Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 110, Issue 26, Pages E2390-E2399Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1219809110
Keywords
genome assembly; metagenomics; single-cell genomics; MDA; symbiotic bacteria
Categories
Funding
- Alfred P. Sloan Foundation [Sloan Foundation-2007-10-19]
- National Institutes of Health (NIH) [3P41RR024851-02S1]
- NIH [2R01 HG003647, UL1TR000100]
- Government of the Russian Federation [11.G34.31.0018]
- NIH National Institute of General Medical Sciences [1R01GM095373]
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1262565] Funding Source: National Science Foundation
Ask authors/readers for more resources
The dark matter of life describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing cells using a highly automated single-cell genomics platform. We developed an approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow-sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a mini-metagenome. A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes. A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated to represent 90% of its genome. High nucleotide identity between a total of three TM6 genome drafts generated from pools that were independently captured, amplified, and assembled provided strong confirmation of a correct genomic sequence. TM6 is likely a Gram-negative organism and possibly a symbiont of an unknown host (nonfree living) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most amino acids and vitamins. Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available