Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth

Doris A. van Bergeijk; Hannah E. Augustijn; Somayah S. Elsayed; Joost Willemse; Victor J. Carrión; Chao Du; Mia Urem; Lena V. Grigoreva; Maksim Y. Cheprasov; Semyon Grigoriev; Hans Jansen; Bas Wintermans; Andries E. Budding; Herman P. Spaink; Marnix H. Medema; Gilles P. van Wezel

doi:10.1111/1462-2920.16589

Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth

Doris A. van Bergeijk, Hannah E. Augustijn, Somayah S. Elsayed, Joost Willemse, Victor J. Carrión, Chao Du, Mia Urem, Lena V. Grigoreva, Maksim Y. Cheprasov, Semyon Grigoriev, Hans Jansen, Bas Wintermans, Andries E. Budding, Herman P. Spaink, Marnix H. Medema, Gilles P. van Wezel^* (Corresponding author)

^*Corresponding author for this work

NIOO - Microbial Ecology (ME)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

1 Citation (Scopus)

Abstract

Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.

Original language	English
Article number	e16589
Journal	Environmental Microbiology
Volume	26
Issue number	2
DOIs	https://doi.org/10.1111/1462-2920.16589
Publication status	Published - Feb 2024

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van Bergeijk, D. A., Augustijn, H. E., Elsayed, S. S., Willemse, J., Carrión, V. J., Du, C., Urem, M., Grigoreva, L. V., Cheprasov, M. Y., Grigoriev, S., Jansen, H., Wintermans, B., Budding, A. E., Spaink, H. P., Medema, M. H., & van Wezel, G. P. (2024). Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth. Environmental Microbiology, 26(2), Article e16589. https://doi.org/10.1111/1462-2920.16589

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title = "Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth",

abstract = "Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.",

author = "{van Bergeijk}, {Doris A.} and Augustijn, {Hannah E.} and Elsayed, {Somayah S.} and Joost Willemse and Carri{\'o}n, {Victor J.} and Chao Du and Mia Urem and Grigoreva, {Lena V.} and Cheprasov, {Maksim Y.} and Semyon Grigoriev and Hans Jansen and Bas Wintermans and Budding, {Andries E.} and Spaink, {Herman P.} and Medema, {Marnix H.} and {van Wezel}, {Gilles P.}",

note = "Data archiving: no NIOO data",

year = "2024",

month = feb,

doi = "10.1111/1462-2920.16589",

language = "English",

volume = "26",

journal = "Environmental Microbiology",

issn = "1462-2912",

publisher = "Wiley-Blackwell",

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van Bergeijk, DA, Augustijn, HE, Elsayed, SS, Willemse, J, Carrión, VJ, Du, C, Urem, M, Grigoreva, LV, Cheprasov, MY, Grigoriev, S, Jansen, H, Wintermans, B, Budding, AE, Spaink, HP, Medema, MH & van Wezel, GP 2024, 'Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth', Environmental Microbiology, vol. 26, no. 2, e16589. https://doi.org/10.1111/1462-2920.16589

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T1 - Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth

AU - van Bergeijk, Doris A.

AU - Augustijn, Hannah E.

AU - Elsayed, Somayah S.

AU - Willemse, Joost

AU - Carrión, Victor J.

AU - Du, Chao

AU - Urem, Mia

AU - Grigoreva, Lena V.

AU - Cheprasov, Maksim Y.

AU - Grigoriev, Semyon

AU - Jansen, Hans

AU - Wintermans, Bas

AU - Budding, Andries E.

AU - Spaink, Herman P.

AU - Medema, Marnix H.

AU - van Wezel, Gilles P.

N1 - Data archiving: no NIOO data

PY - 2024/2

Y1 - 2024/2

N2 - Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.

AB - Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.

U2 - 10.1111/1462-2920.16589

DO - 10.1111/1462-2920.16589

M3 - Article

SN - 1462-2912

VL - 26

JO - Environmental Microbiology

JF - Environmental Microbiology

IS - 2

M1 - e16589

ER -

Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth

Abstract

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