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Title: Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia

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 (est. >85% of gene complement) genome sequences for 17 of the 20 detected member species and revealed two Halomonas spp. and two Rhodobacteraceae sp. variants indistinguishable by amplicon analysis. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggest different mechanisms may result in 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 (9x – 2700x).
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Resource Type:
Journal Article
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Journal Name: Applied and Environmental Microbiology, 82(1):255-267
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
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Country of Publication:
United States
microdiversity; metagenomic sequencing; parallel consortia