|KOLMOGOROV, MIKHAIL - University Of California, San Diego|
|TSENG, ELIZABETH - Pacific Biosciences Inc|
|PORTIK, DANIEL - Pacific Biosciences Inc|
|KOROBEYNIKOV, ANTON - St Petersburg State University|
|TOLSTOGANOV, IVAN - St Petersburg State University|
|URITSKIY, GHERMAN - Phase Genomics, Inc|
|LIACHKO, IVAN - Phase Genomics, Inc|
|SULLIVAN, SHAWN - Phase Genomics, Inc|
|ZOREA, ALVAH - Ben Gurion University Of Negev|
|ANDREU, VICTORIA PASCAL - Wageningen University|
|MEDEMA, MARNIX - Wageningen University|
|MIZRAHI, ITZIK - Ben Gurion University Of Negev|
|PEVZNER, PAVEL - University Of California, San Diego|
|Smith, Timothy - Tim|
Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 5/5/2021
Publication Date: 5/5/2021
Citation: Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., Zorea, A., Andreu, V., Panke-Buisse, K., Medema, M., Mizrahi, I., Pevzner, P., Smith, T.P. 2021. Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing. bioRxiv. https://doi.org/10.1101/2021.05.04.442591.
Interpretive Summary: Metagenomics is a field of study that looks at the genomes of microscopic organisms. It is very difficult to capture individual microorganisms in the environment, so we often must identify them through remnants of their DNA. Until now, this has been very complicated due to limits in DNA sequencing technologies. We have developed a new method using state of the art sequencing technologies that makes this process incredibly easy. Using our method, it is possible for clinicians, microbiologists and other researchers to start analyzing this data immediately and without need for expert curation.
Technical Abstract: 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.