Generating Lineage-resolved, Complete Metagenome-assembled Genomes from Complex Microbial Communities

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2022 Jan 4

PMID 34980911

Citations 79

Authors

Derek M Bickhart

Mikhail Kolmogorov

Elizabeth Tseng

Daniel M Portik

Anton Korobeynikov

Ivan Tolstoganov

Gherman Uritskiy

Ivan Liachko

Shawn T Sullivan

Sung Bong Shin

Alvah Zorea

Victoria Pascal Andreu

Kevin Panke-Buisse

Marnix H Medema

Itzhak Mizrahi

Pavel A Pevzner

Timothy P L Smith

Affiliations

Soon will be listed here.

Abstract

Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.

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