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The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans

Johannes Zimmermann, Nancy Obeng, Wentao Yang, Barbara Pees, Carola Petersen, Silvio Washina, Kohar Annie Kissoyan, Jack Aidley, Marc P. Hoeppner, Boyke Bunk, Cathrin Sproer, Matthias Leippe, Katja Dierking, Christoph Kaleta, Hinrich Schulenburg
doi: https://doi.org/10.1101/554345
Johannes Zimmermann
Research Group Medical Systems Biology, Kiel University, Germany;
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  • For correspondence: j.zimmermann@iem.uni-kiel.de
Nancy Obeng
Research Group of Evolutionary Ecology and Genetics, Kiel University, Germany;
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  • For correspondence: nobeng@zoologie.uni-kiel.de
Wentao Yang
Research Group of Evolutionary Ecology and Genetics, Kiel University, Germany;
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  • For correspondence: wyang@zoologie.uni-kiel.de
Barbara Pees
Research Group of Comparative Immunobiology, Kiel University, Germany;
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  • For correspondence: bpees@zoologie.uni-kiel.de
Carola Petersen
Research Group of Comparative Immunobiology, Kiel University, Germany;
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  • For correspondence: cpetersen@zoologie.uni-kiel.de
Silvio Washina
Research Group Medical Systems Biology, Kiel University, Germany;
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  • For correspondence: s.waschina@iem.uni-kiel.de
Kohar Annie Kissoyan
Research Group of Evolutionary Ecology and Genetics, Kiel University, Germany;
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  • For correspondence: kkissoyan@zoologie.uni-kiel.de
Jack Aidley
Research Group of Evolutionary Ecology and Genetics, Kiel University, Germany;
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  • For correspondence: jaidley@zoologie.uni-kiel.de
Marc P. Hoeppner
Institute of Clinical Molecular Biology, Kiel University, Germany;
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  • For correspondence: m.hoeppner@ikmb.uni-kiel.de
Boyke Bunk
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany;
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  • For correspondence: boyke.bunk@dsmz.de
Cathrin Sproer
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany;
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  • For correspondence: ckc@dsmz.de
Matthias Leippe
Research Group of Comparative Immunobiology, Kiel University, Germany;
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  • For correspondence: mleippe@zoologie.uni-kiel.de
Katja Dierking
Research Group of Evolutionary Ecology and Genetics, Kiel University, Germany;
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  • For correspondence: kdierking@zoologie.uni-kiel.de
Christoph Kaleta
Research Group Medical Systems Biology, Kiel University, Germany;
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  • For correspondence: c.kaleta@iem.uni-kiel.de
Hinrich Schulenburg
University of Kiel
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  • For correspondence: hschulenburg@zoologie.uni-kiel.de
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Abstract

The microbiome is generally assumed to have a substantial influence on the biology of multicellular organisms. The exact functional contributions of the microbes are often unclear and cannot be inferred easily from 16S rRNA genotyping, which is commonly used for taxonomic characterization of the bacterial associates. In order to bridge this knowledge gap, we here analyzed the metabolic competences of the native microbiome of the model nematode Caenorhabditis elegans. We integrated whole genome sequences of 77 bacterial microbiome members with metabolic modelling and experimental characterization of bacterial physiology. We found that, as a community, the microbiome can synthesize all essential nutrients for C. elegans. Both metabolic models and experimental analyses further revealed that nutrient context can influence how bacteria interact within the microbiome. We identified key bacterial traits that are likely to influence the microbe's ability to colonize C. elegans (e.g., pyruvate fermentation to acetoin) and the resulting effects on nematode fitness (e.g., hydroxyproline degradation). Considering that the microbiome is usually neglected in the comprehensive research on this nematode, the resource presented here will help our understanding of C. elegans biology in a more natural context. Our integrative approach moreover provides a novel, general framework to dissect microbiome-mediated functions.

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Posted February 19, 2019.
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The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans
Johannes Zimmermann, Nancy Obeng, Wentao Yang, Barbara Pees, Carola Petersen, Silvio Washina, Kohar Annie Kissoyan, Jack Aidley, Marc P. Hoeppner, Boyke Bunk, Cathrin Sproer, Matthias Leippe, Katja Dierking, Christoph Kaleta, Hinrich Schulenburg
bioRxiv 554345; doi: https://doi.org/10.1101/554345
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The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans
Johannes Zimmermann, Nancy Obeng, Wentao Yang, Barbara Pees, Carola Petersen, Silvio Washina, Kohar Annie Kissoyan, Jack Aidley, Marc P. Hoeppner, Boyke Bunk, Cathrin Sproer, Matthias Leippe, Katja Dierking, Christoph Kaleta, Hinrich Schulenburg
bioRxiv 554345; doi: https://doi.org/10.1101/554345

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