CLR-Seq: A pipeline to identify bacterial microbiota species with immune-relevant glycan moieties through human C-type lectin receptor interaction.

Bacterial glycans are key components in immune interactions. We lack insight into the diverse glycan landscape present in complex microbial communities since current -omics techniques do not capture this post-translational information. Here we employed C-type lectin receptors (CLRs), which are dedicated innate glycan-sensing receptors, as probes for bacterial cell sorting in combination with 16S rRNA gene sequencing to identify microbiota species with a specific CLR-reactive glycan profile. We established our experimental CLR-sequencing (CLR-seq) pipeline using soluble fluorescently-labeled human macrophage galactose C-type lectin (MGL, CD301) and langerin (CD207). Both receptors identified known langerin- or MGL-interacting Staphylococcus aureus strains in a synthetic microbial community even when present at low abundance. Subsequent application of CLR-seq on fecal microbiota samples from healthy donors identified specific langerin- and MGL-interacting bacterial species that were subsequently validated as monocultures. In summary, CLR-seq is a modular platform that allows identification of human microbiota species based on CLR-interacting glycans with easy expansion to other CLRs or microbiota samples from patients. Given that CLRs are densely expressed on dendrites of antigen-presenting cells, this pathway may play a role in cross-barrier recognition and sampling of the environment during homeostasis.