Microbiota shows major difference in case of two shorebird species with different feeding strategy.

Despite the well-known effects of the gut microbiota on mammals, other vertebrates have only recently begun receiving attention in research. Our study focused on describing the cloacal microbiome of Common Snipe (Gallinago gallinago) and Wood Sandpiper (Tringa glareola), using 16S rRNA metabarcoding, to understand how different foraging methods can affect their microbiome. Assessing the host microbial diversity, we found that Shannon- (W = 253, p = 0.099), Simpson- (W = 268, p = 0.168) and inverse Simpson- diversities (W = 268, p = 0.168) did not differ significantly, however, there was a tendency towards the Wood Sandpiper having the higher values. SIMPER analysis revealed that the differences were caused by several bacterial taxa, the biggest contributor being Catellicoccus marimammalinum (mean contribution = 2.76%, p = 0.003) which had greater abundances in Common Snipe (mean relative abundance = 22.76%) than in the Wood Sandpiper (8.27%). We found great differences in Fusobacteria abundances between the hosts, as this phylum had an average abundance of 29.4% in Wood Sandpiper and 8.8% in Common Snipe samples. This difference in their microbiome may be explained by the higher chitin consumption of Wood Sandpiper which is associated with higher Fusobacteria abundance. We found multiple important animal (Mycoplasma iowae, Brachyspira hyodysenteriae) and human pathogens (Campylobacter jejuni, Aeromonas veronii, Vibrio cholerae), some of which are also associated with the growing problem of antimicrobial resistance (Escherichia coli, Enterococcus faecalis). The high prevalence of these pathogens in wild waterbirds should be considered important when assessing human and environmental health hazards.