Júnia Schultz standing in a JGI conference room with her presentation. Photo courtesy of Júnia Schultz
Júnia Schultz is currently a postdoctoral fellow at the Biological and Environmental Sciences and Engineering Division at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. She spent the summer working with Nikos Kyrpides, head of the JGI’s Microbiome Data Science group, and his team to characterize the virome associated with the previously unknown hydrothermal vents in the Red Sea. The hydrothermal vents are something that Schultz’s collaborators and her own team discovered (read more here) and her initial goal in coming to the JGI was to understand the “composition, the abundance, and how unique the viral samples from the vents in the Red Sea are,” while also comparing them to other hydrothermal vents around the world. Once she got to the JGI, however, she learned there was more that could be done.
Nikos Kyrpides (left) and the rest of his team out for a team meal with Júnia Schultz (center). Photo courtesy of Júnia Schultz
Her first interaction with Kyrpides was virtual. Since they both work on genomes and metagenomes, she had been aware of his work after coming across several of his papers on the subject. They briefly met in person at KAUST in 2022 when he came for a metagenomics conference. After that, she dove into her work with her team on hydrothermal vents and realized that within the microbiome that was associated with it, nobody was doing research on the viruses associated with this extreme environment. This was something that was exciting to her as it was a new challenge and outside of her usual realm of bacterial work. She started on the analysis herself, but ended up struggling. This led to her pausing that portion of the project until she saw Kyrpides speak about global viromes at another KAUST conference in 2023. She learned about the tools he and his team were developing and using and thought it would be helpful for her own research. Sensing an opportunity for collaboration, she connected with her PI to reach out to Kyrpides about working together. He was immediately interested in her work and project goals and before she knew it, Júnia was off to the JGI in May as a visiting researcher.
Upon arriving in Berkeley, Schultz got right to work on comparing her hydrothermal vent research with what Kyrpides and his team had analyzed. After chatting with other researchers and scientists, she discovered that the work she was doing for the viruses could also be done for plasmids as well. Using the “know-how and tools” that the team had, Schultz noted that while “we started out with the virome of the hydrothermal vents, we ended up with the mobilome of the Red Sea.” The mobilome consists of the genetic elements that can move within a genome and between different genomes, including transposable elements, bacteriophages and plasmids. Essentially, she took her work on hydrothermal vents and applied it to a global scale. It was an ambitious project with several objectives to complete in just two months and she knew it would be a daunting task. With the “great support from Nikos and his team,” however, Schultz was able to engage in the additional research to the fullest.
When talking about her time at the JGI, Júnia described it as a “game changer for her professional career.” She enjoyed working with Nikos and his team as they were incredibly friendly and welcoming and she felt comfortable in her work environment. Additionally, she enjoyed taking the shuttle up through campus and seeing the sights of Berkeley and the rest of the Bay Area. With regards to the JGI staff, she mentioned that she felt “a part of the team, even though I was only there for two months. That really made a difference.” She also enjoyed that the JGI being, in her words, “a very multicultural/international space.” She liked meeting other scientists and researchers from other countries outside of the US like Brazil (where she’s originally from), Greece, France, Colombia, and Nepal. Lastly, she also loved seeing the variety of wildlife that are on the Berkeley Lab campus. She noted that, “it was great that I could be working in my office and look out the window to see deer or turkeys walking around.”
In terms of what the JGI has to offer potential visiting scientists and faculty, Júnia expressed that she thought it was a great opportunity for those interested in bioinformatics analysis. Furthermore, she mentioned that “there are great computational resources available at the JGI, and everyone is there to help you and give you guidance and support.”
She also liked the weekly seminars that were hosted and that it was “great to meet people and connect with groups outside of my own along with seeing what other researchers are developing.” Several researchers come to visit the JGI. Two she enjoyed meeting with were Dr. Robert Edgar, who specializes in tools for phylogenetic analysis, and Australian Professor Luis Pedro Coelho, who develops and works on the tools that Júnia was using.
When asked about what she learned from Nikos and his team that she’s using in her current position, she laughed and said “everything.” More specifically, she was “there to learn something new, and I’d never worked with viruses or mobilome before.” Additionally, she hadn’t had much prior experience with bioinformatic analysis and had never worked on it by herself without support. After this experience, however, she described it as a “complete shift, because now I’m working on all of these things by myself that I couldn’t do before.”
Something else that she’s taken back with her to apply not only to her own work but the work of her colleagues is how Nikos and his team operate. She described them as a “very creative bunch who had regular brainstorming sessions that really fueled the work that we completed while I was there. I felt like I was really ‘doing science’ in these sessions and it’s something I’m trying to incorporate into my own team as well.”
Byline: Graham Rutherford