Exploring retropharyngeal lymph node metabarcoding as a tool for characterizing microbial signatures in white-tailed deer from urban and non-urban areas

Evaluating the effects of urbanization on wildlife has become increasingly important for understanding how host-associated microbial communities respond to environmental change. Characterizing these communities can improve our understanding of shifts in disease pressure and provide information for early detection of changes. Wildlife disease screening programs may also provide a source of opportunistically collected samples for research and monitoring. Here, we evaluated the use of retropharyngeal lymph nodes from white-tailed deer (Odocoileus virginianus) collected in Florida as part of chronic wasting disease surveillance to assess bacterial community composition across urban and non-urban areas. We detected no differences in alpha or beta microbial diversity between deer from urban versus non-urban environments. However, we found evidence of isolation-by-distance in beta diversity, with communities becoming more dissimilar as geographic distance increased and localized clustering near some urban areas. This study explores how lymph nodes collected during routine surveillance can be used to monitor spatial variation and temporal changes in host-associated microbial communities, and we provide recommendations for researchers interested in applying and improving this approach in future studies.