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  A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

Sabin, S., Herbig, A., Vagene, A. J., Ahlström, T., Bozovic, G., Arcini, C., et al. (2019). A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biology: Biology for the Post-Genomic Era, 21: 201 (2020). doi:10.1186/s13059-020-02112-1.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-A279-E Version Permalink: http://hdl.handle.net/21.11116/0000-0006-DFE7-B
Genre: Journal Article

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 Creators:
Sabin, Susanna1, Author              
Herbig, Alexander1, Author              
Vagene, Ashild J.1, Author              
Ahlström, Torbjörn, Author
Bozovic, Gracijela, Author
Arcini, Caroline, Author
Kuehnert, Denise2, Author              
Bos, Kirsten I.2, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2tide, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2591691              

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Free keywords: Ancient DNA, Metagenomics, Molecular dating, Mycobacterium tuberculosis, Tuberculosis
 Abstract: BACKGROUND: Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). - RESULTS: A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. - CONCLUSIONS: The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.

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Language(s): eng - English
 Dates: 2019-03-25
 Publication Status: Published online
 Pages: 24
 Publishing info: -
 Table of Contents: Results
- Pathogen identification
- Genomic enrichment and reconstruction
- Phylogeny and dating
Discussion
Conclusions
Methods
- Lung nodule identification
- Sampling and extraction
- Library preparation and shotgun screening sequencing
- Pathogen identification and authentication
- In-solution capture probe design
- UDG library preparation and in-solution capture
- Genomic reconstruction, heterozygosity, and SNP calling
- Phylogenetic analysis
- Bayesian phylogenetic analysis of full MTBC and L4 datasets
 Rev. Type: Peer
 Identifiers: DOI: 10.1186/s13059-020-02112-1
DOI: 10.1101/588277
Other: shh2229
 Degree: -

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Title: Genome Biology : Biology for the Post-Genomic Era
Source Genre: Journal
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Affiliations:
Publ. Info: London : BioMed Central Ltd.
Pages: - Volume / Issue: 21 Sequence Number: 201 (2020) Start / End Page: - Identifier: ISSN: 1465-6906
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000224390

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Title: bioRxiv
Source Genre: Journal
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Publ. Info: Cold Spring Harbor : Cold Spring Harbor Laboratory
Pages: - Volume / Issue: - Sequence Number: 588277 Start / End Page: - Identifier: URI: https://www.biorxiv.org/