Peter Wildy Prize 2021 Q&A – Dr Elisabeth Bik

28 April 2021

The Microbiology Society Prizes recognise excellence and are awarded to those making significant contributions in the field of microbiology, based on nominations received from our membership. They are awarded at our Annual Conference, where the winners also present their lectures. Ahead of the Peter Wildy Prize Lecture 2021: Hashtag microbiome: how to be an effective 21st century science communicator, taking place today, Robert Will, Communications Representative of the Society’s Early Career Microbiologists’ Forum Executive Committee, interviewed Dr Elisabeth Bik to find out more about her work and how it feels to win a Microbiology Society prize.

How did you feel when you found out you would be receiving the 2021 Peter Wildy Prize?

Absolutely thrilled, I was doing a little dance across the room! I’m very grateful, it’s nice to be recognised. I have hopefully done work to support others by putting the Microbiome Digest together, which is now run by a team, but it was not really looked at as ‘science’. In my previous lab, I had to do it outside of work hours because my boss did not appreciate the amount of time I was putting into it. It is just so great to be recognised and that other labs have benefitted from it. Also, to be recognised by a UK Society, as I am from the Netherlands and live in the USA, is very nice. It was just an absolutely fantastic day when I heard that news.

Could you describe your career journey up to now?

I feel I have had an unusual career, but it started traditionally working in a research lab at the Dutch National Institute of Health where I did my PhD. I was the only cholera person in a Bordetella lab, and that felt a little bit lonely at some points, but I started to embrace it. After my PhD, I moved to the clinical world to work in a hospital. I joined the Microbiology Department and set up a brand-new Molecular Unit and used my knowledge from the research world and applied it to patient diagnostics and epidemiology.

I worked there for four years. Then my husband was asked to move to the USA for his job and I had to move from my lab. That was hard, because for him it was a natural career move, but for me it felt like I was breaking what I had started to build up. Luckily, I was able to join a lab at Stanford University, thanks to connections through my PhD mentor, and worked there for 15 years working on the microbiome. That was when that field was just starting and didn’t even have a name yet. We called it ‘Indigenous Microbial Communities’ or convoluted wordings like that. We started to work on Crohn’s disease, then, realising nobody had really looked in detail at which bacteria live in a healthy gut, we started with that. Later on, we worked on oral communities and gastric communities in humans, working with fantastic people through collaborations. That was one of the nice things about working in a lab at Stanford; it opens so many doors. I was very fortunate to work with great people in the microbiome field that turned out to be very well-known and famous, and on so many interesting projects. I worked on dolphins! We had a collaboration with the US Navy; they were managing a group of dolphins living in San Diego and they wanted to know what the microbial communities were in the dolphins' mouths and stomachs.

I left Stanford in 2016 and worked at a company called uBiome which was making kits for people to have their microbiome sequenced. The first year was fantastic, the second year the science became less important for the company and I didn’t really feel it was my place anymore. I worked three more months in an industry job, but it turned out not to be a great fit. It was a great company, but the job was not a good match for me as an introvert.

I left that and now work full time unpaid! Again, another very weird career move. I work now on science integrity. It was fantastic to work in research, in the clinical world, and in industry. They are all very different. I really look back at all the things I did, and I enjoyed all the experiences and seeing what other people do. I have always been amazed at the expertise of people in completely different jobs.

Did you ever think it would be that broad when you started?

No! When I started, I thought I’d start teaching and do some research on the side. I also think that when I started my PhD in 1991, the internet was not yet commonplace, so you didn’t really have a good idea which careers were possible. Science papers for me were something you went to the library for. I did not realise there was a whole group of people making these papers, fields like journalism and editors. It seemed like an academic career was pretty much the only thing – or teaching in a community college or high school. That never excited me, I liked research, so I assumed I would be doing that my whole life back then.

Was there a point where you knew microbiology was for you?

Probably in my first or second year of college. We had a microbiology class, and I really, really enjoyed that. In the Netherlands, the curriculum in the first one-and-a-half years consisted of six- or eight-week blocks of different biology-orientated topics. Eight weeks of plants, eight weeks of maths, eight weeks of physics. I really enjoyed being in a lab, pipetting, doing molecular biology. The technicians would bring in these plates, all colourful. Just being able to see there are techniques to make bacteria – which are invisible to the naked eye – visible, that they grow into a colony and then you can see them. That was something that blew my mind. Of course, what one enjoys in college is also dependent on your professor for that class, and our microbiology professor was a fantastic person. I really enjoyed his style, and that made me interested in the field.

I also enjoyed molecular biology, so I saw it as a combination. You had to do two internships in the third and fourth year of college. My first one was more in molecular biology, which was a nice lab. It was the first time I had really worked in a lab, so I enjoyed that, but my project didn’t really work. I stayed there way too long trying to make it work. My second project was in a microbiology lab, where I knew some of the other students who worked there. I really got enthusiastic there. It was at the Dutch National Institute of Health, and I stayed for my PhD.

