Tap water as a natural vehicle for microorganisms shaping the human gut microbiome

Abstract

Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.

Fig. 1

Microbial composition of 16 drinking water samples collected from different locations of the Parma District and delivered by the city water supply system. Panel A displays a histogram with the relative abundance of each microbial species identified in the analysed samples. From left to right, the colour‐coding order of the legend reflects average abundances from largest to smallest, i.e. 55% Acidovorax delafieldii in sample W012, 38.9% Sphingomonas spp. in sample W013, and so on. Panel B shows the percentage of unknown and known bacterial species profiled, while Panel C depicts the prevalent bacterial taxa identified among all processed samples.

Fig. 2

Microbial composition of 132 drinking water samples as obtained from NCBI. Panel A exhibits the PCoA, based on microbial distribution, represented in different colours by means of 10 projects (P1 to P10) using the Bray–Curtis index. Panel B displays a heat map with the prevalence of major microbial players between projects. Panel c reports a schematic overview of the most prevalent bacterial species between projects. Species names and numbers in hexagons represent those taxa prevalent in samples from a number of projects written in circles. P4 data were excluded from the comparisons to avoid bias in the analyses' outcome.

Fig. 3

Investigation of the colonization of drinking water bacteria in humans. Panel A shows the percentage of human faecal samples in which the 10 core microorganisms associated with drinking water were identified through read mapping. Panel B represents a schematic representation of the pilot experiment with drinking and sampling periods (T1, T2 and T3). Panel C illustrates the qPCR data of Curvibacter spp. in tap water (W001‐T1 and W001‐T3) and faecal samples of the subject (F01‐T1, F01‐T2 and F01‐T3).