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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #384575

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing

item Bickhart, Derek
item KOLMOGOROV, MIKHAIL - University Of California, San Diego
item TSENG, ELIZABETH - Pacific Biosciences Inc
item PORTIK, DANIEL - Pacific Biosciences Inc
item KOROBEYNIKOV, ANTON - St Petersburg State University
item TOLSTOGANOV, IVAN - St Petersburg State University
item URITSKIY, GHERMAN - Phase Genomics, Inc
item LIACHKO, IVAN - Phase Genomics, Inc
item SULLIVAN, SHAWN - Phase Genomics, Inc
item Shin, Sung
item ZOREA, ALVAH - Ben Gurion University Of Negev
item ANDREU, VICTORIA PASCAL - Wageningen University
item Panke-Buisse, Kevin
item MEDEMA, MARNIX - Wageningen University
item MIZRAHI, ITZIK - Ben Gurion University Of Negev
item PEVZNER, PAVEL - University Of California, San Diego
item 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.

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.