs influences take place at the strain level rather than at the genus or species levels. Thus, a human gut symbiont, Ruminococcus gravis was recently reported to display a strain-specific repertoire of glycosidases, one of them showing specificity for a blood group A tetrasaccharide (Wu et al, 2021). Microbiota composition could also be affected by the strain-specific display of HBGA-specific bacterial adhesins such as the blood group A and B-specific adhesin of a Lactobacillus mucosae strain (Watanabe et al, 2010).…”

“…Nonetheless, associations with the microbiota composition and FUT2 polymorphisms have been reported (Rausch et al, 2011;Wacklin et al, 2011;Tong et al, 2014;Wacklin et al, 2014;Gampa et al, 2017;Kumbhare et al, 2017;Rodríguez-Díaz et al, 2017;Pan et al, 2021;Rühlemann et al, 2021;Lopera-Maya et al, 2022). Although these remain debated and not fully consistent across studies (Davenport et al, 2016;Turpin et al, 2018), there are strong indications that microbiota composition is partly dependent on gut mucosal glycan composition through either bacterial adhesion molecules or through bacterial use of fucosylated glycans as nutrients (Coyne et al, 2005;Watanabe et al, 2010;Kashyap et al, 2013;Pickard et al, 2014;Wu et al, 2021).…”

Developmental stage variation in the gut microbiome of South China tigers

“…The genus of Fusobacterium in the gut microbiome is often associated with meat digestion as reported in other predators ( Ley et al, 2008 ; Keenan et al, 2013 ; Nelson et al, 2013 ; Nishida and Ochman, 2018 ). Ruminococcus gnavus , an early colonizer of the human gut ( Kelly, 2016 ; Wu et al, 2021 ), was reported to be associated with mucin glycan utilization, which is important for the colonization of bacteria in the gut ( Tailford et al, 2015 ; Lim et al, 2017 ). Species of Bacteroides are important for metabolizing polysaccharides and oligosaccharides, which could provide nutrition and vitamins to the host and other intestinal microbial residents ( Wexler, 2007 ; Zafar and Saier, 2021 ).…”

Human gut metagenomes encode diverse GH156 sialidases

“…Enzymes from several GH families have been demonstrated to contribute to host-glycan Mann et al, 6 breakdown (27,41,(48)(49)(50)(51), and new N-and O-glycan-targeting enzymes are being actively reported (52)(53)(54)(55). Together, these factors hinder bioinformatic annotation of a given GH's macromolecular target and a microbe's carbohydrate preferences.…”

“…Critically, the mucous layer is often thinner during inflammation, and bacteria encroach towards the epithelial surface where they are better positioned to induce an immune response (24,25), akin to mice with genetically compromised mucous barriers. breakdown (27,41,(48)(49)(50)(51), and new N-and O-glycan-targeting enzymes are being actively reported (52)(53)(54)(55). Together, these factors hinder bioinformatic annotation of a given GH's macromolecular target and a microbe's carbohydrate preferences.…”