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  Evolution of the human oral microbiome and resource development for ancient metagenomics

Fellows Yates, J. A. (2022). Evolution of the human oral microbiome and resource development for ancient metagenomics. PhD Thesis, Friedrich Schiller University Jena, Faculty of Biosciences, Jena.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000C-8200-0 Version Permalink: https://hdl.handle.net/21.11116/0000-000C-8203-D
Genre: Thesis

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OA. - Dissertation, Friedrich Schiller University Jena, 2022
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 Creators:
Fellows Yates, James A.1, Author           
Warinner, Christina G.1, Referee                 
Krause, Johannes1, Referee                 
Rasmussen, Simon, Referee
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

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Free keywords: Alte DNA Genomik Mikrobiom <Genetik> Zahnstein Archäologie Bioinformatik
 Abstract: The microbes that live in and on our bodies play major roles in health and disease due to their symbiotic relationship with the host. Understanding how these communities adapt to changes in their environment - either by natural or anthropological forces - is currently a critical area of research for improving holistic healthcare. The aim of this thesis was to demonstrate the potential of large-scale shotgun-sequenced ancient dental calculus to study the wider diversity of the oral microbiome. In Manuscript A, I have shown that ancient dental calculus can be used to improve the understanding of past human oral microbiome diversity, after analysing the largest and oldest ancient dental calculus dataset to date. In this manuscript I also present new tools to help improve authentication of ancient microbiomes. Manuscript B describes the repository AncientMetagenomeDir, a community-level resource that lists all public ancient metagenomic sequencing datasets. The resource will allow researchers to efficiently re-use public data to ensure the robusticity and improve the statistical power of future studies. Manuscript C presents an entirely rewritten user-friendly palaeogenomics pipeline following latest software development and bioinformatics best practices. The pipeline nf-core/eager, has been developed in a way that allows for easy integration with large scale computing infrastructure required for such analyses. Importantly, I have extended this genomics pipeline to have in-parallel metagenomic profiling and screening of ancient DNA characteristics. These manuscripts have contributed new insights into the biology and evolution of oral biofilms, but also introduced new open-source and sustainable tools and resources that will allow further investigation of ancient microbiomes.

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Language(s): eng - English
 Dates: 2021-09-232022-05-172022-05-172022-05-17
 Publication Status: Issued
 Pages: 142
 Publishing info: Jena : Friedrich Schiller University Jena, Faculty of Biosciences
 Table of Contents: 1 Introduction
1.1 Background
1.2 The human microbiome
1.3 Evolution of the oral microbiome
1.4 Reconstruction of ancient oral microbiomes
1.5 Challenges in ancient metagenomics
1.6 Aims
2 Overview of the manuscripts
2.1 Manuscript A
2.2 Manuscript B
2.3 Manuscript C
3 Manuscript A: The evolution and changing ecology of the African hominid oral microbiome
3.1 Overview and contribution
3.2 Article
4 Manuscript B: Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir
4.1 Overview and contribution
4.2 Article
5 Manuscript C: Reproducible, portable, and effcient ancient genome reconstruction with nf-core/eager
5.1 Overview and contribution
5.2 Article
6 Discussion
6.1 Research directions for future ancient dental calculus microbiome research
6.2 Sample sizes in ancient microbiome research
6.3 Improving throughput in ancient metagenomics analysis
6.4 Improving authentication in ancient metagenomics analysis
6.5 Outstanding challenges for ancient metagenomics analysis
7 Conclusion
8 Summary / Zusammenfassung
8.1 English
8.2 Deutsch
9 References
10 Ehrenwörtliche Erklärung
11 Annexes
11.1 Candidate-specific contributions to publications
11.2 Supplementary information
 Rev. Type: -
 Identifiers: URN: https://nbn-resolving.org/urn:nbn:de:gbv:27-dbt-20220721-150818-002
URN: https://www.db-thueringen.de/receive/dbt_mods_00053042
Other: shh3369
 Degree: PhD

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