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Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data.

ABSTRACT: BACKGROUND:Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. RESULTS:We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. CONCLUSIONS:Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.

SUBMITTER: Arumugam K

PROVIDER: S-EPMC6469205 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data.

Arumugam Krithika K Bağcı Caner C Bessarab Irina I Beier Sina S Buchfink Benjamin B Górska Anna A Qiu Guanglei G Huson Daniel H DH Williams Rohan B H RBH

Microbiome 20190416 1

<h4>Background</h4>Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible.<h4>Results</h4>We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromoso ...[more]

PMID: 30992083

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