CLR-Seq: a pipeline to identify bacterial microbiota species with immunomodulatory potential 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 currentomics 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.