Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

Genome Biology
Derek M BickhartTimothy P L Smith

Abstract

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

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Citations

Dec 27, 2019·Briefings in Functional Genomics·Zhichao Xu, Jesse R Dixon
Mar 20, 2020·Genome Research·Lin-Xing ChenJillian F Banfield
Jul 17, 2020·FEMS Microbiology Reviews·Christina C SaakRachel J Dutton
Sep 7, 2019·Genome Biology·Rob KnightElizabeth A Grice
Jun 12, 2020·Archives of Microbiology·Elakshi DekaboruahAnil Kumar Verma
Jul 19, 2020·The Journal of Antimicrobial Chemotherapy·Agnes P ChanDerrick E Fouts
Oct 7, 2020·Nature Methods·Mikhail KolmogorovPavel A Pevzner
May 26, 2020·Trends in Microbiology·Victoria R CarrDavid L Moyes
Feb 27, 2021·Nature Microbiology·Eric G SakowskiSarah P Preheim
Mar 26, 2021·Nature Reviews. Microbiology·Adrienne M S CorreaJoshua S Weitz
Apr 14, 2021·Nature Reviews. Microbiology·Ilana Lauren Brito
Jun 15, 2021·Current Opinion in Virology·Clément Coclet, Simon Roux
Jun 17, 2021·Bioinformatics·Ahmed A ZayedMatthew B Sullivan
Jul 25, 2021·Nature Communications·Riccardo VicedominiRayan Chikhi
Sep 2, 2021·Annual Review of Biomedical Data Science·Lee CallNikos C Kyrpides

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Methods Mentioned

BETA
Hi-C
proximity ligation

Software Mentioned

PacBio
Fragment Analyzer
ProxiMeta MASH
Proximeta
Metabat
mapper
CheckM
Metabat2
tool
BWA

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