DNA Analysis of Potable Water Biology



Potable Water Biology DNA Analysis

Potable water, also known as drinking water, comes from surface and ground sources and is treated to levels that meet state and federal standards for consumption. With Microbe Detectives’ Potable Water 16S and 18S ribosomal DNA amplicon sequencing plus qPCR quantitation analysis, one can attain an intimate understanding of their potable water system’s microbial community and translate that into improved protection of human health and capital assets.

Problems with Microbial Contamination of Potable Water

Water from natural sources is treated for problematic microbes, toxic chemicals, and fecal matter. The US EPA’s National Primary Drinking Water Regulations (NPDWR) establish maximum contaminant levels (MCLs) for public water systems. Despite these measures of protection, potable water can be contaminated with microbes posing threats to the health of people. According to the Centers for Disease Control, 6,939 deaths and 477,000 hospitalizations were caused by waterborne pathogens in 2017 costing $3.8 billion. Microbial contamination can also be a threat to capital assets due to Microbial Influenced Corrosion (MIC), a leading cause of corrosion damage and leaks in water lines.

Advancements in Molecular Test Methods

Advancements in molecular methods (i.e., DNA analysis) have opened a new window to the microbial world of water. Our 2.0 DNA Analysis identifies, quantifies and tracks the following microbes.

Waterborne Pathogens

Fecal Contamination

  • Coliform fecal contamination indicators Buttiauxella, Citrobacter, Enterobacter, Erwinia, Escherichia, Hafnia, Klebsiella, Kluyvera, Morganella, Obesumbacterium, Pantoea, Proteus, Providencia, Rahnella, Raoultella, Serratia, Shigella, Trabusiella, and Yersinia, and
  • Non-coliform fecal contamination indicators Bacteroides, Enterococcus, Lachnospiraceae, Leptospira, Prevotella, and Ruminococcaceae


  • Bacterial biofilm slime formers Bacillus, Klebsiella, Pseudomonas, and Sphingomonas,
  • Cyanobacteria slime formers Anabaena and Anacystis,
  • Fungal slime formers Candida and Trichoderma, and
  • Algal slime formers Chlorella and Scenedesmus.
  • Shannon’s Diversity Index. The biodiversity of each sample is quantified using Shannon’s Diversity Index. Potable water should normally have a relatively low biodiversity.

Microbial Influenced Corrosion (MIC)

  • Iron Reducing Bacteria Geothermobacter, Pseudomonas and Shewanella,
  • Iron/Manganese Oxidizing Bacteria Acidiferrobacter, Acidithiobacillus, Crenothrix, Ferribacterium, Ferritrophicum, Ferrovibrio, Gallionella, Geobacter, Leptospirillum, Leptothrix, Mariprofundus, Sediminibacterium, Sideroxydans, and Sphareotilus,
  • Sulfate Reducing Bacteria Desulfatirhabdium, Desulfobacteraceae, Desulfobacterium, Desulfobulbaceae, Desulfocapsa, Desulfomicrobium, Desulfomonile, Desulfonatronospira, Desulfosporosinus, Desulfurivibrio, Desulfuromonas and Thermodesulforhabdus,
  • Sulfide Oxidizing Bacteria Clostridium, Desulfarculaceae, Desulfatibacillum, Desulfobacteraceae, Desulfomicrobium, Desulfomonas, Desulfonatronum, Desulforegula, Desulforudis, Desulfosalsimonas, Desulfovibrio, Magnetovibrio, Sulfuricella, Sulfuricurvum, Sulfurimonas, Sulfuritalea, Sulfurospirillum, Syntrophobacter, Thiobacillus, Thiorhodospira and Thiothrix, and
  • Acid Reducing Fungi Fusarium, Hormoconis and Penicillium

Molecular Test Methods

DNA amplicon sequencing of the 16S rRNA gene, identifies nearly all bacteria and archaea at the genus level or above and their relative percentage abundance. qPCR quantitation measures the total quantity of 16S rRNA genes, which is extrapolated to each identified microbial group, measured in 16S rRNA gene copies per milliliter of sample. DNA amplicon sequencing of the 18S rRNA gene identifies nearly all eukarya at the genus level or above and their relative percentage abundance. qPCR quantitation measures the total quantity of 18S rRNA genes, which is extrapolated to each identified microbial group, measured in 18S rRNA gene copies per milliliter of sample. Shannon’s Diversity Index is used to quantify biological diversity.

Molecular Negative Screen (136)

The above 136 genera are organized under two categories for microbial control: Protection of Human Health and Protection of Capital Assets. The number in parenthesis is the number of genus identities.

Protection of Human Health (73)
Waterborne Pathogens (48)
Fecal Contamination Indicators (25)
Protection of Capital Assets (63)
Biofilm Slime Forming Microbes (10)
Microbial Influenced Corrosion (53)

DNA Analysis Report

The DNA Analysis Report lists all 136 target microbes. Detected microbes are highlighted in yellow to indicate caution. Microbes are noted as “Not Detected” to provide written validation of microbes that were not present in each sample.

Key Benefits of Potable Water DNA Analysis

Know if microbial contamination occurs, and the source of the contamination, during distribution to your facility

Potable water quality at the point of entry to a commercial facility may not always be the same as it was at the water utility before being distributed miles and miles across an aging water infrastructure. Microbial contamination can and does occur. This report will identify and characterize the contamination.

Know if microbial contamination occurs, and the source of the contamination, in your ground water wells or non-public potable water system

Urban and agricultural pollution can and does contaminate ground water wells. Fecal contamination from animals can occur near agricultural operations. Fecal contamination can occur in more urban areas by municipal sewage. This DNA Analysis will detect the contamination and help determine the source.

Validate the Absence of Potential Contaminants

Using a molecular negative screen validate microbes that are not present among 136 that are known to be of potential harm to human health or capital assets. This can help establish what contamination did not or does not occur.

Example DNA Analysis Dashboards for Potable Water Biology

Dashboards show how microbial contamination changes over time, or how it compares to other sample locations, or similar potable water systems. Below are a few examples.

npdwr regulated microbial contamination
coliform identities
bacteria genera containing pathogens
eukarya genera containing pathogens
microbiologically influenced corrision
MIC iron reducing bacteria

Types of Potable Water Analyzed by Microbe Detectives

Ground water wells, non-public potable water systems, distributed potable water at the point-of-entry to food processors, healthcare and commercial facilities, fire sprinkler and irrigation potable water systems.



  1. Waterborne Pathogens.AWWA MANUAL M48 Second Edition, 2019
  2. Opportunistic Pathogens of Premise Plumbing.” Healthcare Environmental Infection Prevention (online), Centers for Disease Control and Prevention.
  3. Chadee, Amanda B. and Skovhus, Torben Lund. “Linking Microbiologically Influenced Corrosion to Microbiological Activity Using Molecular Microbiological Methods.” Materials Performance, May 2020.
  4. Mapping the microbiome of… everything.The Forefront, University of Chicago, November 2017.
  5. Thompson, L., Sanders, J., McDonald, D. et al. “A communal catalogue reveals Earth’s multiscale microbial diversity.” Nature, November 2017.
  6. Keele, Jacque. “Using eDNA to test for pathogens in reused water.” U.S. Department of the Interior, Bureau of Reclamation, September 2016.
  7. Ghylin, Trevor. “DNA based microbial analysis detects and locates potential contamination in distribution systems.” Journal AWWA, March 2014.

Your Microbiome Analyst will provide guidance on the DNA analysis methods that will meet your needs and objectives.