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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 #384372

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: Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

item Bickhart, Derek
item KOLMOGOROV, MIKHAIL - University Of California
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 - University Of Wageningen
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: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2021
Publication Date: 1/3/2022
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. 2022. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature Biotechnology. 40:711-719.

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 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.