5,000-Year-Old Bacteria Discovered in Frozen Cave May Help Fight Modern Superbugs

Microorganisms preserved for thousands of years in ice caves not only help us understand how life adapts to extreme environments, but also reveal the ancient history of antibiotic resistance. By studying these bacteria from the past, science can find valuable clues to face one of the greatest challenges of modern medicine: combating infections caused by multidrug-resistant microorganisms.

About 20% of the Earth's surface is made up of cold or permanently frozen environments. These places, such as glaciers, polar regions, and ice caves, are often seen as inhospitable and poor in life.

However, science has shown exactly the opposite: these environments harbor highly specialized microorganisms, capable of surviving, growing, and even remaining active in extreme temperatures. With the advance of climate change, understanding who these microbes are and how they function has become even more important.

These cold-adapted microorganisms are not just biological curiosities. They represent a huge source of genetic and biochemical diversity. Many of these bacteria produce enzymes and molecules that function best at low temperatures, which sparks great interest for industrial, environmental, and medical applications.

Furthermore, cold environments can act as "time capsules," preserving microbial life forms virtually intact for thousands of years.

Scarisoara Ice Cave in Romania. Credit: Paun V.I.

Despite the growing interest in microorganisms from polar regions and permafrost, ice deposits inside caves are still largely unexplored. This is surprising, since these caves offer very particular conditions: low and stable temperatures, few nutrients, and isolation from the external environment.

All of this creates an ideal scenario for the preservation of ancient microorganisms, which can reveal what microbial life was like in the past.

An emblematic example is the Scărișoara Ice Cave in Romania, which houses one of the largest and oldest underground ice blocks in the world. This ice is up to 13,000 years old and has been extensively studied from a climatic and geological point of view.

More recently, molecular analyses have shown that it also harbors rich and complex microbial communities, influenced by the environmental conditions existing at the time the ice formed.

The team drilled a 25-meter ice core in the area of ​​the cave known as the Great Hall. Credit: Itcus C.

Beyond their ecological value, these ancient microbial communities are especially relevant for understanding antibiotic resistance. Although antimicrobial resistance is now seen as a consequence of the overuse of antibiotics, it is, in fact, a much older phenomenon.

Bacteria have been developing defense mechanisms against antimicrobial substances for millions of years. Isolated environments with little human impact, such as ice caves, can preserve these ancestral mechanisms.

In this study, researchers isolated a bacterium of the genus Psychrobacter from approximately 5,000-year-old ice from the Scărișoara Cave. This bacterium showed an impressive profile: resistance to several types of modern antibiotics and, at the same time, the ability to inhibit the growth of bacteria dangerous to humans, including multidrug-resistant hospital pathogens. This suggests that ancient microorganisms may carry both resistance genes and genes linked to the production of antimicrobial compounds.

A complete analysis of this bacterium's genome revealed dozens of genes associated with adaptation to cold, environmental stress, and antibiotic resistance, as well as genes potentially involved in the production of bioactive molecules.

These findings reinforce the idea that ice caves are poorly explored reservoirs of microbial diversity, with great potential for the discovery of new antibiotics and for understanding the evolutionary origin of antimicrobial resistance.

READ MORE:

First genome sequence and functional profiling of Psychrobacter SC65A.3 preserved in 5,000-year-old cave ice: insights into ancient resistome, antimicrobial potential, and enzymatic activities

Victoria Ioana Paun, Corina Itcus, Paris Lavin, Mariana Carmen Chifiriuc, and Cristina Purcarea

Frontiers in Microbiology. Volume 16 - 2025. 18 December 2025 DOI: 10.3389/fmicb.2025.1713017

Abstract:

Ancient cryospheric environments may preserve overlooked reservoirs of antimicrobial resistance (AMR) and bioactive potential. This study reports the first whole-genome sequencing and functional characterization of Psychrobacter sp. SC65A.3 isolated from 5,000-year-old ice from Scărișoara Ice Cave, revealing a multidrug-resistance phenotype alongside antimicrobial activity. Whole-genome sequencing combined with phenotypic characterization for extremotolerance, antibiotic susceptibility and biochemical profile were used to identify and functionally characterize the ancient Psychrobacter sp. SC65A.3. SC65A.3 is a polyextremophile, growing up to 15 °C and tolerating 1.9 M NaCl and 0.9 M MgCl₂. Phylogenetic analysis classified it within P. cryohalolentis. Functional assays showed broad hydrolytic activity and resistance to 10 antibiotics across 8 classes, including third-generation cephalosporins, fluoroquinolones, aminoglycosides, and rifampicin. Whole-genome analysis identified >100 AMR-associated genes, including clinically relevant determinants (e.g., ampC, gyrA, gyrB, parC, parE, dfrA, rpoB, tetA, tetC, and mcr-1), as well as multiple heavy-metal resistance and multidrug efflux genes. SC65A.3 inhibited 14 ESKAPE-group pathogens (including MRSA, Enterococcus faecium, Enterobacter sp., Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii), consistent with genes linked to antimicrobial compounds such as glycopeptides and bacitracin. In addition, 45 stress-response genes related to cold/heat adaptation were detected, including distinctive htpX, htpG, and pka genes among cold-adapted Psychrobacter. SC65A.3 represents an ancient, ice-adapted Psychrobacter with a dual profile of multidrug resistance and antimicrobial activity, highlighting ice caves as underexplored reservoirs of ancient resistomes and bioactive traits. To our knowledge, this is the first genome analysis of a Psychrobacter isolate from an ice cave and the first characterization of an ancient resistome from this environment, supporting future ecological, biotechnological, and medical exploration.