Profiling Antibiotic Resistance Determinants in Ancient Permafrost Microbiomes

Antimicrobial resistance presents a formidable challenge, yet its existence predates the introduction of antibiotics. Our study delves into the presence of antimicrobial resistance determinants (ARDs) in ancient permafrost microbiomes, comparing them with contemporary soil and pristine environments. Majority of the samples are from regions around Beringia, encompassing parts of Russia and Alaska, with only one sample originating from the Tien Shan Mountain range in Kyrgyzstan. From over 2.3 tera base pairs of raw metagenomic data, we assembled about 1.3 billion metagenomic contigs and explored the prevalence of ARDs in them. Our findings reveal a diverse array of ARDs in ancient microbiomes, akin to contemporary counterparts. On average, we identified 2 ARDs per ribosomal protein gene in ancient samples. Actinomycetota, Bacillota, and several thermophiles were prominent carriers of ARDs in Chukochi and Kamchatkan samples. Conversely, ancient permafrost from the Tien Shan Mountain range exhibited no Thermophiles or Actinomycetota carrying ARDs. Both ancient and contemporary microbiomes showcased numerous divergent ARDs, with approximately 40% identity to genes in antibiotic resistance gene databases. Antibiotic inactivation-type ARDs exhibited purifying selection with contemporary resistance genes, as estimated by dN/dS ratio. Importantly, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARDs.