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Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.
Rausch, Philipp; Rühlemann, Malte; Hermes, Britt M; Doms, Shauni; Dagan, Tal; Dierking, Katja; Domin, Hanna; Fraune, Sebastian; von Frieling, Jakob; Hentschel, Ute; Heinsen, Femke-Anouska; Höppner, Marc; Jahn, Martin T; Jaspers, Cornelia; Kissoyan, Kohar Annie B; Langfeldt, Daniela; Rehman, Ateequr; Reusch, Thorsten B H; Roeder, Thomas; Schmitz, Ruth A; Schulenburg, Hinrich; Soluch, Ryszard; Sommer, Felix; Stukenbrock, Eva; Weiland-Bräuer, Nancy; Rosenstiel, Philip; Franke, Andre; Bosch, Thomas; Baines, John F.
Afiliación
  • Rausch P; Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany. philipp.rausch@bio.ku.dk.
  • Rühlemann M; Institute for Experimental Medicine, Kiel University, Kiel, Germany. philipp.rausch@bio.ku.dk.
  • Hermes BM; Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen Ø, Denmark. philipp.rausch@bio.ku.dk.
  • Doms S; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
  • Dagan T; Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
  • Dierking K; Institute for Experimental Medicine, Kiel University, Kiel, Germany.
  • Domin H; Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
  • Fraune S; Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
  • von Frieling J; Institute for Experimental Medicine, Kiel University, Kiel, Germany.
  • Hentschel U; Institute of General Microbiology, Kiel University, Kiel, Germany.
  • Heinsen FA; Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany.
  • Höppner M; Zoological Institute, Kiel University, Kiel, Germany.
  • Jahn MT; Zoological Institute, Kiel University, Kiel, Germany.
  • Jaspers C; Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany.
  • Kissoyan KAB; Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
  • Langfeldt D; Kiel University, Kiel, Germany.
  • Rehman A; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
  • Reusch TBH; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
  • Roeder T; Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
  • Schmitz RA; Kiel University, Kiel, Germany.
  • Schulenburg H; Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
  • Soluch R; Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany.
  • Sommer F; Institute of General Microbiology, Kiel University, Kiel, Germany.
  • Stukenbrock E; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
  • Weiland-Bräuer N; Kiel University, Kiel, Germany.
  • Rosenstiel P; Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
  • Franke A; Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany.
  • Bosch T; Institute of General Microbiology, Kiel University, Kiel, Germany.
  • Baines JF; Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany.
Microbiome ; 7(1): 133, 2019 09 14.
Article en En | MEDLINE | ID: mdl-31521200
BACKGROUND: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. METHODS: In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. CONCLUSION: While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ARN Ribosómico 16S / Metagenoma / Secuenciación de Nucleótidos de Alto Rendimiento / Microbiota Límite: Animals / Humans Idioma: En Revista: Microbiome Año: 2019 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ARN Ribosómico 16S / Metagenoma / Secuenciación de Nucleótidos de Alto Rendimiento / Microbiota Límite: Animals / Humans Idioma: En Revista: Microbiome Año: 2019 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido