Microbial diversity in water and animal faeces: a metagenomic analysis to assess public health risk

Environmental DNA (eDNA) offers a new avenue for investigating changes in the water microbial community associated with faecal contamination. Faeces in drinking water might include pathogens, which result in serious waterborne diseases in humans. Therefore, drinking water requires comprehensive information about microbial diversity that comes from faecal contamination of different sources to reduce the risk of gastrointestinal diseases. Here, we investigated the microbial diversity of water and faecal samples at 15 recreational campgrounds in New Zealand. In total, 42 faecal (two rabbits, seven ducks, seven ruminants, seven passerines, nine possum and ten Pukeko) and 75 water (37 intakes and 38 taps) samples were analysed using 16S rRNA metabarcoding. Our results suggested that water samples harbour a higher microbial diversity than faeces. Canonical correspondence analysis of bacterial communities and NeighborNet tree of recognised pathogens showed clustering of samples from similar sources. Phylogenetic analyses showed evidence for the presence of Arcobacter and Sulfurospirillum and indicator organisms Escherichia and enterococci in water, while Campylobacter was mainly found in faeces. These findings provide novel insights toward understanding the quality of drinking water and allow future use for the identification of faecal contamination in water.