Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads

Authors: Bickhart, Derek; KOLMOGOROV, MIKHAIL - University Of California, Davis; MEDEMA, MARNIX - Wageningen University; KOROBEYNIKOV, ANTON - St Petersburg State University; MIZRAHI, ITZIK - Ben Gurion University Of Negev; PEVZNER, PAVEL - University Of California, Davis; Smith, Timothy - Tim

Submitted to: Cold Spring Harbor Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 8/1/2020
Publication Date: 10/23/2020
Citation: Bickhart, D.M., Kolmogorov, M., Medema, M.H., Korobeynikov, A., Mizrahi, I., Pevzner, P., Smith, T.P. 2020. Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads. Cold Spring Harbor Laboratory's Microbiome Conference. October 20-23, 2020. Virtual Meeting.

Interpretive Summary:

Technical Abstract: Metagenome assembly is complicated by the prevalence of repetitive genes and differences in abundance of members of the community. These obstacles often mean that resultant assemblies are highly fragmented and that microbial assembled genomes (MAG) must be binned, post-hoc, from hundreds of contigs. Our group has previously shown that longer DNA sequence reads can reduce this complexity and improve the continuity of assembled contigs; however, the higher error rate of these reads often prevents the assembly of single chromosome contigs for many MAGs in complex metagenomes. Using high-fidelity, circular consensus sequence (CCS) sequence reads that have an ~1% error rate and an N50 fragment size of 12.6 Kbp, we demonstrate a marked improvement in bacterial assembly continuity on a sheep fecal microbial community from an individual infected by nematodes from the Strongyloides genus. We assembled 134 contigs that had greater than 90% completeness and less than 5% contamination as estimated by CheckM, with 19 of these contigs being 100% complete and 0% contaminated. Binning with Hi-C linkage maps and sequence composition metrics resulted in 29 additional MAGs with similar completeness statistics, producing a total of 163 high quality MAGs from a single sequenced metagenome. Additionally, more than 821 Mbp of this assembly was present in contigs with lengths greater than 1 Mbp, representing an unprecedented level of continuity for a gastrointestinal metagenome assembly. We show that high fidelity, CCS reads assembled with metaFlye produce high quality MAGs in single contigs. Our methodology enables better bacterial strain resolution and improved gene annotation over other workflows and is recommended for metagenome assembly of complex communities in the future.