Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Matsumoto N, Habu J, Matsui A. Subsistence, sedentism, and social complexity among Jomon hunter-gatherers of the Japanese Archipelago. In: Habu J, Lape PV, Olsen JW, editors. Handbook of East and Southeast Asian archaeology. New York, NY: Springer New York; 2017. https://doi.org/10.1007/978-1-4939-6521-2_27.
Kanzawa-Kiriyama H, Kryukov K, Jinam TA, Hosomichi K, Saso A, Suwa G, et al. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet. 2017. https://doi.org/10.1038/jhg.2016.110.
Kanzawa-Kiriyama H, Jinam TA, Kawai Y, Sato T, Hosomichi K, Tajima A, et al. Late jomon male and female genome sequences from the funadomari site in Hokkaido, Japan. Anthropol Sci. 2019. https://doi.org/10.1537/ase.190415.
Eisenhofer R, Weyrich LS. Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ. 2019. https://doi.org/10.7287/peerj.preprints.27166v1.
Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, et al. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature. 2017. https://doi.org/10.1038/nature21674.
Mühlemann B, Jones TC, De Barros Damgaard P, Allentoft ME, Shevnina I, Logvin A, et al. Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature. 2018. https://doi.org/10.1038/s41586-018-0097-z.
Larsen BB, Cole KL, Worobey M. Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents. Virus Evol. 2018. https://doi.org/10.1093/ve/vey014.
Spyrou MA, Bos KI, Herbig A, Krause J. Ancient pathogen genomics as an emerging tool for infectious disease research. Nat Rev Genet. 2019. https://doi.org/10.1038/s41576-019-0119-1.
Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature. 2011. https://doi.org/10.1038/nature10549.
Keller M, Spyrou MA, Scheib CL, Neumann GU, Kröpelin A, Haas-Gebhard B, et al. Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750). Proc Natl Acad Sci USA. 2019. https://doi.org/10.1073/pnas.1820447116.
Adler CJ, Dobney K, Weyrich LS, Kaidonis J, Walker AW, Haak W, et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet. 2013. https://doi.org/10.1038/ng.2536.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009. https://doi.org/10.1093/bioinformatics/btp324.
Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013. https://doi.org/10.1089/cmb.2013.0084.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009. https://doi.org/10.1093/bioinformatics/btp352.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009. https://doi.org/10.1186/1471-2105-10-421.
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018. https://doi.org/10.1371/journal.pcbi.1005944.
Herbig A, Maixner F, Bos KI, Zink A, Krause J, Huson DH. MALT: fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman. bioRxiv. 2016. https://doi.org/10.1101/050559.
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010. https://doi.org/10.1093/bioinformatics/btq033.
Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007. https://doi.org/10.1101/gr.5969107.
Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics. 2011. https://doi.org/10.1093/bioinformatics/btr347.
Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L. MapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013. https://doi.org/10.1093/bioinformatics/btt193.
Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, et al. Clades of huge phages from across Earth’s ecosystems. Nature. 2020. https://doi.org/10.1038/s41586-020-2007-4.
Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM. CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genom. 2016. https://doi.org/10.1186/s12864-016-2627-0.
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006. https://doi.org/10.1093/bioinformatics/btl158.
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012. https://doi.org/10.1093/bioinformatics/bts565.
Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007. https://doi.org/10.1093/nar/gkm360.
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018. https://doi.org/10.1093/nar/gky425.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010; https://doi.org/10.1186/1471-2105-11-119.
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7:e1002195. https://doi.org/10.1371/journal.pcbi.1002195.
Rice P, Longden L, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16:276–277.
Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006. https://doi.org/10.1093/nar/gkl315.
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007. https://doi.org/10.1093/molbev/msm088.
Fernandes F, Pereira L, Freitas AT. CSA: an efficient algorithm to improve circular DNA multiple alignment. BMC Bioinform. 2009. https://doi.org/10.1186/1471-2105-10-230.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013. https://doi.org/10.1093/molbev/mst010.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009. https://doi.org/10.1093/bioinformatics/btp348.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014. https://doi.org/10.1093/bioinformatics/btu033.
Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA, et al. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 2012;6:915–926.
Rascovan N, Huynh H, Chouin G, Adekola K, Georges-Zimmermann P, Signoli M, et al. Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth. npj Biofilms Microbiomes. 2016. https://doi.org/10.1038/s41522-016-0008-8a.
Schmidt C. The virome hunters. Nat Biotechnol. 2018. https://doi.org/10.1038/nbt.4268.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. Uncovering Earth’s virome. Nature. 2016. https://doi.org/10.1038/nature19094.
Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, et al. Natural mummification of the human gut preserves bacteriophage DNA. FEMS Microbiol Lett. 2015;363:1–8.
Appelt S, Fancello L, Le Bailly M, Raoult D, Drancourt M, Desnues C. Viruses in a 14th-century coprolite. Appl Environ Microbiol. 2014;80:2648–2655.
Abeles SR, Robles-Sikisaka R, Ly M, Lum AG, Salzman J, Boehm TK, et al. Human oral viruses are personal, persistent and gender-consistent. ISME J. 2014. https://doi.org/10.1038/ismej.2014.31.
Achtman M, Zhou Z. Analysis of the human oral microbiome from modern and historical samples with SPARSE and EToKi. bioRxiv. 2019. http://biorxiv.org/content/early/2019/11/15/842542.abstract.
Cato EP, Moore WEC, Nygaard G, Holdeman LV. Actinomyces meyeri sp. nov., specific epithet rev. Int J Syst Bacteriol. 1984. https://doi.org/10.1099/00207713-34-4-487.
Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, et al. Host genetic control of the oral microbiome in health and disease. Cell Host Microbe. 2017. https://doi.org/10.1016/j.chom.2017.08.013.
Aleti G, Baker JL, Tang X, Alvarez R, Dinis M, Tran NC, et al. Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease. MBio. 2019. https://doi.org/10.1128/mBio.00321-19.
We thank the members of the Human Genetics Laboratory at the National Institute of Genetics for providing many suggestions. This project was supported by Deciphering Origin and Establishment of Yaponesians mainly based on genome sequence data project (Yaponesia Genome Project) supported by JSPS KAKENHI Grant Number JP 18H05506. Some computations were performed on the NIG supercomputer at ROIS National Institute of Genetics. We would like to thank Enago (https://www.enago.jp) for English editing. This work was supported in part by The Graduate University for Advanced Studies, SOKENDAI.
Conflict of interest
The authors declare that they have no conflict of interest.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Nishimura, L., Sugimoto, R., Inoue, J. et al. Identification of ancient viruses from metagenomic data of the Jomon people. J Hum Genet 66, 287–296 (2021). https://doi.org/10.1038/s10038-020-00841-6