What was it like moving across the globe?

It was really scary. I wasn’t scared so much of working in a different lab, but moving across the world to a different country where you have to speak a different language and be with different people. That is just, in general, scary, but only for the first weeks or so. It’s also a lot of work because you have to set up everything again. Everything in the USA is tied to each other, you cannot get a driver’s licence before you get a social security number, and you cannot get a social security number before you get a visa application, so there are all these steps. The first couple of months I did not have a job, I was waiting for my visa so I could start working at Stanford. So I was sitting at home waiting for my husband to come home, working with very slow internet in 2001. My husband was so happy in the office, I could see him having a good time, then we bought a house, and then things started to become really fantastic.

Could you detail an average day for you?

I open my inbox, then I close it again because I see so many new emails! I get a ton of requests to do talks. Each of these talks is a lot of emails back and forth, then rearranging and a lot of administration. I also get several requests every day to look at papers that may have image duplications. Then there are requests to check the work of particular suspect authors, or administration because I sent emails to journals and then they have to get back to me or ask some questions or I have to report new datasets. On a good day, I would just go and work down my spreadsheet and see if there is missing data, see if there are still things I need to post online on PubPeer, or communicate with people on Twitter who ask me questions.

There is no real ‘typical day’, and it is just sitting behind a computer basically, usually from 08:00 or 09:00 until midnight. I am most happy when I work on a set of a particular group or person who has a lot of findings. I will check out a lot of duplicated images, because if you search 200 papers and you don’t find anything, it doesn’t really feel like I’ve done something good for science that day. But if I find 20 papers or so with problems, then I can post them and I feel that I’ve had a good day. The researchers would probably not agree with me, but I feel like I am flagging these papers for other people who can then see that these papers might have a problem.

Your daily digest of scientific microbiome papers, Microbiome Digest, now has over 84,000 followers on Twitter and 40 volunteers. Did you ever think it would get this big when you started it?

No, not this big. I did hope that it would get 500 people following the blog every day, and that is actually the page hits per day. That has been fairly stable over the past few years. I had hoped the page views would be that high, but I had not anticipated that my Twitter account would grow so big. That was just incredible.

Microbiology is a relatively small field, and 20,000 followers felt like a good number, but the remaining 60,000 I think I got two years ago since I switched full time to Science Integrity. That appeals to a lot more scientists, I think. I still do some microbiology, to stay loyal to my old followers!

Were you always interested in education and communication of science?

Since college yes. When I did my PhD and I wrote my thesis, for my introduction I did a little bit on the history of cholera. I got some good feedback and people enjoyed that too, reading that introduction. Then I was encouraged to give talks about those sorts of topics. When I was working in the hospital, I also gave several classes for technicians who weren’t really educated in molecular techniques. I enjoyed it, and the class, I felt, also liked it. I was then discovering that I enjoyed teaching other people.

You do a lot of outreach on social media, especially using the #ImageForensics tag on Twitter. Is education and engagement something you have always thought was important?

Yes, I have always felt when I know something, I need to share it. I am now aware that sometimes images can be duplicated, so I feel this urge to tell other people to be aware that this can happen. So, I turned it into a game, and remove the identifiers. I usually don’t tweet which paper it is from; although if you are a really good detective you could probably figure it out. Later on, when people do a peer review or read a paper, they may automatically apply this new insight, and they might find more duplications, as they are more on the lookout for these things. If you do peer review, just checking out the figures would probably only add a couple of seconds or minutes.

Of course, on Twitter when you see something that gets a lot of likes, you feel encouraged to do more of that, so I do feel like those #ImageForensics tweets are appreciated. People specifically look for these hashtags and reply to them. I give them awards when they get it right, and people are like, "yay, I won my first award", but of course it has a very serious underlayer, because this is, in some cases, science misconduct. Why do people do that? That may be because they are desperate to get a paper or in some desperate situation, not just doing this for fun. I do want to be respectful to those people. I am not going to sympathise too much with them, but I also feel there are sad stories behind these things, so that is why I usually don’t link to papers. Sometimes I do; when it’s way too much or it’s not just a one-time thing, then I’ll call them out.

You made the jump from academia to industry, and then to be a full-time scientific integrity consultant. How did you decide to make these steps?

At Stanford, I felt I was a little stuck in my job. There’s a hierarchy of a professor in a lab and the people in their lab. I still wanted to stay in academia, but I applied for one job at Stanford and I was laughed at. I tried several times to teach at Stanford and was told, "no you are not an MD so you cannot teach". I tried some other faculty jobs in other positions around where I live in San Jose and San Francisco. Every time my application was completely ignored, I never heard back and you have to put a lot of effort in writing these tenure track applications, weeks of work. To not hear back on anything, ever, was frustrating.

