Metagenomic analysis of ancient human and microbial DNA preserved under unusual taphonomic conditions

Sarhan, Mohamed Sabry Mohamed (2023): Metagenomic analysis of ancient human and microbial DNA preserved under unusual taphonomic conditions. Dissertation, LMU München: Fakultät für Biologie

Abstract

In this dissertation, I analyzed different types of ancient organic and inorganic materials preserved under different taphonomic conditions from different time points (~2900-235 BP). During the analysis, I tried to improve the currently used in situ, in vitro, and in silico methods of ancient DNA analysis. The results of this dissertation are summarized and published in three research articles. In the first article, we analyzed skeletal remains of a late Bronze Age individual found in the Wimsener water caves in Germany. In addition to the skeletal remains, we analyzed the calcite deposits, found surrounding the bones of the individuals, from which we were able to retrieve ancient human DNA fragments, enough to reconstruct the full mitochondrial genome and to assign molecular sex to the individual. We demonstrated the ancient human and microbial DNA fragments diffused from the bones to the calcite stone deposits in the same direction of gravity. This study exemplifies using alternative source for obtaining ancient human and/or microbial DNA without causing destruction to the valuable archeological finding. In the second article, we analyzed different paleofeces specimens from Hallstatt mines, Austria (dated to the Bronze Age – the Baroque times). We subjected them to microscopic, proteomic, and metagenomic analyses. The collective analysis allowed unveiling the following: i) the molecular sex and the mitochondrial haplogroups of the individuals; ii) consumption of fibrous plant-based diet as well as animal components; iii) non-Westernized gut microbiome composition until the Baroque times; iv) presence of gut parasites; and finally, v) consumption of fermented food (cheese-like) and beverages (beer). During this study, we reconstructed, for the first time, complete ancient fungal genomes of Saccharomyces cerevisiae and Penicillium roqueforti, and by comparative genomic analyses, we presented different lines of evidence on their being used in beer and cheese fermentation, respectively. The study presented a comprehensive interdisciplinary workflow for the analysis of such precious archeological materials. In the third article, we analyzed different tissue specimens from the mummy of Anna Catharina Bischoff (ACB), from Basel, Switzerland. Initially, we aimed to find any molecular proof of presence of the syphilis-causing bacterium Treponema pallidum, which was not successful. However, by employing de novo metagenomic assembly, we were able to reconstruct a complete genome of a pathogen from the brain sample, belonging to the Mycobacteriaceae family. The genome analysis of the de novo detected pathogen supports the assumption of its pathogenicity and was very congruent with the radiological symptoms and its survival in the brain under high concentrations of mercury. The study presented a proof-of-concept on using metagenomic assembly to detect extinct or previously undescribed pathogens. Overall, throughout this dissertation, I tried to use different analytical methods beyond what is already known and commonly used in the field of ancient DNA.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: De novo assembly, Metagenomics, Mummies, Iceman, Barfüsser Mummy, Wimsenerhöle, Hallstatt, Ancient Microbiome, Blue Cheese, Ancient beer, Paleopathology, Paleogenetics, Bacteriophage, Nontuberculous Mycobacteria, SedaDNA, aDNA, Mercury, Brain infection, Bioinformatics, Diet analysis, Ancient diseases, Evolution
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 25. Oktober 2023
• 1. Bericht­erstatter:in: Zink, Albert