Diverse microbial community with zoonotic potentials characterized in the gut of migratory birds

Identifying gut microbiome shall potentially provide information on the yearly biological course of species, particularly those that are carriers of pathogenic or zoonotic microbes. This study aimed to elucidate the diversity and composition of gut microbiomes and zoonotic consortia in wild and migratory birds from three distinct areas of the Chattaogram division of Bangladesh. Based on their feeding locations, the nine faecal samples collected were divided into three metagenomic groups (e.g., urban, suburban and rural). The collected faecal samples underwent DNA extraction and ribosomal (16S rRNA) gene sequencing targeting the amplification of the V3 - V4 regions. We detected similar bacterial communities in birds' faeces from the same habitat (urban and suburban), and divergent communities from the remaining group (rural). We detected 10 phyla, 16 classes, 27 orders, 52 families, 79 genera, and 121 species of bacteria shared across the sample categories. Variations in the community abundance and variation between the various species were found by analyzing Shannon diversity, Observed species, and Simpson index. Firmicutes, with an average relative abundance of 76%, was detected as the most predominant bacterial phylum across all groups, whilst the genera Carnobacterium and Lactobacillus predominated in semi-urban and rural samples, respectively. The microbial community makeup of the faecal samples from the urban and suburban birds grouped more closely. In contrast, the faecal samples from the rural birds clustered independently, according to principal component and cluster analyses showing significant (p < 0.05, Kruskal Wallis tests) disparity in microbiome composition across the sample categories. Additionally, there were few differences across bird species in the most prevalent bacterial species. The birds' feeding patterns and environmental living conditions may be significant key contributors to the reported discrepancies since several avian gut bacteria are obtained from the food. The makeup of the avian gut microbiota is not significantly affected by relatively brief alterations to food and ecological conditions. This work provides a logical foundation for bird preservation, including disease prevention and management.