PT  - JOURNAL ARTICLE
AU  - Derek M. Bickhart
AU  - Mikhail Kolmogorov
AU  - Elizabeth Tseng
AU  - Daniel M. Portik
AU  - Anton Korobeynikov
AU  - Ivan Tolstoganov
AU  - Gherman Uritskiy
AU  - Ivan Liachko
AU  - Shawn T. Sullivan
AU  - Sung Bong Shin
AU  - Alvah Zorea
AU  - Victòria Pascal Andreu
AU  - Kevin Panke-Buisse
AU  - Marnix H. Medema
AU  - Itzik Mizrahi
AU  - Pavel A. Pevzner
AU  - Timothy P.L. Smith
TI  - Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing
AID  - 10.1101/2021.05.04.442591
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.05.04.442591
4099  - http://biorxiv.org/content/early/2021/05/04/2021.05.04.442591.short
4100  - http://biorxiv.org/content/early/2021/05/04/2021.05.04.442591.full
AB  - Microbial communities in many environments include distinct lineages of closely related organisms which have proved challenging to separate in metagenomic assembly, preventing generation of complete metagenome-assembled genomes (MAGs). The advent of long and accurate HiFi reads presents a possible means to address this challenge by generating complete MAGs for nearly all sufficiently abundant bacterial genomes in a microbial community. We present a metagenomic HiFi assembly of a complex microbial community from sheep fecal material that resulted in 428 high-quality MAGs from a single sample, the highest resolution achieved with metagenomic deconvolution to date. We applied a computational approach to separate distinct haplotype lineages and identified haplotypes of hundreds of variants across hundreds of kilobases of genomic sequence. Analysis of these haplotypes revealed 220 lineage-resolved complete MAGs, including 44 in single circular contigs, and demonstrated improvement in overall assembly compared to error-prone long reads. We report the characterization of multiple, closely-related microbes within a sample with potential to improve precision in assigning mobile genetic elements to host genomes within complex microbial communities.Competing Interest StatementET and DMP are employees of Pacific Biosciences. GU, IL and STS are employees of Phase Genomics. All other authors have no competing interests.