DNA analysis from a Turkish cave has unveiled evidence that prehistoric people used charcoal-based remedies to treat digestive ailments as much as 5,000 years ago, while simultaneously revealing that antibiotic resistance genes existed millennia before modern pharmaceuticals. This groundbreaking discovery from İnönü Cave in Turkey's Zonguldak province challenges our understanding of both ancient medicine and microbial evolution.
The research, recently published in PLoS ONE, represents one of Turkey's first large-scale ancient DNA soil studies. Using cutting-edge metagenomic sequencing, scientists from Zonguldak Bülent Ecevit University have reconstructed 5,000 years of microbial communities, revealing fascinating insights into prehistoric healthcare practices.
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Prehistoric Coal Medicine Uncovered
Excavations at İnönü Cave, led by Associate Professor Dr. Hamza Ekmen since 2017, have revealed continuous habitation from the Chalcolithic Age through the Iron Age, reveals Arkeonews. The volcanic cave's unique geology provided abundant natural resources, including coal deposits that prehistoric inhabitants cleverly utilized for medicinal purposes.
Soil analysis from four distinct cultural layers revealed that ancient people treated nausea, diarrhea, stomach pain, and other digestive disorders using coal-derived substances. This practice demonstrates remarkable continuity with modern activated charcoal therapies, suggesting sophisticated understanding of natural remedies thousands of years before recorded medical knowledge.
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Soil DNA analysis from İnönü Cave reveals prehistoric microbial communities and ancient medical practices. (Öztürk et al., 2025/PLoS ONE)
Ancient Antibiotic Resistance Discovered
Perhaps most significantly, the study identified antibiotic resistance genes dating back millennia: the tetA gene from 4300 BC, the intl1 gene from 3000 BC, and the OXA-58 gene from 1400 BC. These findings support the "resistome hypothesis," which argues that antibiotic resistance evolved naturally in soil bacteria long before human pharmaceutical development.
"Antibiotic resistance is not only a consequence of modern drug use but a deeply rooted ecological trait," explained Dr. İkran Öztürk, lead researcher from ZBEU's Faculty of Pharmacy. Environmental factors including volcanic geology, mineral-rich water sources, and prehistoric medical practices likely shaped microbial evolution over thousands of years.
The research team identified major bacterial groups including Acidobacteriota, Proteobacteria, and Cyanobacteria, mapping how microbial communities shifted alongside human activities. Early Bronze Age samples showed increased Proteobacteria linked to animal husbandry, while Chalcolithic samples revealed Cyanobacteria suggesting aquatic resource utilization.
This interdisciplinary approach, part of Turkey's One Health initiative, demonstrates how archaeological DNA analysis can illuminate both prehistoric daily life and modern health challenges. As humanity faces rising antibiotic resistance, these discoveries highlight archaeology's valuable role in understanding medical evolution.
Top image: İnönü Cave archaeological excavation site in Turkey's Zonguldak province. Source: İnönü Cave Project Archive/PLoS ONE
By Gary Manners
References
Öztürk, İ., Ekmen, F.G., Ekmen, H. et al. 2025. Decoding past microbial life and antibiotic resistance in İnönü Cave's archaeological soil. Available at: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0326358
Arkeonews. 2025. Ancient DNA From Turkish Cave Reveals 5,000-Year-Old Charcoal Therapy and Hidden Antibiotic Resistance. Available at: https://arkeonews.net/ancient-dna-from-turkish-cave-reveals-5000-year-old-charcoal-therapy-and-hidden-antibiotic-resistance/
