Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

van Bergeijk, D. A.; Augustijn, H.; Elsayed, S. S.; Willemse, J.; Carrion, V. J.; Urem, M.; Grigoreva, L. V.; Cheprasov, M.; Grigariev, S.; Wintermans, B.; Budding, A. E.; Spaink, H. P.; Medema, M. H.; van Wezel, G.

doi:10.1101/2022.12.22.521380

bioRxiv · 10.1101/2022.12.22.521380

Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

van Bergeijk, D. A.·Augustijn, H.·Elsayed, S. S.·Willemse, J.·Carrion, V. J.·Urem, M.·Grigoreva, L. V.·Cheprasov, M.·Grigariev, S.·Wintermans, B.·Budding, A. E.·Spaink, H. P.·Medema, M. H.·van Wezel, G.

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Abstract

Ancient microbial communities of permafrost soils and frozen animal remains represent an archive that has barely been explored. This yet unexplored microbial world is a vast resource that can provide us with new evolutionary insights, metabolic pathways and novel chemistry. Here, we reveal that Actinobacteria isolated from a faecal sample from the intestinal tract of a 28,000-year-old Siberian mammoth are phylogenetically and metabolically distinct from currently known modern siblings. Ancient Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of the ancestors show a large phylogenetic distance to strains isolated today and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides a snapshot into Actinobacteria of the past, yielding unexplored genomic information that is not yet present in current databases.

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van Bergeijk, D. A., Augustijn, H., Elsayed, S. S., Willemse, J., Carrion, V. J., Urem, M., Grigoreva, L. V., Cheprasov, M., Grigariev, S., Wintermans, B., Budding, A. E., Spaink, H. P., Medema, M. H., van Wezel, G.. 2022-12-22. Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth. https://doi.org/10.1101/2022.12.22.521380

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