Millennial-Scale Microbiome Analysis Reveals Ancient Antimicrobial Resistance Conserved Despite Modern Selection Pressures

Abstract

Background 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.Results 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, majority of which have identity between 40%-60% to genes in antibiotic resistance gene databases. Antibiotic inactivation-type ARDs exhibited purifying selection with contemporary resistance genes, as estimated by dN/dS ratio.Conclusion Antibiotic resistance has always existed and will continue to do so, as it is inherently encoded in the genomes of microbes. The classes of antimicrobial resistance genes profiled and the function of antibiotic-inactivating enzymes from ancient permafrost microbiomes do not seem to be very different from the genes found in the antibiotic era. Additionally, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARDs.