Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

Bhavya Papudeshi, J. Matthew Haggerty, Michael Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G.Z. Silva, Fabiano Thompson, Robert A. Edwards, Elizabeth A. Dinsdale

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Abstract

Background: Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to taxa/function and facilitates discovery of novel organisms. Genome reconstruction incorporates sequence assembly and sorting of assembled sequences into bins, characteristic of a genome. However, the microbial community composition, including taxonomic and phylogenetic diversity may influence genome reconstruction. We determine the optimal reconstruction method for four microbiome projects that had variable sequencing platforms (IonTorrent and Illumina), diversity (high or low), and environment (coral reefs and kelp forests), using a set of parameters to select for optimal assembly and binning tools. Methods: We tested the effects of the assembly and binning processes on population genome reconstruction using 105 marine metagenomes from 4 projects. Reconstructed genomes were obtained from each project using 3 assemblers (IDBA, MetaVelvet, and SPAdes) and 2 binning tools (GroopM and MetaBat). We assessed the efficiency of assemblers using statistics that including contig continuity and contig chimerism and the effectiveness of binning tools using genome completeness and taxonomic identification. Results: We concluded that SPAdes, assembled more contigs (143,718 ± 124 contigs) of longer length (N50 = 1632 ± 108 bp), and incorporated the most sequences (sequences-assembled = 19.65%). The microbial richness and evenness were maintained across the assembly, suggesting low contig chimeras. SPAdes assembly was responsive to the biological and technological variations within the project, compared with other assemblers. Among binning tools, we conclude that MetaBat produced bins with less variation in GC content (average standard deviation: 1.49), low species richness (4.91 ± 0.66), and higher genome completeness (40.92 ± 1.75) across all projects. MetaBat extracted 115 bins from the 4 projects of which 66 bins were identified as reconstructed metagenome-assembled genomes with sequences belonging to a specific genus. We identified 13 novel genomes, some of which were 100% complete, but show low similarity to genomes within databases. Conclusions: In conclusion, we present a set of biologically relevant parameters for evaluation to select for optimal assembly and binning tools. For the tools we tested, SPAdes assembler and MetaBat binning tools reconstructed quality metagenome-assembled genomes for the four projects. We also conclude that metagenomes from microbial communities that have high coverage of phylogenetically distinct, and low taxonomic diversity results in highest quality metagenome-assembled genomes.

Original languageEnglish
Article number915
Number of pages13
JournalBMC Genomics
Volume18
Issue number1
DOIs
Publication statusPublished - 28 Nov 2017
Externally publishedYes

Bibliographical note

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Keywords

  • Metagenome-assembled Genomes
  • Binning Tools
  • SPAdes Assembler
  • Chimeric Contigs
  • MetaVelvet

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    Papudeshi, B., Haggerty, J. M., Doane, M., Morris, M. M., Walsh, K., Beattie, D. T., Pande, D., Zaeri, P., Silva, G. G. Z., Thompson, F., Edwards, R. A., & Dinsdale, E. A. (2017). Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes. BMC Genomics, 18(1), [915]. https://doi.org/10.1186/s12864-017-4294-1