As a part of our microbiome research interview series, we spoke with Dr. Elisabeth Bik, Scientific Editorial Director at uBiome, the leading microbial genomics company. Dr. Bik received her PhD at Utrecht University in the Netherlands and later joined the Department of Microbiology and Immunology at Stanford University School of Medicine. She is a recipient of Stanford’s prestigious Microbiome Pioneer Award, recognizing her contributions to this scientific field. We interviewed Dr. Bik to discuss her research, her typical work day and her hobbies.
Give us some idea about your background and how you got interested in science?
I wanted to study biology already in elementary school. At that age, I was imagining studying bird migration or zoology. But once I went to college, I fell in love with microbiology and molecular techniques. During a lab rotation at the Dutch National Institute of Health, I worked in an infectious diseases lab and was captivated by the drive and motivation of all the researchers in that group, who worked hard to better understand diseases such as tuberculosis or whooping cough. I decided to stay in that group and did my PhD on Vibrio cholerae, the bacterium that causes the devastating disease cholera.
Can you give a summary of your project?
Since 2016, I work at uBiome in San Francisco, the world’s leading company in microbial genomics. Last year, I helped to develop a microbiome-based women’s health test. This was a challenging project to work on because we wanted the test to report the relative abundance of three different sets of microbes. These include 19 different strains of human papillomavirus that cause cervical cancer or genital warts, four bacterial species that cause sexually transmitted diseases and a set of bacteria associated with bacterial vaginosis and other vaginal health issues. There were a lot of targets to validate, but we successfully combined them all in an easy self-sampling format that will appeal to a lot of women. Developing such a product is a huge team effort, from the laboratory team to the marketing department. My main role was to write a scientific paper, but I also did some bioinformatics analysis and laboratory validation. I am very proud of the end product, which is called SmartJaneTM. We hope that this test will enable women to learn more about their vaginal health.
Are you working on any other new projects in the field of microbiome research? If so can you tell us a little about these?
We are working hard on some exciting new products that we hope to share with you and the rest of the world in the near future! One project I can share with you is an upcoming paper demonstrating the reproducibility of our analysis. Some competitors have claimed that our test is not reproducible – this paper will prove otherwise.
What is a typical day for you in the lab?
I don’t work in the lab anymore, and I miss that a lot, especially DNA extraction. In my previous work at Stanford University, I extracted large amounts of samples – and we were big fans of the QIAGEN and MO BIO products. Here at uBiome, a typical day for me will include reading the latest literature, editing a manuscript or copy for blog posts or products, meetings with the product or marketing teams and preparing for conference lectures and posters.
What do you find most interesting about your work? What is the most interesting or surprising result you have found?
How fun it is to work at uBiome. We talk about poop a lot and there is no shame in walking into the bathroom with a swab to obtain some research material or discussing each other’s results. Although I miss some parts of working in academia, working in industry has taught me many new skills. I never realized how many aspects there are to developing a new assay. It has been an amazing experience to work in such a big team and together make a great new product.
What are the important benefits of your research to science/human or animal health?
On an individual level, the research we do at uBiome has led to the development of products that enable people to learn about their microbiome and take action to improve their health. On a much larger scale, we have the largest microbiome dataset in the world – 250,000 samples – so we can use those data to learn more about associations between microbiome composition and health conditions.
What are your hobbies?
I love gardening, although I am better at repairing irrigation systems than growing anything edible. I also collect turtles (not real ones!). However, I spend most of my off-hours searching for duplicated or manipulated images in scientific literature and trying to decrease science misconduct.
What are the major challenges you face in your research with regards to sample collection, nucleic acid isolation and data analysis?
Nowadays, DNA extraction kits such as those made by MO BIO or QIAGEN have become very good and consistent. Two big challenges in the microbiome analysis field are reproducibility between labs and background levels of nucleic acids. Each lab uses their own favorite DNA extraction method and personal tweaks, making microbiome profiles hard to compare between labs. Also, human microbiome research has moved from the high-yield sample types, such as gut and mouth, into samples that contain minute amounts of microbial DNA or might even be sterile, such as placenta or blood. In those samples, it is hard or even impossible to distinguish background from signal.
Which MO BIO or QIAGEN products do you use/have you used in the past and what did you like about the products?
I have used the QIAamp DNA extraction kits on hundreds of human and marine mammal samples, as well as seawater. My most unusual DNA extractions were done on human breast milk, infant meconium samples, honeybees and whole fish. I was very pleased to find that the QIAamp kit successfully extracted whatever you threw at it! What I loved most about the QIAamp kits was the process of unpacking each new strip of columns and placing them lovingly in my DNA extraction rack.
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