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Comparative Study
. 2020 Apr 9;15(4):e0231210.
doi: 10.1371/journal.pone.0231210. eCollection 2020.

A comparative analysis of drinking water employing metagenomics

Kyle D Brumfield  1   2 , Nur A Hasan  2   3 , Menu B Leddy  4 , Joseph A Cotruvo  5 , Shah M Rashed  1   3 , Rita R Colwell  1   2   3 , Anwar Huq  1
Affiliations
Comparative Study

A comparative analysis of drinking water employing metagenomics

Kyle D Brumfield et al. PLoS One. .

Abstract

The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.

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Conflict of interest statement

The authors declare the follow potential conflicts of interest with respect to the research, authorship and/or publication of this article: RRC is the founder of CosmosID, Inc., Rockville, MD and also a Professor at the University of Maryland; NAH and SMR are employees of CosmosID, Inc., Rockville, MD; JAC is the founder of Joseph Cotruvo and Associates LLC, Washington, DC; MBL is an employee of Essential Environmental and Engineering Systems, Huntington Beach, CA. The specific roles of these authors are articulated in the ‘author contributions’ section. This does not alter our adherence to PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors (https://journals.plos.org/plosone/s/competing-interests).

Figures

Fig 1
Fig 1. Principal coordinate analysis of bacterial communities in drinking water microbiomes.
Fig 2
Fig 2. Krona plot of bottled sparkling natural mineral water microbiome.
Species composition percentages are displayed as the normalized proportion of organism specific k-mers observed relative to the total microbial species diversity detected in the sample. Red, bacteria; green, fungi; purple, protozoa; teal, archaea.
Fig 3
Fig 3. Krona plot of normalized bottled non-mineral water, including spring, artesian, and reprocessed tap water sample microbiomes.
Species composition percentages are displayed as average number of organism specific k-mers detected, normalized to represent the proportion of organism specific k-mers observed relative to total microbial species diversity detected. Red, bacteria; green, fungi; purple, protozoa; teal, archaea.
Fig 4
Fig 4. Krona plot of municipal tap water microbiome.
Species composition percentages are displayed as the normalized proportion of organism specific k-mers observed relative to total microbial species diversity detected in the sample. Red, bacteria; green, fungi; purple, protozoa; teal, archaea.
Fig 5
Fig 5. Krona plot of public drinking fountain water microbiome.
Species composition percentages are displayed as the normalized proportion of organism specific k-mers observed relative to the total microbial species diversity detected in the sample. Red, bacteria; green, fungi; purple, protozoa; teal, archaea.
Fig 6
Fig 6. Heatmap of relative abundance of bacterial, fungal, protozoan, and archaeal species DNA in drinking water microbiomes.
Species composition percentages are displayed as the normalized proportion of the microorganism specific k-mers observed in each sample relative to the total microbial species diversity of the sample. Color gradient key displays the scale of relative abundance percentages. Sample A, bottled sparkling natural mineral water; sample B, bottled spring water; sample C, bottled artesian water; sample D, bottled reprocessed tap water; sample E, municipal tap water; sample F, public drinking fountain water.
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