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

• Main Authors: Krithika Arumugam, Caner Bağcı, Irina Bessarab, Sina Beier, Benjamin Buchfink, Anna Górska, Guanglei Qiu, Daniel H. Huson, Rohan B. H. Williams
• Format: Article
• Language: English
• Published: BMC 2019-04-01
• Series: Microbiome
• Subjects: Microbiome; Long-read sequencing; Microbial genomics; Sequence assembly; Frame-shifts; Algorithms
• Online Access: http://link.springer.com/article/10.1186/s40168-019-0665-y

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.