Linking Taxonomic and Functional Microbiome Diversity with Population Density and Habitat Urbanization in an Urban Exploiter Bird

Microbiome of vertebrate gastrointestinal tract has multifaceted effects on hosts, but is itself modulated by host diet, social interactions, and external environments. Here, we investigated microbiome composition in the feral pigeon Columba livia domestica , an iconic urban bird renowned for extreme population densities, which should facilitate horizontal transmission of microbes and enhance microbiome diversity. We collected faecal samples from 200 individuals at study plots varying in habitat urbanization and pigeon population density within five large cities in Poland. We used high-throughput 16S rRNA gene sequencing to characterize gut microbiome composition. We found relatively high levels of taxonomic and functional gut microbiome diversity in the feral pigeon, with nearly 35 thousand Amplicon Sequence Variants (ASVs) representing 561 bacterial families and 75 functional groups. We detected a negative relationship between habitat urbanization and microbiome taxonomic richness, likely associated with a decline of habitat heterogeneity in more urbanized areas. In the functional dimension, bacteria classified as human and mammal gut commensals, human pathogens, and nitrate-reducers increased in abundance along the urbanization gradient, consistent with the so-called humanization of the gut microbiome in urban birds. Nevertheless, we found no associations between taxonomic or functional microbiome diversity and pigeon population density. There was, however, evidence for significant turnover of microbiome composition among study plots characterized by different urbanization levels and population densities. Our study is among the first addressing the links between population density and gut microbiome diversity in urban contexts and it pinpoints potential fitness consequences of gut microbiome modulations in urban wildlife.