uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Metagenomic analysis of a distal gut sample from the Tyrolean Iceman
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
Show others and affiliations
(English)Manuscript (preprint) (Other academic)
National Category
URN: urn:nbn:se:uu:diva-206206OAI: oai:DiVA.org:uu-206206DiVA: diva2:645062
Available from: 2013-09-03 Created: 2013-08-29 Last updated: 2014-01-23
In thesis
1. Microbial Metagenomics: A Tale of the Dead and the Living
Open this publication in new window or tab >>Microbial Metagenomics: A Tale of the Dead and the Living
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

It is a microbial world we live in: microbes outnumber other organisms by several orders of magnitude, and they have great importance for the environment. However, environmental microbes are notoriously difficult to grow in the laboratory, and using culture independent techniques is necessary to expand our view. In this thesis, I apply metagenomics and single-cell genomics to environmental samples from ancient human remains and lakes.

First, I used metagenomics to learn about bacteria from a Neanderthal’s bone and the gut of Ötzi, a frozen natural mummy. Both were exploratory studies where the main question was what kind of bacteria are present. I found out that Streptomyces dominated this particular Neanderthal fossil, and the DNA lacked the damage that is often seen in ancient samples. Ötzi's gut sample was dominated by Clostridia and fungi belonging to Basidiomycota.

Second, ten single-cell amplified genomes of freshwater Alphaproteobacterium LD12 and three metagenomes from Swedish lakes were sequenced. Comparative metagenomics allowed hypothesizing about which functions are important for microbe proliferation in freshwater, pointing to osmoregulation and transport proteins and, possibly, to different strategies of metabolizing sugars. I also focused on SAR11 sister-groups in oceans and lakes. Phylogenies and sequence evolutionary distance estimates indicated the existence of microclusters within LD12, showing variation in abundance between lakes. The most striking difference was the relative amount of recombination compared to mutation, the estimated r/m ratio. SAR11 marine and their freshwater cousins are found at the opposite extremes of the r/m range, lowest and highest, respectively. The genetic background or sequence diversity did not explain the observed dramatic difference, so it is possibly connected to environmental adaptation or population dynamics.

In addition, I have spent a substantial amount of effort benchmarking available metagenomic methods, for example fragment recruitment of metagenomes to reference genomes.

In conclusion, my exploratory metagenomic studies have shed some light on the bacteria present in ancient human remains; comparative metagenomics has suggested the importance of substrate preference on functional differences between lakes and oceans; finally, single-cell genomes have allowed some insight into molecular evolutionary processes taking place in the freshwater LD12 bacterium. 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2013. 108 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1067
single-cell genomics, single cell, fossil metagenome, freshwater metagenome, LD12
National Category
Microbiology Bioinformatics and Systems Biology
urn:nbn:se:uu:diva-206702 (URN)978-91-554-8742-3 (ISBN)
Public defence
2013-10-18, B41, Husargatan 3, Uppsala, 13:15 (English)
Available from: 2013-09-25 Created: 2013-09-03 Last updated: 2014-01-23

Open Access in DiVA

No full text

By organisation
Molecular Evolution

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 280 hits
ReferencesLink to record
Permanent link

Direct link