Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia

William C. Nelson, Yukari Maezato, Yu Wei Wu, Margaret F. Romine, Stephen R. Lindemann

研究成果: 雜誌貢獻文章

19 引文 (Scopus)

摘要

To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9 × to 2,700×) within the metagenomic data set.
原文英語
頁(從 - 到)255-267
頁數13
期刊Applied and Environmental Microbiology
82
發行號1
DOIs
出版狀態已發佈 - 2016
對外發佈Yes

指紋

Metagenomics
genome
Halomonas
Genome
Population
Rhodobacteraceae
genomics
complement
Rhizobiales
Microbial Genome
Microbial Interactions
interspecific variation
Sequence Analysis
microbial communities
microbial community
sequence analysis
Sensitivity and Specificity
species diversity
gene
Genes

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology

引用此文

Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia. / Nelson, William C.; Maezato, Yukari; Wu, Yu Wei; Romine, Margaret F.; Lindemann, Stephen R.

於: Applied and Environmental Microbiology, 卷 82, 編號 1, 2016, p. 255-267.

研究成果: 雜誌貢獻文章

Nelson, William C. ; Maezato, Yukari ; Wu, Yu Wei ; Romine, Margaret F. ; Lindemann, Stephen R. / Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia. 於: Applied and Environmental Microbiology. 2016 ; 卷 82, 編號 1. 頁 255-267.
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