Every time astronauts blast off into orbit, so do a slew of microorganisms that quietly colonize spacecraft equipment and living spaces. As the next era of space exploration ramps into gear, keeping track of those invisible stowaways is vital for astronaut health and spacecraft safety, and this summer, a Rice University undergraduate helped equip NASA scientists with a custom tool for the task.
Ankhi Banerjee, a junior pursuing a computer science and biology double major at Rice, spent 10 weeks over the summer building a data-analysis pipeline to help NASA Johnson Space Center scientists track microbes aboard the International Space Station (ISS). Her project took shape through Genome Sleuths, a research program led by computer scientist Todd Treangen that engages undergraduates in developing computational tools for studying microbial genomes and metagenomes.
Banerjee’s project involved close collaboration with Sarah Wallace and the microbiology lab at Johnson Space Center and aimed to find useful ways to interpret the sequencing data extracted from microbiome samples collected on the ISS. Over the course of the summer, she built visualizations to show how different bacteria were distributed across the station’s modules and began designing an anomaly-detection tool that could flag unusual microbial signatures.
“I was absolutely thrilled to team up with Dr. Wallace to co-mentor Ankhi for this exciting summer project facilitated by Dr. Wallace’s team at NASA JSC,” Treangen said.
The patterns she uncovered told everyday stories about life in orbit. Sweat-loving bacteria clustered around gym equipment. Food-associated microbes turned up near dining areas. Bathroom handrails proved to be microbial hot spots.
“I had a lot of fun finding these patterns,” Banerjee said.
At the end of the 10-week program, Banerjee presented her findings at Johnson Space Center, where she faced a larger audience than expected.
“I thought it would be a small group I already knew,” she said. “Then I walked in and there were around 30 people in attendance. It was very intimidating at first, but everyone was kind and welcoming. They all just wanted me to learn.”
Treangen has run Genome Sleuths since he joined Rice’s faculty in 2018, supporting up to eight undergraduates with paid internships each summer. He estimates he has mentored more than 50 students through the program with many co-authoring papers or contributing to open-source software tools as a result of their participation.
“This was the eighth summer of Genome Sleuths, and it was one of the top undergraduate projects I have seen,” said Treangen, associate professor of computer science at Rice and the lead of the AI and Computational Biology for Human Health, or AI2Health, research cluster at Rice’s Ken Kennedy Institute. “Ankhi developed software that impressed a full team of NASA scientists, and she is just getting started.”
Genome Sleuths itself is part of the Vertically Integrated Projects (VIP) program, an education-and-research model adopted by universities worldwide. VIPs embed undergraduates in faculty-led research groups for multiple semesters or years, allowing them to build deeper skills and leadership roles than short-term lab experiences usually allow. At Rice, the program is coordinated through the Office of Undergraduate Research and Inquiry (OURI).
Banerjee’s anomaly-detection tool is still under development this semester with the goal of producing a polished software tool that aids scientists both at Johnson Space Center and on the ISS. The software could also potentially serve to support monitoring on Artemis missions and lunar Gateway ⎯ NASA’s planned staging platform for travel to the moon and Mars.
For Banerjee, the experience was also a glimpse into what a career in science might look like.
“I would love to continue this project for as long as possible,” she said. “Right now, I am thinking about going to grad school for a Ph.D. in computational biology.”
Wallace, who leads the Johnson Space Center’s microbiology group, served as Banerjee’s NASA mentor and co-mentor overall of this project.
“I am beyond excited to have this collaboration with Dr. Treangen as I have long admired his computational microbiology achievements, and there are also many benefits that accompany proximity,” Wallace said. “Ankhi truly highlights this benefit, and I was blown away by her enthusiasm, intellect and ability to continually ask the right questions. Her tool is something that we have long sought, and I look forward to its use to enhance crew health and safety.”
Wallace will be on campus this fall to deliver a keynote at an upcoming Ken Kennedy Institute workshop on microbes and microbiomes in health, which is part of this year’s AI in Health Conference set for Sept. 22-25. Interested participants can register for the workshop here.
Opportunities like Banerjee’s are not isolated. Rice undergraduates from any major can apply to join a VIP team through OURI, earning course credit while contributing to research projects tackling real-world challenges from microbial genomics to robotics.
“Positive experiences like this show what undergraduates at Rice are capable of when it comes to contributing to research on campus and provides me with endless motivation to keep Genome Sleuths going for many years to come,” Treangen said.