Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
Show others and affiliations
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Aquatic microorganism are key drivers of global biogeochemical cycles and form the basis of aquatic food webs. However, there is still much left to be learned about these organisms and their interaction within specific environments, such as the Baltic Sea. Crucial information for such an understanding can be found within the genome sequences of organisms within the microbial community.

In this study, the previous set of Baltic Sea clusters, constructed by Hugert et al., is greatly expanded using a large set of metagenomic samples, spanning the environmental gradients of the Baltic Sea. In total, 124 samples were individually assembled and binned to obtain 2,032 Metagenome Assembled Genomes (MAGs), clustered into 353 prokaryotic and 14 eukaryotic species- level clusters. The prokaryotic genomes were widely distributed over the prokaryotic tree of life, representing 20 different phyla, while the eukaryotic genomes were mostly limited to the division of Chlorophyta. The large number of reconstructed genomes allowed us to identify key factors determining the quality of the genome reconstructions.

The Baltic Sea is heavily influenced of human activities of which we might not see the full implications. The genomes reported within this study will greatly aid further studies in our strive for an understanding of the Baltic Sea microbial ecosystem.

National Category
Bioinformatics and Systems Biology Microbiology
Identifiers
URN: urn:nbn:se:kth:diva-227963OAI: oai:DiVA.org:kth-227963DiVA, id: diva2:1205873
Funder
BONUS - Science for a better future of the Baltic Sea region, Art 185Swedish Research Council, 2011-5689
Note

QC 20180516

Available from: 2018-05-15 Created: 2018-05-15 Last updated: 2018-05-16Bibliographically approved
In thesis
1. Bioinformatic Methods in Metagenomics
Open this publication in new window or tab >>Bioinformatic Methods in Metagenomics
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Microbial organisms are a vital part of our global ecosystem. Yet, our knowledge of them is still lacking. Direct sequencing of microbial communities, i.e. metagenomics, have enabled detailed studies of these microscopic organisms by inspection of their DNA sequences without the need to culture them. Furthermore, the development of modern high- throughput sequencing technologies have made this approach more powerful and cost-effective. Taken together, this has shifted the field of microbiology from previously being centered around microscopy and culturing studies, to largely consist of computational analyses of DNA sequences. One such computational analysis which is the main focus of this thesis, aims at reconstruction of the complete DNA sequence of an organism, i.e. its genome, directly from short metagenomic sequences.

This thesis consists of an introduction to the subject followed by five papers. Paper I describes a large metagenomic data resource spanning the Baltic Sea microbial communities. This dataset is complemented with a web-interface allowing researchers to easily extract and visualize detailed information. Paper II introduces a bioinformatic method which is able to reconstruct genomes from metagenomic data. This method, which is termed CONCOCT, is applied on Baltic Sea metagenomics data in Paper III and Paper V. This enabled the reconstruction of a large number of genomes. Analysis of these genomes in Paper III led to the proposal of, and evidence for, a global brackish microbiome. Paper IV presents a comparison between genomes reconstructed from metagenomes with single-cell sequenced genomes. This further validated the technique presented in Paper II as it was found to produce larger and more complete genomes than single-cell sequencing.

Abstract [sv]

Mikrobiella organismer är en vital del av vårt globala ekosystem. Trots detta är vår kunskap om dessa fortfarande begränsad. Sekvensering direkt applicerad på mikrobiella samhällen, så kallad metagenomik, har möjliggjort detaljerade studier av dessa mikroskopiska organismer genom deras DNA-sekvenser. Utvecklingen av modern sekvenseringsteknik har vidare gjort denna strategi både mer kraftfull och mer kostnadseffektiv. Sammantaget har detta förändrat mikrobiologi-fältet, från att ha varit centrerat kring mikroskopi, till att till stor del bero på dataintensiva analyser av DNA-sekvenser. En sådan analys, som är det huvudsakliga fokuset för den här avhandlingen, syftar till att återskapa den kompletta DNA-sekvensen för en organism, dvs. dess genom, direkt från korta metagenom-sekvenser.

Den här avhandlingen består av en introduktion till ämnet, följt av fem artiklar. Artikel I beskriver en omfattande databas för metagenomik över Östersjöns mikrobiella samhällen. Till denna databas hör också en webbsida som ger forskare möjlighet att lätt extrahera och visualisera detaljerad information. Artikel II introducerar en bioinformatisk metod som kan återskapa genom från metagenom. Denna metod, som kallas CONCOCT, används för data från Östersjön i artikel III och Artikel V. Detta möjliggjorde återskapandet av ett stort antal genom. Analys av dessa genom presenterad i Artikel III ledde till hypotesen om, och belägg för, ett globalt brackvattenmikrobiom. Artikel IV innehåller en jämförelse mellan genom återskapade från metagenom och individuellt sekvenserade genom. Detta validerade metoden som presenterades i Artikel II ytterligare då denna metod visade sig producera större och mer kompletta genom än sekvensering av individuella celler.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2018. p. 51
Series
TRITA-CBH-FOU ; 2018:25
Keywords
Bioinformatics, Metagenomics, Microbiome, Binning, Baltic Sea, Bioinformatik, Metagenomik, Mikrobiom, Binning, Östersjön
National Category
Bioinformatics and Systems Biology Bioinformatics (Computational Biology) Microbiology
Identifiers
urn:nbn:se:kth:diva-227965 (URN)978-91-7729-799-4 (ISBN)
Public defence
2018-06-08, Air and Fire, Science for Life Laboratory, Tomtebodavägen 23, Solna, 10:00 (English)
Opponent
Supervisors
Funder
BONUS - Science for a better future of the Baltic Sea region, Art 185
Note

QC 20180516

Available from: 2018-05-16 Created: 2018-05-15 Last updated: 2018-05-16Bibliographically approved

Open Access in DiVA

No full text in DiVA

Authority records BETA

Alneberg, JohannesAndersson, Anders F.

Search in DiVA

By author/editor
Alneberg, JohannesAndersson, Anders F.
By organisation
Science for Life Laboratory, SciLifeLabGene Technology
Bioinformatics and Systems BiologyMicrobiology

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 854 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf