Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach

Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible the overall signal detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus migratory trajectories feeding impact their shape, rare address comparison to other sources develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers detect such Thus, by using 16S rRNA amplicon high-throughput sequencing, aims this study were (i) explore compare fecal bacterial communities from (i.e., six families 15 species, n = 275 samples) that poultry, cattle, pigs, influent/effluent wastewater treatment plants ( 150 (ii) new MST for waterbirds. Significant differences observed between four groups. We identified 7,349 Amplicon Sequence Variants (ASVs) hypervariable V3–V4 region. Firmicutes Proteobacteria and, lesser extent, Actinobacteria Bacteroidetes ubiquitous while Fusobacteria Epsilonbacteraeota mainly present The clustering samples non-metric multidimensional scaling (NMDS) ordination indicated by-group with diversity within In addition, structure was distinct according bird and/or animal species (Adonis R 2 0.13, p 10 –4 , Adonis 0.11, respectively). Analysis Composition Microbiomes (ANCOM) showed waterbird group differed others significant presence sequences Fusobacteriaceae W 566) Enterococcaceae 565) families, corresponding Cetobacterium 1427) Catellicoccus genera, respectively. Altogether, our results suggest some members microbiomes allowing design qPCR markers. For instance, swan- an oystercatcher-associated (named Swan_2 Oyscab, respectively) have been developed. Moreover, genera harboring potential human pathogens associated droppings detected dataset, including enteric pathogens, i.e., Arcobacter Clostridium Helicobacter Campylobacter environmental Burkholderia Pseudomonas . Future involving wildlife hosts may improve microbiome marker development, helping mitigation yet unknown sources.