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Tytuł:
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Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.
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Autorzy:
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Herold M; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.; Epidemiology and Microbial Genomics, Laboratoire National de Santé, 1 rue Louis Rech, 3555, Dudelange, Luxembourg.
Martínez Arbas S; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Narayanasamy S; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.; Megeno S.A., 6A Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
Sheik AR; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Kleine-Borgmann LAK; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Lebrun LA; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Kunath BJ; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Roume H; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.; MetaGenoPolis, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université Paris-Saclay, Domaine de Vilvert, Bâtiment 325, 78350, Jouy-en-Josas, France.
Bessarab I; Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore, 637551, Singapore.
Williams RBH; Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore, 637551, Singapore.
Gillece JD; The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA.
Schupp JM; The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA.
Keim PS; The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA.
Jäger C; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Hoopmann MR; Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA.
Moritz RL; Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA.
Ye Y; School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA.
Li S; School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA.
Tang H; School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA.
Heintz-Buschart A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany.; Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Str. 4, 06120, Halle, Germany.
May P; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Muller EEL; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.; Equipe Adaptations et Interactions Microbiennes, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France.
Laczny CC; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.
Wilmes P; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg. .; Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg. .
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Źródło:
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Nature communications [Nat Commun] 2020 Oct 19; Vol. 11 (1), pp. 5281. Date of Electronic Publication: 2020 Oct 19.
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Typ publikacji:
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Journal Article; Research Support, Non-U.S. Gov't
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Język:
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English
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Imprint Name(s):
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Original Publication: [London] : Nature Pub. Group
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MeSH Terms:
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Microbiota*
Bacteria/*genetics
Bacteria/*metabolism
Wastewater/*microbiology
Bacteria/classification ; Bacteria/isolation & purification ; Bioreactors/microbiology ; Ecosystem ; Metabolomics ; Metagenome ; Metagenomics ; Proteomics ; Time Factors
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Grant Information:
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R01 AI108888 United States AI NIAID NIH HHS; R01 AI143254 United States AI NIAID NIH HHS
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Substance Nomenclature:
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0 (Waste Water)
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Entry Date(s):
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Date Created: 20201020 Date Completed: 20201110 Latest Revision: 20221207
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Update Code:
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20240105
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PubMed Central ID:
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PMC7572474
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DOI:
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10.1038/s41467-020-19006-2
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PMID:
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33077707
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The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.
