Meet a microbiome researcher: Q&A with Dr. Nicolette Zhou

Zhou Rhino

As a part of our microbiome research interview series, we spoke with Dr. Nicolette Zhou who is a Postdoctoral Research Fellow in the Environmental and Occupational Health Microbiology Lab, Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, USA. Dr. Zhou received her Ph.D. from the University of Washington and in collaboration with the Nielsen Lab at Aalborg University focused on enhanced biological trace organic contaminant removal (EBTCR) during wastewater treatment. We interviewed Dr. Zhou to discuss her research, her typical day in the lab and her hobbies.

What is your background and how did you become interested in science? 

Growing up in the Seattle area, I was surrounded by nature every day. I knew that I wanted to do something to help the environment for as long as I can remember; I was just not sure what path that would take. I earned my BS in chemical engineering with the plan to switch to environmental engineering for graduate school. However, my path to the microbial realm was not as clear. I got my first exposure to E. coli and coliforms during a summer research experience for undergraduates, during which I went sampling at Santa Monica pier every day, though I didn’t get fully immersed in microbiology until graduate school. With my background and love of chemistry, I anticipated working on drinking water physical-chemical treatment processes, but when I was offered the opportunity to work on a wastewater project focused on biological removal of trace organics contaminants, I jumped on it. I had a lot of catching up to do, with only one introduction to biology course taken during my undergraduate studies, but I made it through and have loved the microbial world ever since.

Can you provide a summary of your project?

Poliovirus is a pathogen of international concern, and the World Health Organization (WHO) is seeking to eradicate it through the Global Polio Eradication Initiative. I am working on a multiinstitutional project funded by the Bill and Melinda Gates Foundation, which seeks to improve poliovirus environmental surveillance sampling with the development of the bag-mediated filtration system (BMFS). The BMFS is being tested alongside the WHO’s gold standard method of two-phase separation in both Kenya and Pakistan. The BMFS utilizes in-field gravity filtration to process large sample volumes (3–6 liters of wastewater), compared to the two-phase separation method which processes 500 ml. This results in a greater effective volume assayed of the original sample processed, with 900–1800 ml for BMFS samples compared to 150 ml for two-phase samples. In conjunction with BMFS development, a device was created to elute ViroCap filters prior to further concentration and analysis. This device is biologically enclosed, manually powered and low-cost, making it a viable option for resource-limited laboratories.

Additionally, we are collaborating with Andrew Adey’s laboratory at Oregon Health & Science University to develop a novel synthetic long-read next-generation sequencing [NGS] method for the identification of multiple poliovirus serotypes and strains in complex environmental samples. This method works by barcoding individual poliovirus VP1 molecules prior to amplification. After further processing, individual poliovirus VP1 molecules are sequenced, and then subassembled for a full-length read of the VP1 region. This allows multiple mutations in a single virion to be associated with the isolate that they are from, and with increased likelihood of detection of poliovirus present in low concentrations.

Can you describe a typical day for you in the lab?

My typical day consists of manuscript and proposal preparation, analyzing data from the ongoing BMFS studies and coordinating with collaborators on current and future projects. I do spend some time doing wet lab work, though typically in labs of collaborators. My time in the lab generally involves a great deal of RNA extraction and RT-qPCR, as well as optimization of the sample preparation for sequencing.

Zhou workbench

What do you find most interesting about your project? What is the most interesting or surprising result you have found?

The most exciting outcome of our research has been the decision by the WHO to conduct supplementary immunization activities in response to poliovirus wild type detection in BMFS samples. The most interesting part of this project to me has been how broad it is, and how we have had a chance to collaborate with a number of people and institutions. I look forward to continuing work on the sequencing method, and connecting our results to what we found with the current gold standard detection methods.

What are the important benefits of your research to science/human or animal health?

Eradication of poliovirus is hopefully close at hand. This pathogen, which once effected hundreds of thousands annually, is now down to 16 wild type cases this year. However, as cases of wild type poliovirus-related paralysis decrease with successful vaccination campaigns, environmental surveillance is crucial for monitoring low-level, silent circulation of poliovirus within a population. This project provides an additional sampling and concentration tool and a novel sequencing approach for the poliovirus environmental surveillance world to utilize. These tools can help to detect poliovirus present at low concentrations in the environment, and provide rapid identification, potentially guiding supplementary immunization activities to prevent outbreaks.

What are your hobbies?

I spend a majority of my free time goofing off with my pup, doing a variety of crafting projects, and attending musicals with my family and friends. I also love traveling, and my husband and I are on a mission to go to all US National Parks. I’ve been to over 25, but still have a long way to go.

What are the major challenges you face in your research with regards to sample collection, nucleic acid isolation and data analysis?

The main challenge our research team and collaborators have faced during this large project has actually been shipping the collected samples in a timely fashion and at a proper temperature to ensure minimal loss of the target organisms. This was addressed through the introduction of preservatives to the filter cartridges, temperature loggers in the shipments and use of timely couriers.
The main challenge when isolating nucleic acids is the isolation of high-quality DNA or RNA for downstream applications. Particular challenges I have faced include isolation of RNA without DNA contamination for targeted NGS work and isolation of DNA from complex samples with inhibitors present.

Which QIAGEN products for microbiome analysis do you use/have you used in the past and what did you like about the products?

I have used a variety of QIAGEN products, including the QIAamp Viral RNA Mini Kit, QIAquick PCR Purification Kit, QIAquick Gel Extraction Kit, and MO BIO Ultraclean Microbial DNA Isolation Kit [now called DNeasy UltraClean Microbial Kit].

I was particularly pleased with the UltraClean Microbial DNA Isolation Kit during my graduate studies for bacterial DNA extraction from activated sludge. It worked well, allowing for detection of low gene copy numbers of specific organisms within these complex samples containing inhibitors.

Currently, I regularly use the QIAamp Viral RNA Mini Kit for RNA preparation for both poliovirus detection by RT-qPCR and NGS methods. I particularly like how rapid these protocols can be completed, while producing good quality RNA.

At QIAGEN, we are excited to support your microbiome research. Find out more about our microbiome research solutions.

Vishwadeepak Tripathi

Vishwadeepak Tripathi, PhD is a Global Market Manager at QIAGEN. He received his PhD in biochemistry at the Faculty of Medicine from Ruhr-University Bochum, Germany. Dr. Tripathi studied the role of chaperones and co-chaperones in protein folding and quality control and authored a number of scientific publications. He was also at RIKEN Institute in Japan where he studied the pathogenesis of Huntington's disease in cellular and mice models. He is currently interested in biomarker research, NGS and neurodegeneration.

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