High-resolution phylogenetic microbial community profiling
| Autor: | Philip Hugenholtz, Hans-Peter Klenk, Asaf Levy, Tanja Woyke, Steven J. Hallam, Susannah G. Tringe, Brett Bowman, Esther Singer, Brian Bushnell, Esther A. Gies, Alex Copeland, Robert M. Bowers, Jan Fang Cheng, Devin Coleman-Derr |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
16S Technology 030106 microbiology Computational biology Biology Microbiology 03 medical and health sciences symbols.namesake Microbial ecology Phylogenetics RNA Ribosomal 16S Genetics Taxonomic rank Ecology Evolution Behavior and Systematics Phylogeny Sanger sequencing Ribosomal Phylogenetic tree Bacteria British Columbia Phylum Ecology Community structure Genetic Variation High-Throughput Nucleotide Sequencing DNA Sequence Analysis DNA Biological Sciences Archaea Lakes Microbial population biology symbols RNA Original Article Sequence Analysis Environmental Sciences |
| Zdroj: | The ISME Journal The ISME journal, vol 10, iss 8 Singer, E; Bushnell, B; Coleman-Derr, D; Bowman, B; Bowers, RM; Levy, A; et al.(2016). High-resolution phylogenetic microbial community profiling. ISME Journal, 10(8), 2020-2032. doi: 10.1038/ismej.2015.249. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/22p8307r |
| ISSN: | 1751-7370 1751-7362 |
| DOI: | 10.1038/ismej.2015.249. |
| Popis: | © 2016 International Society for Microbial Ecology All rights reserved. Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential. |
| Databáze: | OpenAIRE |
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