RT Journal Article
SR Electronic
T1 De novo assembly of microbial genomes from human gut metagenomes using barcoded short read sequences
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 125211
DO 10.1101/125211
A1 Eli L. Moss
A1 Alex Bishara
A1 Ekaterina Tkachenko
A1 Joyce B. Kang
A1 Tessa M. Andermann
A1 Christina Wood
A1 Christine Handy
A1 Hanlee Ji
A1 Serafim Batzoglou
A1 Ami S. Bhatt
YR 2017
UL http://biorxiv.org/content/early/2017/04/07/125211.abstract
AB Shotgun short-read sequencing methods facilitate study of the genomic content and strain-level architecture of complex microbial communities. However, existing methodologies do not capture structural differences between closely related co-occurring strains such as those arising from horizontal gene transfer and insertion sequence mobilization. Recent techniques that partition large DNA molecules, then barcode short fragments derived from them, produce short-read sequences containing long-range information. Here, we present a novel application of these short-read barcoding techniques to metagenomic samples, as well as Athena, an assembler that uses these barcodes to produce improved metagenomic assemblies. We apply our approach to longitudinal samples from the gut microbiome of a patient with a hematological malignancy. This patient underwent an intensive regimen of multiple antibiotics, chemotherapeutics and immunosuppressants, resulting in profound disruption of the microbial gut community and eventual domination by Bacteroides caccae. We significantly improve draft completeness over conventional techniques, uncover strains of B. caccae differing in the positions of transposon integration, and find the abundance of individual strains to fluctuate widely over the course of treatment. In addition, we perform RNA sequencing to investigate relative transcription of genes in B. caccae, and find overexpression of antibiotic resistance genes in our de novo assembled draft genome of B. caccae coinciding with both antibiotic administration and the appearance of proximal transposons harboring a putative bacterial promoter region. Our approach produces overall improvements in contiguity of metagenomic assembly and enables assembly of whole classes of genomic elements inaccessible to existing short-read approaches.