Reference : Comparative integrated omics: identification of key functionalities in microbial comm...
Scientific journals : Article
Life sciences : Environmental sciences & ecology
Life sciences : Genetics & genetic processes
Life sciences : Microbiology
http://hdl.handle.net/10993/21557
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
English
Roume, Hugo [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Buschart, Anna mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Muller, Emilie mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Satagopam, Venkata mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Laczny, Cédric mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Narayanasamy, Shaman mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Lebrun, Laura mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Hoopmann, Michael [> >]
Schupp, James [> >]
Gillece, John [> >]
Hicks, Nathan [> >]
Engelthaler, David [> >]
Sauter, Thomas mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
Keim, Paul [> >]
Moritz, Robert [> >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
2015
Biofilms and Microbiomes
1
15007
Yes (verified by ORBilu)
International
2055-5008
[en] BACKGROUND: Mixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships is essential for ultimately driving these systems towards desired outcomes, e.g., the enrichment in organisms capable of accumulating valuable resources during BWWT.
METHODS: A comparative integrated omic analysis including metagenomics, metatranscriptomics and metaproteomics was carried out to elucidate functional differences between seasonally distinct oleaginous mixed microbial communities (OMMCs) sampled from an anoxic BWWT tank. A computational framework for the reconstruction of community-wide metabolic networks from multi-omic data was developed. These provide an overview of the functional capabilities by incorporating gene copy, transcript and protein abundances. To identify functional genes, which have a disproportionately important role in community function, we define a high relative gene expression and a high betweenness centrality relative to node degree as gene-centric and network topological features, respectively.
RESULTS: Genes exhibiting high expression relative to gene copy abundance include genes involved in glycerolipid metabolism, particularly triacylglycerol lipase, encoded by known lipid accumulating populations, e.g., Candidatus Microthrix parvicella. Genes with a high relative gene expression and topologically important positions in the network include genes involved in nitrogen metabolism and fatty acid biosynthesis, encoded by Nitrosomonas spp. and Rhodococcus spp. Such genes may be regarded as ‘keystone genes’ as they are likely to be encoded by keystone species.
CONCLUSION: The linking of key functionalities to community members through integrated omics opens up exciting possibilities for devising prediction and control strategies for microbial communities in the future.
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) ; Institute for Systems Biology (ISB) ; The Translational Genomic Research Institute-North (Tgen) ; University of Luxembourg: High Performance Computing - ULHPC ; University of Luxembourg: Life Science Research Unit
Fonds National de la Recherche - FnR ; National Science Foundation ; National Institute of General Medical Sciences
http://hdl.handle.net/10993/21557
10.1038/npjbiofilms.2015.7

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