Join Our Bio Nutrient Removal
Microbiome Study

Join Our Bio Nutrient Removal Microbiome Study

Microbe Detectives, along with support from CH2M and Donohue & Associates is conducting a multi-client study focused on optimizing Biological Nutrient Removal (BNR) programs at municipal wastewater treatment facilities. Here are the basics:

What are we providing?

An ability to optimize your BNR program by directly measuring and monitoring microbes that remove phosphorus (BioP) and nitrogen, using next generation DNA sequencing. A multi-client summary report “Performance Comparison of Bio Nutrient Removal Systems Using Next Generation DNA Sequencing” – free of charge.

What is the benefit?

This DNA sequencing technology has already enabled annual operating savings in excess of $300,000 for a medium sized municipality by reducing chemicals, energy and solids. See videos below for more information:

View “DNA Sequencing in Wastewater” presented by Leon Downing, Ph.D., Senior Technologist, CH2M

BNR + Metagenomics = $360,000 Annual Savings

Biological Nutrient Removal [BNR] What we’re looking at is finding ways to remove phosphorus and nitrogen from the wastewater biologically instead of chemically. That results in a lower net resource consumption. It also allows us to actually recover phosphorus and nitrogen. Instead of treating it, where we are removing it from the water but have another environmental impact (which is the disposal of solid waste), it actually allows us to concentrate those nutrients, pull them out, and get them back into the fertilizer cycle. Biological Nutrient Removal really drives a lot that is protecting the waterways. It’s recovering valuable resources and at the end of day it actually uses less energy to treat water than conventional processes.

A really great success story of using metagenomics in wastewater treatment and resource recovery involves a facility outside of Dallas, Texas. They’ve been doing metagenomic sequencing for about three years now and over that period of time they’ve used that to understand their ecology and give them confidence in operating their facility in a different way. With that they’ve been able to change operational strategies that reduced annual costs by three-hundred and sixty-thousand dollars a year.

Trevor Ghylin, Ph.D., P.E.
Founder/CTO, Microbe Detectives

How can DNA sequencing help BNR operators?

DNA sequencing can help operators that are trying to do BNR in their plant finally see the bacteria that are necessary for that process. Without DNA data it’s really hard to know what’s going on in a plant. You can see phosphorus levels going down but you don’t know if that’s just normal biological uptake or are your chemicals doing something? With DNA data you can actually see you have the biological phosphorous bacteria in there, there’s only a couple different types to do that. Either you’ve got them or you don’t and you can see how many are, and you can track those populations over time. The same goes for ammonia removers and denitrifying.

How can you learn more?

We welcome an opportunity to discuss this program and answer any questions you may have. Please email or call direct at 630-310-9353.

Order DNA analysis kits below to join BNR study

Study Instructions:

1. Order DNA Analysis for Study

After receipt of order, we will ship our kit to you which contains supplies for collecting samples.

2. Collect Representative Sample

Wear gloves to prevent contamination. For liquid samples, use instructions below. For solids, add sample and yellow dessicant card to the Whirl-Pak bag and seal.

3. Fill out Chain of Custody Card 

Add Whirl-Pak bag or filter housing (dry off housing with a clean paper towel first) to zip loc bag with completed COC form and yellow desiccant card. EACH SAMPLE AND COC CARD MUST BE KEPT IN SEPARATE BAGS.

4. Register and Enter Sample Data

Sample ID number is on the red label, located on the COC card. Enter data for each sample in Study Registration, please note we cannot process  until study registration is completed.

5. Ship to Microbe Detectives

Freeze samples taken to ship all at once, or ship samples overnight individually (Monday-Thursday) to:

Microbe Detectives c/o STUDY
935 Curtiss Street, Suite 3
Downers Grove, IL 60515

DNA Analysis Kit


DNA analysis of submitted sample, includes kit with collection supplies.

dna analysis pricing

Include shipping of samples to lab?

Send analysis report to email address below *

SKU: RET-KIT Categories: , ,


DNA analysis of submitted sample, includes kit with collection supplies. The DNA Analysis will be produced by a doctoral-level application expert and will include a summary of the total data, focusing on bacteria that are typically important in water systems. The full data is also provided in a spreadsheet. Data presented are bacterial relative abundance (% of total bacteria in the sample). For example 0.12% Actinobacteria means that 0.12% of bacteria in the sample are Actinobacteria. Interpretation of the results that is application specific is communicated in a detailed report via email. Consulting services are available for an additional fee, subject to a scope of work, contact us to discuss options.

Additional information

Weight 5.3 oz
Dimensions 6.5 x 4.5 x 1.5 in

Performance Comparison of Bio Nutrient Removal Systems – Available June 2018


Comparative study of bio nutrient removal (BNR) systems based on DNA sequencing of samples collected. Includes the DNA sequencing results of each sample, grouped and analyzed for each BNR program. Survey data will be included to augment DNA testing. Available in June 2018.


Instructions for Collecting Liquid Samples:

draw water
A. Draw 1ml of wastewater or  or until you feel back pressure, indicating filter clogging.
screw housing
B. Screw the filter housing onto the syringe. The housing contains a filter to collect microbes.
push water
C. Push the syringe plunger to force sample through the filter housing. Stop forcing through the filter if you feel back pressure indicating filter clogging. Record the actual volume.
unscrew housing
D. Unscrew the filter housing from the syringe. Discard syringe after total amount is collected. DO NOT DISASSEMBLE FILTER HOUSING. This would expose and contaminate sample.

John Tillotson, CEO of Microbe Detectives, recently got together with wastewater expert Leon Downing, PhD., CH2M, to get his perspectives on using DNA analysis in BNR programs.

Why is DNA sequencing important to the wastewater industry?

I think it’s really in the understanding of new processes so we can come up with a new idea of how we might be able to treat water more efficiently and recover resources from it more effectively. It’s being able to understand the biology that’s present and getting a better sense of who’s really there. This helps us to better understand the process and not make it a “black box.” This gives us more confidence to apply technologies more rapidly and to to accelerate adoption. That’s a big part of it. The other part is the optimization component, where we have existing processes they aren’t working as well as we need them to, and figuring out how to make them work better.

What are the energy savings of BNR program?

10 to 15 % of the aeration energy, which is half the total plant energy. So it’s not getting rid of energy, but it’s every little bit that makes a big impact as we try to move towards less and less energy intensive processes.

What are the impacts of BNR on chemicals and solids?

By going to biological processes we don’t have to add a lot of expensive iron salts or aluminium salts into our water. We’re making it more of a natural process with the biology, not having to bring in chemicals and that also reduces the chemical sludge that we make. From a utility perspective, the main driver is an overall cost benefit, but from an environmental standpoint it also reduces our impact of treating and reclaiming water.

Why is DNA sequencing (metagenomics) needed with a BNR program?

It really comes down to understanding the biology that’s there. We’ve learned a lot over the past decades on how these processes work from an overall perspective, and how to operate them, but we’ve always been trying to just kind of infer what bacteria are present. As we try to be more innovative, using smaller tanks, using less energy, we’re selecting for a different ecology than we have in the past. Without being able to understand those changes and understand who’s there, it’s very difficult to find better ways to do things. With metagenomics, and with the ease of being able to get these samples, it helps us to really understand what is going on, for instance, when we’re shifting from an old population to a new population because the old population couldn’t make things work under our new conditions. At the end of the day, metagenomics gives the utility the confidence they need to invest tens of millions of dollars in a new technology, that in the end will save them money. They need that confidence to invest rate-payer’s money.

What is the public benefit of metagenomics?

The public benefit for metagenomics really comes down to the bottom line. That’s one part of it, right, just the fact that understanding the biology in a biological system helps you to operate it more efficiently and potentially design smaller tanks, so it cost less. The check you write out for your bill at the end of the month can be reduced. The environmental impacts are also a huge component of this. By understanding the biology that’s there, we can try to concentrate our nutrients and recover them. Instead of just fixing more and more nitrogen from the atmosphere and mining more and more phosphorus, we can actually fix those nutrients from a wastewater treatment process and return them back to the cycle. In addition to the environmental aspect of this, there is also a social benefit. When you think about clean waterways, I think a lot of people forget that the Cuyahoga River used to start on fire, right, or that Lake Erie was dead, and now even the Chicago River has people kayaking on it. So again, using metagenomics, to understand the biology and clean water to a higher level, benefits everyone and the use of our natural resources.


Updates of this study will be presented at the Microbiome Water Summit. The Microbiome Water Summit will be held at the Shedd Aquarium in Chicago on September 29th 2017 (before WEFTEC). The summit features leaders in this ground-breaking field of work, plus an opportunity to network with a new community of innovators.
microbiome water summit

