ArticleProceedings of the National Academy of Sciences of the United States of America2013
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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96 citing papers in PubMed.
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- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Revealing COBiodesign research · 2022Article
- Characteristics, Biodiversity, and Cultivation Strategy of Low Nucleic Acid Content Bacteria.Frontiers in microbiology · 2022Review
- Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases.Frontiers in immunology · 2022Review
- Challenges in exploring and manipulating the human skin microbiome.Microbiome · 2021Review
- A human respiratory tract-associated bacterium with an extremely small genome.Communications biology · 2021Article
- Single-Cell Sequencing Applications in the Inner Ear.Frontiers in cell and developmental biology · 2021Review
- Exploring Changes in the Microbiota ofFrontiers in microbiology · 2021Article
- Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods.Frontiers in microbiology · 2021Review
- Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis.Biochemical Society transactions · 2020Review
- Chlamydiae - What's New?Journal of veterinary research · 2020Article
- Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'.Integrative biology : quantitative biosciences from nano to macro · 2020Article
- Microbial single-cell omics: the crux of the matter.Applied microbiology and biotechnology · 2020Review
- Insights into the dynamics between viruses and their hosts in a hot spring microbial mat.The ISME journal · 2020Article
- Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts.Cell reports · 2020Article
36 more citing papers are in PubMed but not listed here.
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20 authors.
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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.
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