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Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

Brumfield, Kyle D ; Huq, Anwar ; Colwell, Rita R ; Olds, James L ; Leddy, Menu B Gyarmati, Peter

PloS one, 2020-02, Vol.15 (2), p.e0228899 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
Autor: Brumfield, Kyle D ; Huq, Anwar ; Colwell, Rita R ; Olds, James L ; Leddy, Menu B
Gyarmati, Peter
Assuntos: Access to information ; Annotations ; Aquatic ecosystems ; Archaea ; Archaea - genetics ; Bacteria - genetics ; Biogeochemistry ; Biology and Life Sciences ; Biosphere ; Computer and Information Sciences ; Data retrieval ; Data storage ; Databases, Genetic - standards ; Datasets ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA, Bacterial - genetics ; Ecological effects ; Ecological monitoring ; Environmental changes ; Gene sequencing ; Genes ; Genetic engineering ; Genomes ; High-Throughput Nucleotide Sequencing - methods ; High-Throughput Nucleotide Sequencing - standards ; Identification ; Interoperability ; Laboratories ; Metabolism ; Metabolites ; Metadata ; Metagenome ; Metagenomics ; Metagenomics - methods ; Methods ; Microorganisms ; Neon ; Observatories ; Open access ; Open data ; Pathogens ; Protocol (computers) ; Quality standards ; Research and Analysis Methods ; RNA, Ribosomal, 16S - genetics ; Sequence analysis ; Sequence Analysis, DNA - methods ; Sequence Analysis, DNA - standards ; Sequence Analysis, RNA - methods ; Sequence Analysis, RNA - standards ; Soil ; Soil investigations ; Soil microorganisms ; Soil surfaces ; Soils ; Standardization ; Subsystems ; Taxonomy ; Terrestrial ecosystems ; Terrestrial environments ; Viruses ; Whole Genome Sequencing - methods ; Whole Genome Sequencing - standards
É parte de: PloS one, 2020-02, Vol.15 (2), p.e0228899
Notas: Competing Interests: The authors have read the journal's policy and the authors of this manuscript have the following competing interests: RRC, distinguished university professor at University of Maryland, College Park, MD, and PhD advisor for KDB is the founder of CosmosID Inc., Rockville, MD. However, RRC did not receive any support from CosmosID Inc. for this study and manuscript. There are no patents, products in development or marketed products associated with this research to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
Descrição: Microorganisms are ubiquitous in the biosphere, playing a crucial role in both biogeochemistry of the planet and human health. However, identifying these microorganisms and defining their function are challenging. Widely used approaches in comparative metagenomics, 16S amplicon sequencing and whole genome shotgun sequencing (WGS), have provided access to DNA sequencing analysis to identify microorganisms and evaluate diversity and abundance in various environments. However, advances in parallel high-throughput DNA sequencing in the past decade have introduced major hurdles, namely standardization of methods, data storage, reproducible interoperability of results, and data sharing. The National Ecological Observatory Network (NEON), established by the National Science Foundation, enables all researchers to address queries on a regional to continental scale around a variety of environmental challenges and provide high-quality, integrated, and standardized data from field sites across the U.S. As the amount of metagenomic data continues to grow, standardized procedures that allow results across projects to be assessed and compared is becoming increasingly important in the field of metagenomics. We demonstrate the feasibility of using publicly available NEON soil metagenomic sequencing datasets in combination with open access Metagenomics Rapid Annotation using the Subsystem Technology (MG-RAST) server to illustrate advantages of WGS compared to 16S amplicon sequencing. Four WGS and four 16S amplicon sequence datasets, from surface soil samples prepared by NEON investigators, were selected for comparison, using standardized protocols collected at the same locations in Colorado between April-July 2014. The dominant bacterial phyla detected across samples agreed between sequencing methodologies. However, WGS yielded greater microbial resolution, increased accuracy, and allowed identification of more genera of bacteria, archaea, viruses, and eukaryota, and putative functional genes that would have gone undetected using 16S amplicon sequencing. NEON open data will be useful for future studies characterizing and quantifying complex ecological processes associated with changing aquatic and terrestrial ecosystems.
Editor: United States: Public Library of Science
Idioma: Inglês

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Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

Brumfield, Kyle D ; Huq, Anwar ; Colwell, Rita R ; Olds, James L ; Leddy, Menu B Gyarmati, Peter

United States: Public Library of Science

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