Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by c...

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Published in:	Genome research 2015-04, Vol.25 (4), p.534-543
Main Authors:	Sharon, Itai, Kertesz, Michael, Hug, Laura A, Pushkarev, Dmitry, Blauwkamp, Timothy A, Castelle, Cindy J, Amirebrahimi, Mojgan, Thomas, Brian C, Burstein, David, Tringe, Susannah G, Williams, Kenneth H, Banfield, Jillian F
Format:	Article
Language:	eng
Subjects:	Bacterial Proteins - genetics Base Sequence BASIC BIOLOGICAL SCIENCES Biodiversity Chloroflexi - genetics Chloroflexi - isolation & purification Deltaproteobacteria - genetics Deltaproteobacteria - isolation & purification DNA, Bacterial - genetics Genome, Bacterial Geologic Sediments - analysis Geologic Sediments - microbiology Glucose - metabolism Hydrolases - genetics Metagenomics - methods Microbial Consortia - genetics Sequence Analysis, DNA
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Summary:	Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were
ISSN:	1088-9051 1549-5469