For over a hundred years, the unassuming fruit fly has been a key player in numerous vital scientific discoveries. It helped scientists understand how X-rays induce genetic mutations, the transmission of genes through chromosomes, and the role of a gene called period in regulating our internal clocks—issues that can lead to complications like jet lag and increased risks for various diseases. These findings, along with around 90,000 other studies, are compiled in a significant online resource named FlyBase, which researchers regularly access to craft new experiments aimed at uncovering disease causes and developing potential treatments. Good science builds on earlier revelations, and having such a repository is crucial for fostering further innovation.
FlyBase garners around 770,000 visits a month from researchers around the globe, focusing on personalized therapies for rare cancers and studying neurodegenerative diseases, among other things. However, its future now hangs in the balance due to impending layoffs triggered by funding cuts. This spring, the Trump administration terminated a grant that Harvard University used to maintain FlyBase, as part of a broader $2.2 billion funding reduction.
“I rely on FlyBase every day—it’s indispensable,” remarked Celeste Berg, a genome sciences professor at the University of Washington and not on the FlyBase team. “Our understanding of human genes largely stems from model systems like Drosophila.” Interestingly, humans share around 60% of their genes with these fruit flies.
FlyBase’s precarious status showcases how interconnected the research landscape is and illustrates how funding issues in one area can have far-reaching implications. More than 4,000 laboratories utilize FlyBase. Harvard previously received about $2 million annually from federal funds to support FlyBase, constituting a significant portion of its operational budget. Other institutions, including the University of New Mexico, Indiana University, and the University of Cambridge, also work collaboratively on FlyBase and benefit from it.
“This isn’t just a Harvard issue,” said Brian Calvi, a biology professor at Indiana University and part of the FlyBase management team. “The ripple effects extend to the global biomedical research community.” While Harvard’s Faculty of Arts and Sciences provided interim funding to sustain FlyBase, that assistance is set to end in October. A judge recently mandated the Trump administration to restore funds to Harvard researchers who lost support, but no money has yet reached FlyBase, and the administration is currently appealing the court’s decision.
The Transmitter, a site focusing on neuroscience news, was the first to report on the imminent layoffs at FlyBase, a situation also covered by the Harvard Crimson. Calvi noted that the FlyBase grant covered salaries for eight staff members at Harvard, three at Indiana, five at Cambridge, and one at the University of New Mexico. While Indiana and Cambridge managed to secure funding for their parts of the program for next year, the New Mexico position ended in August. Operating since 1992, FlyBase has enjoyed over three decades of federal support, compiling and summarizing research papers, organizing gene findings, and providing data on genetically modified fruit flies to help elucidate gene functions.
Berg uses FlyBase extensively for her work on human development and organ formation, enabling her to identify genes of interest for experimentation. Thousands of fruit fly studies are added each year, and without FlyBase, researchers would struggle to keep pace and might overlook crucial connections.
Researchers associated with the Undiagnosed Diseases Network utilize FlyBase to discern if genetic mutations in children contribute to rare diseases by comparing genetic variants to historical data on those genes in fruit flies. FlyBase is now turning to crowdfunding for support.
“Given how important FlyBase is to the broader scientific community, we hope that other institutions and stakeholders at Harvard will rally support,” said James Chisholm, a spokesperson for the Harvard Faculty of Arts and Sciences, noting that multiple Harvard departments are actively seeking additional funding to secure FlyBase’s future operations. Unfortunately, two staff members from FlyBase have already been laid off, and more layoffs are anticipated soon.
“If we lose key personnel, regaining that expertise to maintain the database would become nearly impossible,” Perrimon warned. “That would mark a turning point for FlyBase.” This funding crisis also threatens plans to transition FlyBase’s data to a long-term facility known as the Alliance of Genome Resources, which aims to streamline research efforts across common model organisms like rats and mice.
The National Institutes of Health has been investing about $5 million annually since 2017 to amalgamate various databases, including FlyBase, WormBase, and others that are essential for human health research. Paul Sternberg, a professor of biology at Caltech leading the Alliance initiative, expressed that the current funding turmoil at FlyBase adds an unforeseen hurdle to making research results more user-friendly and accessible.
“We need to resolve this quickly, but staff reductions complicate things,” he noted. Plans for merging FlyBase with the Alliance in 2029 may need to be expedited, given the financial uncertainties. As for the crowdfunding going on, Calvi mentioned, “So far, it’s less than $100,000; we probably need a million.”
