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Hodgins HP, Chen P, Lobb B, Wei X, Tremblay BJM, Mansfield MJ, Lee VCY, Lee PG, Coffin J, Duggan AT, Dolphin AE, Renaud G, Dong M, Doxey AC. Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. Nat Commun 2023; 14:5475. [PMID: 37673908 PMCID: PMC10482840 DOI: 10.1038/s41467-023-41174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023] Open
Abstract
The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.
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Affiliation(s)
- Harold P Hodgins
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Briallen Lobb
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Xin Wei
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Benjamin J M Tremblay
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Victoria C Y Lee
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Coffin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Alexis E Dolphin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - Andrew C Doxey
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada.
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Stolarek I, Zenczak M, Handschuh L, Juras A, Marcinkowska-Swojak M, Spinek A, Dębski A, Matla M, Kóčka-Krenz H, Piontek J, Figlerowicz M. Genetic history of East-Central Europe in the first millennium CE. Genome Biol 2023; 24:173. [PMID: 37488661 PMCID: PMC10364380 DOI: 10.1186/s13059-023-03013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no earlier than the sixth century CE; the second postulates that they already inhabited this region in the Iron Age (IA). Testing either hypothesis is not trivial given that cremation of the dead was the prevailing custom in Central Europe from the late Bronze Age until the Middle Ages (MA). RESULTS To address this problem, we determined the genetic makeup of representatives of the IA Wielbark- and MA Slav-associated cultures from the territory of present-day Poland. The study involved 474 individuals buried in 27 cemeteries. For 197 of them, genome-wide data were obtained. We found close genetic affinities between the IA Wielbark culture-associated individuals and contemporary to them and older northern European populations. Further, we observed that the IA individuals had genetic components which were indispensable to model the MA population. CONCLUSIONS The collected data suggest that the Wielbark culture-associated IA population was formed by immigrants from the north who entered the region of contemporary Poland most likely at the beginning of the first millennium CE and mixed with autochthons. The presented results are in line with the hypothesis that assumes the genetic continuation between IA and MA periods in East-Central Europe.
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Affiliation(s)
- Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | | | - Anna Spinek
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Artur Dębski
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Marzena Matla
- Department of History, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Hanna Kóčka-Krenz
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Janusz Piontek
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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Ciecierski L, Stolarek I, Figlerowicz M. Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics. Nucleic Acids Res 2023:7175335. [PMID: 37216609 DOI: 10.1093/nar/gkad428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.
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Affiliation(s)
- Lukasz Ciecierski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Toncheva D, Serbezov D, Karachanak-Yankova S, Nesheva D. Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease. PLoS One 2020; 15:e0233666. [PMID: 32970680 PMCID: PMC7514063 DOI: 10.1371/journal.pone.0233666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.
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Affiliation(s)
- Draga Toncheva
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
- Bulgarian Academy of Sciences–BAS, Sofia, Bulgaria
- * E-mail:
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
- Department of Genetics, Faculty of biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
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Philips A, Stolarek I, Handschuh L, Nowis K, Juras A, Trzciński D, Nowaczewska W, Wrzesińska A, Potempa J, Figlerowicz M. Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia. BMC Genomics 2020; 21:402. [PMID: 32539695 PMCID: PMC7296668 DOI: 10.1186/s12864-020-06810-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death. RESULTS In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria. CONCLUSIONS In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.
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Affiliation(s)
- Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Katarzyna Nowis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Dawid Trzciński
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Wioletta Nowaczewska
- Department of Human Biology, Faculty of Biological Sciences, Wroclaw University, 50-138, Wroclaw, Poland
| | - Anna Wrzesińska
- Anthropological Laboratory, Museum of the First Piasts at Lednica, 62-261, Lednogora, Poland
| | - Jan Potempa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland.,Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, 40202, USA
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, 60-965, Poznan, Poland.
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Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry. Sci Rep 2019; 9:16883. [PMID: 31729399 PMCID: PMC6858343 DOI: 10.1038/s41598-019-51045-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022] Open
Abstract
Human ancient DNA studies have revealed high mobility in Europe’s past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300–1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns.
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Perego UA, Bodner M, Raveane A, Woodward SR, Montinaro F, Parson W, Achilli A. Resolving a 150-year-old paternity case in Mormon history using DTC autosomal DNA testing of distant relatives. Forensic Sci Int Genet 2019; 42:1-7. [DOI: 10.1016/j.fsigen.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 01/01/2023]
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Goth migration induced changes in the matrilineal genetic structure of the central-east European population. Sci Rep 2019; 9:6737. [PMID: 31043639 PMCID: PMC6494872 DOI: 10.1038/s41598-019-43183-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/12/2019] [Indexed: 12/05/2022] Open
Abstract
For years, the issues related to the origin of the Goths and their early migrations in the Iron Age have been a matter of hot debate among archaeologists. Unfortunately, the lack of new independent data has precluded the evaluation of the existing hypothesis. To overcome this problem, we initiated systematic studies of the populations inhabiting the contemporary territory of Poland during the Iron Age. Here, we present an analysis of mitochondrial DNA isolated from 27 individuals (collectively called the Mas-VBIA group) excavated from an Iron Age cemetery (dated to the 2nd-4th century A.D.) attributed to Goths and located near Masłomęcz, eastern Poland. We found that Mas-VBIA has similar genetic diversity to present-day Asian populations and higher diversity than that of contemporary Europeans. Our studies revealed close genetic links between the Mas-VBIA and two other Iron Age populations from the Jutland peninsula and from Kowalewko, located in western Poland. We disclosed the genetic connection between the Mas-VBIA and ancient Pontic-Caspian steppe groups. Similar connections were absent in the chronologically earlier Kowalewko and Jutland peninsula populations. The collected results seem to be consistent with the historical narrative that assumed that the Goths originated in southern Scandinavia; then, at least part of the Goth population moved south through the territory of contemporary Poland towards the Black Sea region, where they mixed with local populations and formed the Chernyakhov culture. Finally, a fraction of the Chernyakhov population returned to the southeast region of present-day Poland and established the archaeological formation called the “Masłomęcz group”.
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