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

• Main Authors: Arumugam, Krithika, Bağcı, Caner, Bessarab, Irina, Beier, Sina, Buchfink, Benjamin, Górska, Anna, Qiu, Guanglei, Huson, Daniel H., Williams, Rohan B. H.
• Other Authors: Singapore Centre for Environmental Life Sciences and Engineering
• Format: Article
• Language: English
• Published: 2019
• Subjects: Microbiome; DRNTU::Engineering::Environmental engineering; Long-read Sequencing
• Online Access: https://hdl.handle.net/10356/106705; http://hdl.handle.net/10220/49039
• Institution: Nanyang Technological University

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.