Reference : Integrated time-resolved multi-omics for understanding microbial niche ecology

	Document type :	Scientific congresses, symposiums and conference proceedings : Poster
	Discipline(s) :	Life sciences : Biotechnology Life sciences : Environmental sciences & ecology Life sciences : Microbiology
	Focus Areas :	Systems Biomedicine
	To cite this reference:	http://hdl.handle.net/10993/38046

Title :	Integrated time-resolved multi-omics for understanding microbial niche ecology
Language :	English
Author, co-author :	Herold, Malte [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Narayanasamy, Shaman [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; Megeno Sarl, Luxembourg]
	Martinez Arbas, Susana [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Muller, Emilie [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; Université de Strasbourg > Equipe Adaptations et Interactions Microbiennes]
	Kleine-Borgmann, Anna Luise [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
	Lebrun, Laura [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Roume, Hugo [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; French National Institute for Agricultural Research > MetaGenoPolis]
	Sheik, Abdul [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Bessarab, Irina [Singapore Centre for Environmental Life Sciences]
	Williams, Rohan [Singapore Centre for Environmental Life Sciences]
	Gillece, John [The Translational Genomics Research Institute]
	Schupp, Jim [The Translational Genomics Research Institute]
	Keim, Paul [The Translational Genomics Research Institute]
	Jäger, Christian [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Hoopmann, Michael [Institute for Systems Biology - ISB]
	Li, Sujun [University of Indiana > School of Informatics and Computing]
	Tang, Haixu [University of Indiana > School of Informatics and Computing]
	Heintz, Anna [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; German Centre for Integrative Biodiversity Research (iDiv)]
	May, Patrick [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Laczny, Cedric Christian [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Wilmes, Paul [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Publication date :	Aug-2018
Peer reviewed :	No
Audience :	International
Event name :	17th International Symposium on Microbial Ecology
Event date :	from 12-08-2018 to 17-08-2018
Event place (city) :	Leipzig
Event country :	Germany
Abstract :	[en] Microbial communities are strongly shaped by the niche breadths of their constituent populations. However, a detailed understanding of microbial niche ecology is typically lacking. Integrated multi-omic analyses of host- or environment-derived samples offer the prospect of resolving fundamental and realised niches in situ. In turn, this is considered a prerequisite for niche engineering in order to drive an individual population or a community towards a specific phenotype, e.g., improvement of a biotechnological process. Here, we sampled floating islets on the surface of an activated sludge tank in a time-series spanning 51 time-points over 14 months. Multi-omics datasets (metagenomics, metatranscriptomics, metaproteomics, and (meta-)metabolomics) were generated for all time-points. Leveraging nucleotide sequencing data, we analyzed the community structure and reconstructed genomes for specific populations of interest. Moreover, based on their metabolic potential, three major groups emerged, serving as proxies for their respective fundamental niches . Time-resolved linkage of the proteomic and transcriptomic data to the reconstructed genomes revealed a fine-grained picture of niche realization. In particular, environmental factors (temperature, metabolites, oxygen) were significantly associated with gene expression of individual populations. Furthermore, we subjected the community to controlled oxygen conditions (stable or dynamic) in a bioreactor experiment and measured the transcriptomic response. Our results suggest short-term adaptations of populations of interest with respect to lipid metabolism, among other pathways. In conclusion, our work demonstrates how longitudinal multi-omic datasets can be integrated in order to further our understanding of microbial niche ecology within a biotechnological process with potential applications beyond waste water treatment.
Research centres :	Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group)
Funders :	Fonds National de la Recherche - FnR
Target :	Researchers
Permalink :	http://hdl.handle.net/10993/38046
Framework Programme / European Project :	FP7 ; 321567 - ERASYSAPP - ERASysAPP - Systems Biology Applications
FnR project :	FnR ; FNR8888488 > Paul Wilmes > SysMetEx > Systems Biology of Acidophile Biofilms for Efficient Metal Extraction > 01/03/2015 > 31/07/2018 > 2014

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