The industry job felt like it was written for me. It had science outreach, writing blog posts, writing papers and making sure the science behind the product was up to date. I thought, "that was exactly what I love, and I know everything about the field right now". The people were very nice, and it is a special atmosphere in industry; it felt like I was suddenly part of a team. In academia, it felt like everyone worked for themselves. In the Netherlands it felt like a group, in the USA I felt we were all competitors, all competing for the professor’s time and for the best PhD or lab meeting. If someone had knowledge, it was really hard to get it out of them. People would not share protocols with each other. At uBiome – only for the first year I worked there, because later things weren’t as great anymore – it really felt you were part of a team. You had one person doing the marketing, two people running the lab and the robots, a couple of engineers that built the robots. Someone tried to teach me how to work in SQL – which wasn’t really my thing – but I got to see all these other things that I wasn’t really aware of. You felt like you were a part of a group, regardless of what your function was, or what your salary was, you pitched in and did what needed to be done. That was fantastic. The salary of course was nice; I had not earned so much in my life. The whole atmosphere was great – you never knew what the day would bring, and there was something exciting in that. It was in San Francisco, so every day I had to take an hour train. You go around a corner and you see the skyline of San Francisco every day. I was like, "wow, I work in this city - this is just so amazing".

How widespread would you estimate scientific misconduct is in published papers?

I think it depends on the field, and the countries. I would guess between 5% and 10%. That is based on my searches looking at duplicated images. I look at photos, but I cannot really see if data in a line graph or table has been manipulated. So probably just looking at photos is the tip of the iceberg. There is now the growing issue of completely fake papers, which we have recognised as produced by the same ‘paper mill’ because they all had the same Western Blot background. They were artificially generating bands that looked real, with a background that was all the same. That was how we could recognise these images: 500–600 papers all have the same background but authored by different institutions, all from Chinese hospitals. There is a requirement that you need to have a paper published in a scientific journal in order to make the first step in becoming a staff doctor. These people are clinicians, who often do not want or even have the time to do research, because they work 60 hours a week. So they buy a paper to get through. There must be thousands of papers like that but I cannot prove it. There might be another paper that has the same Western Blot, but how do I find that? Sometimes it’s by sheer luck, or by knowing which journals they target. Reverse images searches do not work. We need software in order to speed up our searches. People are working on that, but it is not good enough yet to screen any image against the entire database of every scientific image published. That would be fantastic if such a thing existed.

Do you have any standout mentors that have helped you along your journey?

There have been a lot throughout my career. Just before my PhD, I did an internship in a lab at the Dutch National Institute of Health, and Peter Hermans was a graduate student there. He was a great mentor, he was so enthusiastic, he kindled my enthusiasm for microbiology and PCRs, and all the things I learned during that time. He lit that fire in me. It was a great lab to work in, but he was definitely the person who made me super enthusiastic to become a microbiology researcher.

Also, my PhD supervisor Frits Mooi, especially later in my PhD. I think in the beginning we had some personality clashes, but you grow towards each other, and he has always been a quiet force, always making sure I combined my enthusiasm with an eye for detail and being very thorough in my investigations.

I had a great time, also, with Judith Kamerbeek, who was a tech and would have been a great PhD student. She brought so much fun and joy and social activity when I still worked at the Dutch National Institute of Health.

At Stanford, Cleber Ouverney was always a good friend to me. The first few days he really helped me, and he brought the craziness that I always need a bit of.

Sara Bird at uBiome was a good friend as well. I was amazed at how much she could do. She was more like a leader than I had seen during my PhD; seeing someone come in as a young researcher and having this capacity to lead a huge group of people and motivate them; making sure the right people meet with each other, realising what is missing, and bringing in other people. She could do that, and I was so amazed by her capacity and working her butt off to get a lot done.

Is there any advice you have – especially for early career researchers – for careers in science?

I don’t think that academia is the only career path, there are many others. There’s industry, there’s journalism, there’s publishing and science integrity is now becoming a new field. Every career is very different, but everything you learn during your PhD will be applicable. If you have worked in a lab, you have learned to handle successes and disappointments, and how to work with other people.

The other one is to grab opportunities when you see them. When you see a job application in a very different field, but you just read it and think, "Wait, I could do all those things. It’s very different from what I thought I would do, but that’s me, they are looking for me. I’m going to apply and do a career switch’. And don’t make plans too far ahead, because something else might come that you would not have expected. I have never made any plans; I have no idea what I will be doing next year. I do not feel I am a very adventurous person, but sometimes opportunities come along that are very different from what you thought you would encounter. I have grabbed those, and never regretted any job I’ve taken.

Could you give a flavour of the Prize Lecture you will be giving later this year?

I don’t really prepare too much in advance, it will be about my crazy career so far and how microbes play a role in that!

The Peter Wildy Prize Lecture 2021: Hashtag microbiome: how to be an effective 21st century science communicator, takes place today at the Microbiology Society Annual Conference Online 2021 at 17:30–18:15.

Inspired by our outstanding prize winners? Nominations for 2022 Prize Lectures and the 2023 Prize Medal are now open. Visit the Prize Lecture pages for more information.


Image: MichelNCo, San Jose, CA.