Karlsson Lindsjö, Oskar
(2016).
Metagenomic characterisation of the gastrointestinal virome of neonatal pigs.
Diss. (sammanfattning/summary)
Uppsala :
Sveriges lantbruksuniv.,
Acta Universitatis Agriculturae Sueciae, 1652-6880
; 2016:84
ISBN 978-91-576-8670-1
eISBN 978-91-576-8671-8
[Doctoral thesis]
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6MB |
Abstract
Microorganisms that colonise the gastrointestinal tract are responsible for a large portion of the genetic diversity of the body. These microorganisms are of bacterial, archaeal and viral origin. The living space of these microorganisms, the microbiome, holds numerous interactions both between each other and the host. The viral part of the microbiome, the virome, consists of a multitude of virus species. These viruses infect and modulate cells from all three domains of life. Even though viruses have been acknowledged for their abilities to induce disease in its host, knowledge about the total diversity of viruses within the virome, and the role it plays in health and disease, is so far scarce. It is thought that the virome co-evolved with the host and that its establishment in mammals occurs early in life.
The virome can be studied by the use of viral metagenomics, the study of all viral genetic material within a sample. Viral metagenomics was used in this thesis to generate datasets for comparative metagenomics. These datasets were then used for disease investigation and to compare similarities in the viromes of two mammalian species, pigs and humans.
This thesis establishes a methodological framework for studying the virome in mammals, by use of viral metagenomics. A methodology for amplifying the metagenome prior to sequencing was assessed and a software for bioinformatics analysis of viral metagenomes was developed. With the methodologies developed herein, the eukaryotic virome of neonatal piglets suffering from diarrhoea was investigated. Several known enteric viruses were detected using viral metagenomics on healthy and diarrhoeic neonatal piglets. However, no virus was present exclusively within sick or healthy piglets and no virologial cause could be established for the neonatal diarrhoea. Comparative viral metagenomics was also used to establish if similarities existed between neonates of porcine and human origin, as well as between adults and neonates. Similarities were detected between adults of both species, who seems to be sharing a considerable part of their virome. There was also a notable difference between neonatal viromes and adult viromes, further supporting established theories about diversification over time of the virome.
Authors/Creators: | Karlsson Lindsjö, Oskar | ||||||||||
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Title: | Metagenomic characterisation of the gastrointestinal virome of neonatal pigs | ||||||||||
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Series Name/Journal: | Acta Universitatis Agriculturae Sueciae | ||||||||||
Year of publishing : | 2016 | ||||||||||
Depositing date: | 1 September 2016 | ||||||||||
Number: | 2016:84 | ||||||||||
Number of Pages: | 83 | ||||||||||
Papers/manuscripts: |
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Place of Publication: | Uppsala | ||||||||||
Publisher: | Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences | ||||||||||
ISBN for printed version: | 978-91-576-8670-1 | ||||||||||
ISBN for electronic version: | 978-91-576-8671-8 | ||||||||||
ISSN: | 1652-6880 | ||||||||||
Language: | English | ||||||||||
Additional Information: | Financial support was obtained from The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, Formas (221-2012-586) awarded to Professor Mikael Berg. - The author would like to express special thanks to the EU FP7 Project reference: 612583: "Developing an European American NGS Network” (DEANN). - The author would like to thank the EU COST Action BM1006 Next Generation Sequencing Data Analysis Network SeqAhead for financial support to participate on workshops, training and discussions. - This work was partially supported by the EU FP7 AllBio project [KBBE.2011.3.6-02]. - Funding was also generously provided by HELGE AX:SON JOHNSONS foundation, used for analysis in paper II, III and manuscript IV. - The authors would like to acknowledge support of the National Genomics Infrastructure (NGI) / Uppsala Genome Center and UPPMAX for providing assistance in massive parallel sequencing and computational infrastructure. Work performed at NGI / Uppsala Genome Center has been funded by RFI/VR and Science for Life Laboratory, Sweden. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | ||||||||||
Publication Type: | Doctoral thesis | ||||||||||
Full Text Status: | Public | ||||||||||
Agris subject categories.: | L Animal production > L10 Animal genetics and breeding L Animal production > L50 Animal physiology and biochemistry L Animal production > L73 Animal diseases | ||||||||||
Subjects: | (A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109) (A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203) (A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Pathobiology | ||||||||||
Agrovoc terms: | swine, piglets, newborn animals, genomics, bioinformatics, diarrhoea, digestive tract microflora, viruses, mammals, mankind | ||||||||||
Keywords: | Metagenomics, Pig, Bioinformatics, Neonatal, Virome, Microbiome, Neonatal diarrhoea, Comparative metagenomics | ||||||||||
URN:NBN: | urn:nbn:se:slu:epsilon-e-3639 | ||||||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-3639 | ||||||||||
ID Code: | 13549 | ||||||||||
Faculty: | VH - Faculty of Veterinary Medicine and Animal Science | ||||||||||
Department: | (VH) > Dept. of Biomedical Sciences and Veterinary Public Health | ||||||||||
External funders: | EU FP7 and FORMAS and Helge Ax:sson Johnsson Foundation | ||||||||||
Deposited By: | Msc Oskar E. Karlsson Lindsjö | ||||||||||
Deposited On: | 05 Sep 2016 08:59 | ||||||||||
Metadata Last Modified: | 10 Sep 2020 13:41 | ||||||||||
Project info: | |||||||||||
Name: | Prevention of and fight against crime | ||||||||||
Acronym: | ANI BIO THREAT | ||||||||||
ID: | HOME/2009/ISEC/AG/191 | ||||||||||
Programme: | DG Home Affairs |
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