TY - BOOK

T1 - Prospects of Meta-Omic Applications on Archaeological Microbiomes

AU - Fotakis, Anna Katerina

PY - 2019

Y1 - 2019

N2 - The human oral microbiome harbours a diverse and dynamic collection of microorganisms and its full impact on our health and wellbeing is only beginning to be understood. It is only recently that fossilised dental plaque (calculus) from osteological remains was found to be an excellent repository for the preservation of ancient biomolecules. These can offer a unique snapshot of the oral microbes of the past. However, limitations regarding data analysis and validation of metagenomic and metaproteomic datasets from archaeological microbes soon became apparent. More specifically, fragmented DNA and proteins, a characteristic of ancient biomolecules, are challenging to utilize in traditional data analysis pipelines. The difficulty of making direct conclusions of microbial composition and dynamics through time is further complicated where, as is often the case, studies are based on few samples from diverse geographic origins and time points. Taking into consideration these drawbacks, this thesis set out to examine new methods to explore metagenomic and metaproteomic datasets from archaeological dental plaque. After a brief Introduction to the field, Chapter 1 explores the options for increasing protein identifications from calculus utilising a metagenomic-guided approach. Chapter 2 comprises the main study of this thesis, whereby shotgun metagenomic and metaproteomic data from a collection of dental plaque samples originating from three neighbouring cemeteries from Trondheim, Norway, spanning almost a millennium are analysed in order to investigate whether it is possible to detect temporal shifts through time within the oral microbiota. In addition, this chapter explores new pipelines for optimising data analysis of ancient microbial samples by utilising current metagenomic pipelines for the recovery of novel or low abundance genomes. Chapters 3 and 4 arecase studies utilising dental calculus in order to reveal disease and lifestyle of the past. We found calculus to be a reservoir of dietary information, as well as non-oral pathogens such as Mycobacterium leprae. Taken together, these studies exemplify how dental calculus can harbour a unique collection of biological and archaeological significant information that warrant its inclusion in future studies.

AB - The human oral microbiome harbours a diverse and dynamic collection of microorganisms and its full impact on our health and wellbeing is only beginning to be understood. It is only recently that fossilised dental plaque (calculus) from osteological remains was found to be an excellent repository for the preservation of ancient biomolecules. These can offer a unique snapshot of the oral microbes of the past. However, limitations regarding data analysis and validation of metagenomic and metaproteomic datasets from archaeological microbes soon became apparent. More specifically, fragmented DNA and proteins, a characteristic of ancient biomolecules, are challenging to utilize in traditional data analysis pipelines. The difficulty of making direct conclusions of microbial composition and dynamics through time is further complicated where, as is often the case, studies are based on few samples from diverse geographic origins and time points. Taking into consideration these drawbacks, this thesis set out to examine new methods to explore metagenomic and metaproteomic datasets from archaeological dental plaque. After a brief Introduction to the field, Chapter 1 explores the options for increasing protein identifications from calculus utilising a metagenomic-guided approach. Chapter 2 comprises the main study of this thesis, whereby shotgun metagenomic and metaproteomic data from a collection of dental plaque samples originating from three neighbouring cemeteries from Trondheim, Norway, spanning almost a millennium are analysed in order to investigate whether it is possible to detect temporal shifts through time within the oral microbiota. In addition, this chapter explores new pipelines for optimising data analysis of ancient microbial samples by utilising current metagenomic pipelines for the recovery of novel or low abundance genomes. Chapters 3 and 4 arecase studies utilising dental calculus in order to reveal disease and lifestyle of the past. We found calculus to be a reservoir of dietary information, as well as non-oral pathogens such as Mycobacterium leprae. Taken together, these studies exemplify how dental calculus can harbour a unique collection of biological and archaeological significant information that warrant its inclusion in future studies.

UR - https://soeg.kb.dk/permalink/45KBDK_KGL/1pioq0f/alma99122029830605763

M3 - Ph.D. thesis

BT - Prospects of Meta-Omic Applications on Archaeological Microbiomes

PB - Natural History Museum of Denmark, Faculty of Science, University of Copenhagen

ER -