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Culture-free generation of microbial genomes from human and marine microbiomes

Authors :
Mikhail Kolmogorov
Ziming Weng
Serafim Batzoglou
Alma E. Parada
Arend Sidow
Alex Bishara
Eli L. Moss
Anne E. Dekas
Ami S. Bhatt
Publication Year :
2018
Publisher :
Cold Spring Harbor Laboratory, 2018.

Abstract

Our understanding of natural microbial communities is shaped by the careful investigation of a relatively small number of isolated and cultured organisms, and by analysis of genomic sequences obtained by culture-free metagenomic sequencing approaches. Metagenomic shotgun sequencing has facilitated partial reconstruction of strain-level community structure and functional repertoire. Unfortunately, it remains difficult to cost-effectively produce high quality genome drafts for individual microbes without isolation and culture. Recent molecular techniques that partition long DNA fragments and then barcode short fragments derived from them produce “read clouds”, which are short-read sequences containing long-range information. Here, we present a novel application of a read cloud technique to microbiome samples, as well as Athena, a de novo assembler that uses these barcodes to produce improved metagenomic assemblies. We apply our approach to sequence human stool samples from two healthy individuals, and compare it to existing short read and synthetic long read metagenomic sequencing approaches. We find that read cloud metagenomic sequencing and Athena assembly produce the most complete individual genome drafts. These genome drafts are also highly contiguous (>200kb N50

Details

Language :
English
Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....6c0559f60a3a1ca785c16f3cbe7c0240
Full Text :
https://doi.org/10.1101/263939