Introduction:

The Puerto Rico IDeA Network of Biomedical Research Excellence (PR-INBRE) was formed in 2005 from funding from the National Institutes of Health (NIH) and the National Institute of General Medical Sciences (NIGMS), award number 5P20GM103475. The PR-INBRE is committed to the continued development of Puerto Rico’s biomedical research infrastructure through the implementation of a strengthened and cohesive structure with common scientific and educational interests, collaborations, and mentoring initiatives. The PR-INBRE is comprised of 5 primary cores: The Administrative Core, the Bioinformatics Resource Core, the Science and Technology Competency Enhancement Core, the Centralized Research Instrumentation Core, and the Developmental Research Project Program Core. In addition to the cores, the PRINBRE has dozens of active students and researchers working to achieve the directives of the organization. 

Dr. Filipa Godoy-Vitorino is the chair of the Microbiology and Medical Zoology department at the University of Puerto Rico Medical Sciences Campus, president of the American Association for the Advancement of Science (AAAS) Caribbean Division, and is a member of the PR-INBRE funded Bioinformatics Resource Core. Dr. Godoy-Vitorino assists in providing bioinformatics-focused workshops and remains an active member of the microbiome field. 

The NAIPI team set out to learn from Dr. Godoy-Vitorino about her journey to bioinformatics and her current experience working with PR-INBRE as a PI and core member to elevate biomedical research across the region. 

Interview Summary:

Dr. Godoy-Vitorino began her work in the microbiome field during her Ph.D. where she worked with the only known folivorous bird, the hoatzin (Opisthocomus hoazin). Folivorous means that the hoatzin’s diet is comprised primarily of leaves, which leaves some interesting questions about the organism’s digestive microbiome. 

“When I came to Puerto Rico I wanted to do something in tropical ecology and I ended up working with hoatzin [Opisthocomus hoazin]. I was working under Dr. Dominguez Bello, one of the pioneers of the microbiome field. We started several studies on different animal microbiomes and my focus was on pre-gastric fermentation. So, I studied bacteria and fungi that are part of the gut microbiota of the only folivorous bird, it’s called the flying cow. I studied the hoatzin microbial ecology through my Ph.D.”

Although Dr. Godoy-Vitorino has experience in bioinformatics, she does not consider herself a bioinformatician. She prefers to use bioinformatics as a tool to answer microbiome-focused questions. 

“I always use bioinformatics as a tool. I don’t see myself as a bioinformatician or a programmer, I adapt programs from other people or pipelines that are already available to study host-microbe interactions.”

Despite the array of pipelines available today, universal pipelines were not available when Dr.Godoy-Vitorino began implementing bioinformatics into her work. 

“…I started learning by myself because about 15 years ago there were no universal pipelines for studying these things… I actually started by learning a lot from papers and from emailing experts. … I started learning from other people and getting information from my own research and I kind of developed with the microbiome field. Because, when I finished my PhD was in 2008 and it was when the microbiome field really kicked off.”

Since the completion of her Ph.D. Dr. Godoy-Vitorino has expanded her work to help answer a variety of questions regarding microbiomes. The two leading projects in her lab focus on how microbiomes influence aspects of cancer and components of climate change. 

“My lab is organized in two ways, we have a more clinical part where we specialize more in microbiome-driven malignancies, so we studied cervical cancer and solid tumors and how the microbiome can drive these phenotypes… and then we have the other, the environmental projects, where we have collaborations with folks studying climate change and how invasive species have different microbiomes that made them more able to colonize corals and kill them.”

Dr. Godoy-Vitorino also shares her expertise through the PR-INBRE by organizing and executing bioinformatics workshops that help teach others how to incorporate bioinformatics into their own work.  

I’m also participating as a part of the BiRC, the Bioinformatics Research Core from Puerto Rico INBRE. And one of the things that we do is we do a lot of workshops on bioinformatics and we collaborate with clinicians and PUI [Primarily Undergraduate Institution] PIs [Principal Investigators] that bring their own projects. We think about ways that they could integrate bioinformatics or ways to integrate the microbiome and I always involve a student from my lab to help them analyze the data and be like a bridge between us and the other groups.”

In addition to her administrative and PR-INBRE roles, Dr. Godoy-Vitorino also enjoys mentoring students, where she emphasizes empowering her students as a great way to build up the future of science. 

“By empowering students, [it’s] the only way they can grow and they can help you grow. So, I think that would be my advice. To, especially for mentors, to empower their students because they’re going to be the future of what we do.” 

For students interested in microbiomes and bioinformatics, Dr. Godoy-Vitorino was able to provide some advice on how to get started.

“If I was a student today, that would be wonderful because there are so many pipelines and tutorials. And everything is digested already so you can apply those tools…My big advice is, don’t get frustrated. Be resourceful and go find someone who can explain that [the problem] to you. Go find a forum. Subscribe to all the forums for all the pipelines that exist. Nowadays people are really generous. At least in microbiome, the data is public and the tools are public. People don’t make money out of it. They want to share their science. We want a field that evolves with knowledge and everything is free. So, you can email the experts, you can go to the forums. But never, never get frustrated because it’s easy to get frustrated.”