For this fabulous world microbiome day, we are absolutely delighted to present you this exclusive interview of Elisabeth Bik. She runs the Microbiome Digest, the daily news for microbes if you want, and everything we know is mostly thanks to her. Marie is fangirling a lot right now, it’s a bit embarrassing..
Could you tell us a bit about yourself and your background?
I grew up in the Netherlands. I was born in Gouda (famous for its cheese, caramel wafers, and a gorgeous city hall) and studied microbiology at Utrecht University. I did my PhD at the Dutch National Institute of Health on cholera and worked in a hospital lab for 4 years after that. I moved to the US in 2001 and worked at Stanford University for 15 years on microbiome research. I have worked both with human samples as well as with dolphin and sea lion samples, in a project funded by the US Navy Office of Naval Research. Since 2016, I work at uBiome, where I am the Scientific and Editorial Director.
Do you remember the first time you heard of the microbiome? What made you decide to go to this part of science?
I worked on the microbiome before it was even called the microbiome! I worked in the lab of David Relman, and we were one of the first labs to analyze “microbial communities” of the human gut. We wanted to look at these communities in Crohn’s disease patients, but we realized that we needed to analyze healthy controls first because there were not many molecular studies done first. That was still in the days of cloning PCR fragments and Sanger sequencing, and we aligned all our sequences by hand. We were super proud to have generated a set of 13,000 sequences from 3 patients, but obviously, that was a very small dataset compared to what we can do nowadays. After that first dataset, we analyzed several other sample sets, from mouth and stomach. It was very exciting to have been part of the first decade of microbiome research – it was all about determining “who is there”, not yet about function, but it was work that no one had done before at that scale.
What gave you the idea of starting the Microbiome Digest?
It all started by sending coworkers some occasional relevant papers that I found during my daily PubMed search. My lab-mates liked that, so I started to send more and more papers. This turned into a weekly, and then daily email to our lab group. As the microbiome field started to grow rapidly, so did the length of this daily email. One day, during a lab happy hour at The Dutch Goose in Menlo Park, one of my coworkers suggested that I should turn these updates into a blog and share with the rest of the world. That night, I bought the domain MicrobiomeDigest.com, set up a WordPress site and started the blog. I sent around some emails to other microbiome labs, and the word spread quickly. I ran the blog all by myself for the first three years or so, but nowadays it is run by a team of 15 amazing scientists, who take turns in compiling all the new papers and writing the blog.
What is your favourite Microbiome amazing fact/ pub quiz fact?
That a healthy microbiome in a person living in Europe or the US is very different than a healthy microbiome in hunter-gatherers in South America or Africa. Therefore, it is impossible to define what a healthy microbiome is. It all depends on where we live, and what we eat. Also, most of us do not eat enough fibre. Increasing the amount of fibre in your diet is a very easy way to feed your gut microbes with the fuel they need to make you feel healthy.
There is a lot of focus on the skin microbiome at the moment, what is the latest study you read that you found interesting and why?
I just read this paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0486-4 It is about the skin microbiome of preterm and full-term infants and shows that a lower diversity and more potentially pathogenic strains in premies. Research like this is important to take better care of preterm infants and make sure that they are off to a good start. In general, skin microbiome has not been the focus of many academic research studies. Most of the attention so far has been gone to the microbiome of the gut. Given this, it is even amazing that the cosmetic industry is moving forward so fast in skin microbiome research and the development of products to take care of our skin microbiome and replenish it with beneficial strains (probiotics) and food for those strains (prebiotics).
You are now working as a Scientific Editorial Director at UBiome. Can you explain to us what the company does, and why do you think citizen science is the future?
uBiome is the leader in microbial genomics. We develop microbiome products for both consumers as well as for patients and clinicians. We have developed two clinical products, SmartGut for gastrointestinal conditions, and SmartJane, which combines vaginal microbiome analysis with STI and HPV genotyping. These clinical products are clinician-prescribed and are reimbursable by most health insurance companies. Explorer is our consumer product that is designed for citizen scientists. The Explorer test allows everyone worldwide to learn about their microbiome and take action. This citizen science product has generated the largest microbiome sample set in the world, with currently over 250,000 datasets. Without the power of citizen scientists, we would not have been able to generate such a huge dataset. This large dataset allows us to apply innovations in machine learning and other computational methods to gain deeper insights into microbiome analysis which we can then apply to the development of new products, in return.
We are slightly obsessed with food at Gallinée. What food do you miss from your native Netherlands?
Raw herring with onions! This probably grosses out most non-Dutchies, but it’s sooooo good. Whenever I go back home, I always make sure to eat a raw herring, either as street food or on a slice of bread for lunch. I have not been able to find raw herring in the San Francisco Bay Area, but there are a lot of sushi and poke restaurants here, so I am still getting my weekly dose of raw fish.
Thank you, Elisabeth! If you want to know more about the microbiome, you can have a look at the microbiome digest blog, right here. Happy Microbiome World Day to everyone!
