Cal Poly Scientists Probe Microbes Trapped in Amber for New Antibiotic Clues — With ‘Jurassic Park’ Overtones

Cal Poly researchers are examining microorganisms preserved in amber and other ancient environments to search for novel antibiotic compounds and to study how antibiotic resistance evolved over millions of years. The project is led by biochemistry Professor Katharine Watts and postdoctoral researcher Rachel Johnson and involves student investigators Safiya Rufino and Kaitlyn Calligan.

The microbial collection was donated by Professor Emeritus Raul Cano, who previously collaborated with the scientist whose work helped inspire Michael Crichton’s novel Jurassic Park. The samples span a wide age range — from roughly 20,000 years to as old as 40 million years — and amber specimens are stored at −80°C to preserve their integrity.

The team is screening these ancient strains for small molecules with antibiotic activity and sequencing their DNA to identify the biosynthetic genes that encode those natural products. By linking chemical profiles to genetic information, researchers can pinpoint the enzymes and pathways microbes used to produce antibiotic compounds.

“We’re specifically searching for antibiotic compounds, and we’re also studying the microbial DNA because it encodes the instructions for making those small molecules,” Johnson said. “The DNA gives us a recipe for the natural products we’re interested in.”

Student researchers have focused tasks: Rufino is profiling secondary metabolites — the natural products microbes produce — to identify candidates that can inhibit modern, nonpathogenic test organisms. Calligan is studying protein structures and other molecular evidence to learn how these bacteria and their metabolites evolved and functioned in ancient ecosystems.

“Working with bacterial strains that lived millions of years ago feels surreal,” said Safiya Rufino. “I’m trying to identify what natural products these microbes produce and whether any of them can suppress the growth of contemporary safe pathogens.”

Although the project has drawn comparisons to Jurassic Park, the researchers emphasize that their work is focused on chemical and genetic discovery, not biological cloning. All laboratory procedures with the ancient samples are conducted under basic biosafety conditions.

“We’re not cloning dinosaurs — at most we may clone some proteins they express,” Johnson noted.

The work responds to the global challenge of rising antibiotic resistance. The team is currently in a discovery phase and does not have immediate plans to develop medicines, but their findings could reveal previously unknown antibacterial mechanisms and genes that inspire future therapeutic research.

Both student leads are participants in Cal Poly’s BEACoN program, which is run by the Office of Diversity, Equity and Inclusion and supports underrepresented students through research opportunities and mentoring. Calligan, who identifies as a first-generation college student, credited BEACoN with helping her access research experience.