RT Journal Article
SR Electronic
T1 Culture-free generation of microbial genomes from human and marine microbiomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 263939
DO 10.1101/263939
A1 Alex Bishara
A1 Eli L. Moss
A1 Mikhail Kolmogorov
A1 Alma Parada
A1 Ziming Weng
A1 Arend Sidow
A1 Anne E. Dekas
A1 Serafim Batzoglou
A1 Ami S. Bhatt
YR 2018
UL http://biorxiv.org/content/early/2018/02/11/263939.abstract
AB 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, <10 contigs), even for bacteria that have relatively low (20x) raw short read sequence coverage. We also apply this approach to a significantly more complex marine sediment sample and obtain 23 genome drafts with valuable 16S ribosomal RNA taxonomic marker sequences, nine of which are complete genome drafts. Read cloud metagenomic sequencing allows culture-free generation of high quality microbial genome drafts using only a single shotgun experiment.