Technical and Operational Advisory Group

leon downing
Dr. Leon Downing is a senior technologist with CH2M and serves as the East Region Technology Lead. A graduate of the University of Wisconsin-Platteville, Leon then received his M.S. and PhD from the University of Notre Dame, focusing on process modeling and energy efficient biological nutrient removal. Read more...
Over the past decade, Dr. Downing has focused on the application of process modeling, innovative technologies, and operational strategies within the wastewater treatment field.  Leon has most recently been contributing the shift in our industry from wastewater treatment to resource recovery.  Leon was the vice chair and contributing author for the recent WEF publication Moving Towards Resource Recovery Facilities, he has served on the Issue Area Team for the WERF Resource Recovery Challenge research program, and he has been involved with the evaluation, design, and/or operation of multiple energy efficiency, biogas utilization, and struvite harvesting projects.
trevor ghylin
Dr. Trevor Ghylin is a professional water process engineer and has more than a decade of experience working for CH2M, the leading consulting firm in the water industry and also a senior process engineer for Xylem, a multi-billion dollar pure play water technology company. Read more...
Dr. Ghylin is passionate about harnessing innovation to utilize and protect water and energy resources and the environment. Dr. Ghylin is a licensed Professional Engineer and holds a Class IV wastewater treatment operators license in the state of Wisconsin. He has a B.S. degree from the University of North Dakota – Grand Forks in Civil Engineering and a Ph.D. degree from the University of Wisconsin – Madison in Civil and Environmental Engineering. Dr. Ghylin is very active in professional societies including the Water Environment Federation (Technical Committee for CSWEA Annual Conference) and Engineers without Borders (Marquette University Mentor). He has also spoken at Regional and National Conferences (CSWEA Annual Seminar, Madison, WI; WEFTEC, Chicago). He has a breadth of experience in environmental projects including greenhouse gas analyses, sustainability assessments, PCB cleanup in rivers as well as drinking water treatment and contaminated site remediation. Additionally, he has gained a deep understanding of environmental protection and water issues by working on numerous wastewater planning and design projects.
jeremy cramer
Dr. Sara Arabi holds a Ph.D. in Chemical Engineering from Western University (Canada) and has 13 years of experience in environmental consulting, research, and process engineering for water/wastewater treatment. Read more...
Her primary background and area of expertise is wastewater treatment plant design, evaluation, and optimization for municipal and industrial applications including landfill leachate, food/beverage, and power/metals for facilities in the U.S. and Canada. Dr. Arabi’s specific expertise includes design, optimization, and troubleshooting of Biological Nutrient Removal (BNR) plants, computer simulation of biological wastewater treatment processes using BioWin®, bench and pilot treatability studies, and process design/evaluation. As a Professional Engineer registered in Ontario and a Board Certified Environmental Engineer, Dr. Arabi participates in industry organizations including the Water Environment Federation (WEF), Illinois Water Environment Association (IWEA), Environment Research and Education Foundation (EREF), Water Environment Association of Ontario (WEAO), and Central States Water Environment Association (CSWEA) with publications in the wastewater treatment and solid waste practice areas. She has published her work in several peer-reviewed journals and presented at several national and international conferences. Dr. Arabi is actively involved in WEF publication sub-committees/Task Forces with authorship and peer review of Manual of Practices (MOP), including MOP 35 (Biofilm Reactor), 36 (MBR), and 37 (Nutrient Removal) and the Nutrient Roadmap. Dr. Arabi was the primary author for the “Process Control with DO and ORP” chapter for MOP 37 and for “Membrane Biofouling” chapter for MOP 35.
jeremy cramer
Jeremy Cramer has 18 years of wastewater and water treatment experience. He is a licensed water and wastewater operator in the state of Wisconsin. Throughout his career, he has been involved in the management, operation, and maintenance of both wastewater and water treatment systems and facilities. Read more...
Under his guidance, two different wastewater facilities have been recognized for operation and performance and have won Utility of the Future Today Awards from WEF. He has also overseen the operation and maintenance of sanitary liftstations, stormwater liftstations, and drinking water wells. Mr. Cramer has had a tremendous amount of experience in the area of wastewater treatment with focus areas in anaerobic digestion, biological nutrient removal, and energy efficient operations. Mr. Cramer holds a B.S. degree in biology and a M.S. degree in business management and is a Senior Process Specialist for Donohue & Associates, Inc.
david garman
Dr. George Wells is an Assistant Professor of Civil and Environmental Engineering at Northwestern University, McCormick School of Engineering. He holds a Ph.D. and M.S. in Civil & Environmental Engineering from Stanford University, and a B.S in Chemical Engineering and B.A. in Environmental Engineering from Rice University. Read more...
Dr. Wells’ doctoral research was focused on elucidating the diversity and relative importance of ammonia-oxidizing bacteria and newly discovered ammonia-oxidizing archaea in nitrifying wastewater treatment plants, and on employing nitrifier microbial ecology to recover energy from nutrient removal processes. After receiving his Ph.D., Wells spent nearly 2.5 years as a postdoctoral scholar at Eawag-the Swiss Federal Institute of Aquatic Science and Technology (near Zürich, Switzerland) studying the microbial ecology and process stability of a new class of low energy, sustainable biological nutrient removal processes that rely on so-called anammox bacteria. He has been awarded the US NSF International Research Fellowship (2011), EAWAG 75th Anniversary Postdoctoral Fellowship (2010), US EPA STAR Fellowship for Graduate Environmental Studies (2007) and US NSF Graduate Research Fellowship (2004). Wells’ primary research interests are microbial nitrogen cycling and short-circuit biological nutrient removal processes, microbial ecology of engineered and natural settings, sustainable biological wastewater treatment, microbial greenhouse gas production, and resource and energy recovery from waste. His research has been published in numerous international journals, including Water Research, Environmental Microbiology, Frontiers in Microbiology, Proceedings of the National Academy of Sciences of the USA, and Applied and Environmental Microbiology. Dr. Wells is excited to explore collaborative possibilities on related research topics within the Civil and Environmental Engineering Department, across the university, and particularly with local industrial or public utility partners. When Wells is not searching for sustainable solutions to pressing environmental and public health problems, he enjoys a myriad of outdoor activities (particularly hiking, backpacking, biking, and canoeing), playing bluegrass and old-time guitar, and exploring the Chicago music scene.