Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms
Abstract 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 Collaborativ...
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BMC
2019-09-01
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Series: | Microbiome |
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Online Access: | http://link.springer.com/article/10.1186/s40168-019-0743-1 |
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doaj-797e6ee94c85445a9c187cd89d19f574 |
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Article |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Philipp Rausch Malte Rühlemann Britt M. Hermes Shauni Doms Tal Dagan Katja Dierking Hanna Domin Sebastian Fraune Jakob von Frieling Ute Hentschel Femke-Anouska Heinsen Marc Höppner Martin T. Jahn Cornelia Jaspers Kohar Annie B. Kissoyan Daniela Langfeldt Ateequr Rehman Thorsten B. H. Reusch Thomas Roeder Ruth A. Schmitz Hinrich Schulenburg Ryszard Soluch Felix Sommer Eva Stukenbrock Nancy Weiland-Bräuer Philip Rosenstiel Andre Franke Thomas Bosch John F. Baines |
spellingShingle |
Philipp Rausch Malte Rühlemann Britt M. Hermes Shauni Doms Tal Dagan Katja Dierking Hanna Domin Sebastian Fraune Jakob von Frieling Ute Hentschel Femke-Anouska Heinsen Marc Höppner Martin T. Jahn Cornelia Jaspers Kohar Annie B. Kissoyan Daniela Langfeldt Ateequr Rehman Thorsten B. H. Reusch Thomas Roeder Ruth A. Schmitz Hinrich Schulenburg Ryszard Soluch Felix Sommer Eva Stukenbrock Nancy Weiland-Bräuer Philip Rosenstiel Andre Franke Thomas Bosch John F. Baines Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms Microbiome Animal microbiome Evolution Phylosymbiosis Holobiont Metaorganism |
author_facet |
Philipp Rausch Malte Rühlemann Britt M. Hermes Shauni Doms Tal Dagan Katja Dierking Hanna Domin Sebastian Fraune Jakob von Frieling Ute Hentschel Femke-Anouska Heinsen Marc Höppner Martin T. Jahn Cornelia Jaspers Kohar Annie B. Kissoyan Daniela Langfeldt Ateequr Rehman Thorsten B. H. Reusch Thomas Roeder Ruth A. Schmitz Hinrich Schulenburg Ryszard Soluch Felix Sommer Eva Stukenbrock Nancy Weiland-Bräuer Philip Rosenstiel Andre Franke Thomas Bosch John F. Baines |
author_sort |
Philipp Rausch |
title |
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms |
title_short |
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms |
title_full |
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms |
title_fullStr |
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms |
title_full_unstemmed |
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms |
title_sort |
comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms |
publisher |
BMC |
series |
Microbiome |
issn |
2049-2618 |
publishDate |
2019-09-01 |
description |
Abstract 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. |
topic |
Animal microbiome Evolution Phylosymbiosis Holobiont Metaorganism |
url |
http://link.springer.com/article/10.1186/s40168-019-0743-1 |
work_keys_str_mv |
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doaj-797e6ee94c85445a9c187cd89d19f5742020-11-25T03:33:33ZengBMCMicrobiome2049-26182019-09-017111910.1186/s40168-019-0743-1Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganismsPhilipp Rausch0Malte Rühlemann1Britt M. Hermes2Shauni Doms3Tal Dagan4Katja Dierking5Hanna Domin6Sebastian Fraune7Jakob von Frieling8Ute Hentschel9Femke-Anouska Heinsen10Marc Höppner11Martin T. Jahn12Cornelia Jaspers13Kohar Annie B. Kissoyan14Daniela Langfeldt15Ateequr Rehman16Thorsten B. H. Reusch17Thomas Roeder18Ruth A. Schmitz19Hinrich Schulenburg20Ryszard Soluch21Felix Sommer22Eva Stukenbrock23Nancy Weiland-Bräuer24Philip Rosenstiel25Andre Franke26Thomas Bosch27John F. Baines28Evolutionary Genomics, Max Planck Institute for Evolutionary BiologyInstitute of Clinical Molecular Biology, Kiel UniversityEvolutionary Genomics, Max Planck Institute for Evolutionary BiologyEvolutionary Genomics, Max Planck Institute for Evolutionary BiologyInstitute of General Microbiology, Kiel UniversityDepartment of Evolutionary Ecology and Genetics, Zoological Institute, Kiel UniversityZoological Institute, Kiel UniversityZoological Institute, Kiel UniversityMolecular Physiology, Zoological Institute, Kiel UniversityMarine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean ResearchInstitute of Clinical Molecular Biology, Kiel UniversityInstitute of Clinical Molecular Biology, Kiel UniversityMarine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean ResearchKiel UniversityDepartment of Evolutionary Ecology and Genetics, Zoological Institute, Kiel UniversityInstitute of General Microbiology, Kiel UniversityInstitute of Clinical Molecular Biology, Kiel UniversityKiel UniversityMolecular Physiology, Zoological Institute, Kiel UniversityInstitute of General Microbiology, Kiel UniversityDepartment of Evolutionary Ecology and Genetics, Zoological Institute, Kiel UniversityInstitute of General Microbiology, Kiel UniversityInstitute of Clinical Molecular Biology, Kiel UniversityEnvironmental Genomics, Max Planck Institute for Evolutionary BiologyInstitute of General Microbiology, Kiel UniversityInstitute of Clinical Molecular Biology, Kiel UniversityInstitute of Clinical Molecular Biology, Kiel UniversityZoological Institute, Kiel UniversityEvolutionary Genomics, Max Planck Institute for Evolutionary BiologyAbstract 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.http://link.springer.com/article/10.1186/s40168-019-0743-1Animal microbiomeEvolutionPhylosymbiosisHolobiontMetaorganism |