title: Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
abstract: 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.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA 92121, USA. jmclean@jcvi.org
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: McLean
authors.forename: Mary-Jane
authors.initials: MJ
authors.lastname: Lombardo
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Badger
authors.forename: Anna
authors.initials: A
authors.lastname: Edlund
authors.forename: Mark
authors.initials: M
authors.lastname: Novotny
authors.forename: Joyclyn
authors.initials: J
authors.lastname: Yee-Greenbaum
authors.forename: Nikolay
authors.initials: N
authors.lastname: Vyahhi
authors.forename: Adam P
authors.initials: AP
authors.lastname: Hall
authors.forename: Youngik
authors.initials: Y
authors.lastname: Yang
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Dupont
authors.forename: Michael G
authors.initials: MG
authors.lastname: Ziegler
authors.forename: Hamidreza
authors.initials: H
authors.lastname: Chitsaz
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.forename: Shibu
authors.initials: S
authors.lastname: Yooseph
authors.forename: Glenn
authors.initials: G
authors.lastname: Tesler
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
authors.forename: Robert M
authors.initials: RM
authors.lastname: Friedman
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Nealson
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
authors.forename: Roger S
authors.initials: RS
authors.lastname: Lasken
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D018441:Biofilms; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D006761:Hospitals; D006801:Humans; D053858:Metabolic Networks and Pathways; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D008969:Molecular Sequence Data; D010802:Phylogeny; D012498:Sanitary Engineering; D014871:Water Microbiology; D014881:Water Supply
chemical_list: D004269:DNA, Bacterial
keywords: MDA; genome assembly; metagenomics; single-cell genomics; symbiotic bacteria