Serena Fraraccio, Senior Scientist

Serena Fraraccio’s road to becoming Micronoma’s first wet lab senior scientist started in her hometown in Isernia, Italy, where an interest in the environment and biology blossomed into a career that has gone from winters in Alaska creating bioremediation methods to cleaning up oil spills to San Diego where her focus on the microbiome now includes leading Micronoma’s wet lab operations.

Serena sat down for a conversation that showed her enthusiasm for science, helping people and the planet, and the importance of Micronoma’s work.

What does an average day at work look like for you?

On a daily basis I feel motivated; happy. I’m a senior scientist for the R&D branch and I do wet lab work. Once I get here and I cross the laboratory door I feel at home. The laboratory is just my natural environment.

I don’t always do the same thing every day. The work that I need to do is variable. Every day I have the freedom of formulating research questions, talking about questions with my colleagues and getting their amazing feedback. Some workflows are already locked into place and I know exactly what I need to do. But then there is the other aspect that is more innovative and changes every day. And then I get to do the exciting part in the wet lab, implementing new ideas into our work.

Take us through setting up the testing procedures and how results are processed.

Every time we have a new project, our CEO, Sandrine and our CSO, Eddie lead the collaboration. Eddie secures the adequate samples we need to work with, samples that have already been collected from cancer research centers, clinics, or other vendors. Once we receive samples, then my role begins.

First from the plasma samples, I purify the nucleic acid (DNA). Once it’s purified, I do some quality control and prepare it for the sequencing analysis. All of this preparation stage consists of many smaller steps which need to be tightly controlled to avoid any risk of contamination or bias in our results. The process takes a couple of days.

Once the samples are sequenced, then I work with Stephen, our senior bioinformatician, to make sure that the data is transferred to him for analysis and he takes it from there.  We then regroup to discuss the experimental results and plan our next experiments.

What is the process for extracting the microbes from the DNA sequence?

We want to analyze specifically the microbiome component. One of the biggest challenges is to isolate microbial DNA from their host DNA; in other words, the microbial signature is hidden in a lot of human genetic material. We are working on several different methods to better highlight microbial signatures from our samples in the wet lab. Many people, in many laboratories in different parts of the world, have tried to do that, but have seen little success. I can’t reveal what we are doing to improve on others, beside the fact that we have been able to make incremental progress in this microbial analysis.

All these daily challenges are what makes our work very interesting and so impactful. We have to come up with new ideas all the time because we have to deal with all the challenges that happen at each step of our workflow. The very motivating aspect is that every time we find a solution, that’s going to be very novel and have a huge impact on the capability to detect early cancer.

What did you study and what inspired you to pursue science?

I’ve always known I wanted to be a scientist. There are no other scientists in my family. There’s a doctor.  Since I was a little kid I would always play outside in nature. I’m a very big outdoors person.

I’m also a very detail oriented person in many ways. Maybe too detailed sometimes…. I don’t know. But I’m always observing everything in the environment–flowers, plants, what happens with them. I knew I wanted to study biology. I’ve always known. And I went for it.

I started with general biology for my bachelors in my hometown in Italy. I had a passion already for microbiology, but also science in general. For my master’s, I moved to the University of Bologna. My major was in molecular and industrial biotechnology. It was a very intense program, and very diverse. My courses included applied chemistry, biochemistry, thermodynamics, and cancer therapy. In those three and a half years, I had a lot of opportunities to test my skills, my passion in different fields of research. Eventually I decided to focus on microbiology applied to bioremediation.

I became what you would call a microbial ecologist because I was, in particular, studying the interactions between microbes and their environment. There are many different applications for this. For example, once you know microdynamics, how microbes survive, live, and how they contribute to the environment they live in, you can leverage that knowledge to develop systems, such as a remedy to clean up a polluted environment.

I was specifically studying the microbial ecology of polluted environments and trying to understand what was happening every time there was an oil spill or polluting event, how that would affect the natural environment and how microbes would react and how we could use the environmental microbes from that specific environment to trigger a natural bioremediation process for the cleanup.

I spent about 10 years working on projects for the bioremediation of different environments–ground water, sea water, soil, sludge, plant litter. I even studied microbes in animal poop, for applications in agriculture. I worked on samples collected from so many different environments: from the desert to urban wastewater to the boreal forest. And, I traveled a lot because of my research interests. I went to Alaska for my second post doc, for two years. The project was looking at microbial ecology processes driven from specific plant species that grow in different regions around the Arctic circle. I studied samples of boreal forests from Alaska, Siberia, Finland, and Iceland.

How did you end up in San Diego?

I knew I wanted to be in the United States because the research, the science here is important, really motivating. There are many, many opportunities for scientists who want to do research in all different fields.

At that point in my career, I had explored so many different environments but I had not worked on human microbiology. I was intrigued. During my first and second post docs, between 2013 and 2020, there had been this boom in the microbiome field. While that was happening, I found myself in a position where I thought I had so many skills that could help. The technical skills; and the knowledge that you have when you work as an ecological microbiologist are complementary to human microbiology.

I happened to find this great opportunity in San Diego, with Sandrine, at the Center for Microbiome Innovation. Rob Knight was my P.I. That was really, really stimulating: new challenges, new things to consider, a new host subject. It gave me the opportunity to do the kind of research that I like, but also applied research. I could do both from a new perspective, looking at the human microbiome. That was a really good change for me.

How has cancer personally impacted you?

Unfortunately, like many, many other people, I’ve also been affected by cancer, relatives and people that I love. Cancer is definitely an enemy. And I’m very happy to be here doing something that will contribute to fighting cancer early on. From that standpoint, I think all of us at Micronoma are probably angry at cancer, different kinds of cancer.

It is very motivating to me that here we have the opportunity to expand our work on more cancer types. And we have so much opportunity to keep growing and expanding. And, at the same time, the research, the science that can happen here is so interesting, so noble. I think there’s an opportunity for us in the future to use our microbiome-based methods to also chase down other diseases.

Do you have any hidden talents or hobbies?

I like sports. I used to be an athlete. I used to be a long-distance runner. In my hometown in Italy I had a race every Sunday, or every other Sunday. I wouldn’t say I was a talent, but I would usually win a prize. The truth is that there weren’t many women competing at that time. Sometimes I was even first. In my region I was well-known, just because I was always on the podium.

I like to live close to the water. I love to play beach volleyball. I’m short, but I’m good at digging the ball. At least I can move fast. I’m not going to be the one spiking the ball. I’m going to be the one in the back.

Do you have a favorite Microbe?

They’re all very cool, to be honest. It’s very hard to choose. I do have a favorite microbe. It’s called Acinetobacter pittii. This was one of the microbes I isolated from some polluted ground water in Czech Republic. This isolate turned out to be a really good degrader of a specific type of pollutants that I was monitoring at the time for a specific project. These pollutants belong to the class of chemicals called chlorinated aliphatic hydrocarbons, that are solvents found in a lot of cleaning agents and degreasers in several industrial production processes. This isolate of the genus Acinetobacter was a microbe that performed really well into the biological assays that I developed and optimized for the biodegradation of these specific pollutants. It was just really nice to me by performing really well. But microbes are all cool.