Comparison of three clustering approaches for detecting novel environmental microbial diversity
Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of...
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| Format: | Article |
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PeerJ Inc.
2016-02-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/1692.pdf |
| _version_ | 1797419801477382144 |
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| author | Dominik Forster Micah Dunthorn Thorsten Stoeck Frédéric Mahé |
| author_facet | Dominik Forster Micah Dunthorn Thorsten Stoeck Frédéric Mahé |
| author_sort | Dominik Forster |
| collection | DOAJ |
| description | Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR2) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR2. Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity. |
| first_indexed | 2024-03-09T06:53:33Z |
| format | Article |
| id | doaj.art-cf3edeff9de946b09cec1a755ba91047 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:53:33Z |
| publishDate | 2016-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-cf3edeff9de946b09cec1a755ba910472023-12-03T10:16:13ZengPeerJ Inc.PeerJ2167-83592016-02-014e169210.7717/peerj.1692Comparison of three clustering approaches for detecting novel environmental microbial diversityDominik Forster0Micah Dunthorn1Thorsten Stoeck2Frédéric Mahé3Department of Ecology, Technische Universität Kaiserslautern, Kaiserslautern, GermanyDepartment of Ecology, Technische Universität Kaiserslautern, Kaiserslautern, GermanyDepartment of Ecology, Technische Universität Kaiserslautern, Kaiserslautern, GermanyDepartment of Ecology, Technische Universität Kaiserslautern, Kaiserslautern, GermanyDiscovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR2) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR2. Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity.https://peerj.com/articles/1692.pdfEnvironmental diversityBarcodingMolecular operational taxonomic unit |
| spellingShingle | Dominik Forster Micah Dunthorn Thorsten Stoeck Frédéric Mahé Comparison of three clustering approaches for detecting novel environmental microbial diversity PeerJ Environmental diversity Barcoding Molecular operational taxonomic unit |
| title | Comparison of three clustering approaches for detecting novel environmental microbial diversity |
| title_full | Comparison of three clustering approaches for detecting novel environmental microbial diversity |
| title_fullStr | Comparison of three clustering approaches for detecting novel environmental microbial diversity |
| title_full_unstemmed | Comparison of three clustering approaches for detecting novel environmental microbial diversity |
| title_short | Comparison of three clustering approaches for detecting novel environmental microbial diversity |
| title_sort | comparison of three clustering approaches for detecting novel environmental microbial diversity |
| topic | Environmental diversity Barcoding Molecular operational taxonomic unit |
| url | https://peerj.com/articles/1692.pdf |
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