Novel insights into immune cell diversity and maturation in the pteropodid bat Eonycteris spelaea via single-cell transcriptome analysis

Bats within the mammalian order Chiroptera are reservoir hosts for various zoonotic viruses, and there is significant interest in understanding and learning from the bat immune system. Here, we utilised single-cell transcriptome sequencing (sc-RNAseq) to profile 123,000 cells and 50 cell types in bone marrow, blood and liver tissue of the nectarivorous bat Eonycteris spelaea . We provide a comprehensive map of immune cell heterogeneity and maturation across these tissues, benchmarking bat immune cell identities against human single-cell atlases. We identify a TREM2 + subset of circulating monocytes lacking a clear counterpart in healthy human peripheral blood, a neutrophil IDO1 associated immunosuppressive signature acquired upon bone marrow egress, and a dominant population of FCER1G expressing innate-like T cells enriched for cytotoxic effector genes across tissue sites. This work provides a rich resource for dissecting the complex interplay between immune tolerance and immune effector mechanisms in bats and expands our understanding of the diversity of the mammalian immune system.