Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

By Yann Marcy, C. Ouverney, E. Bik, T. Lösekann, Natalia N. Ivanova, Héctor García Martín, Ernest Szeto, D. Platt, Philip Hugenholtz, David A. Relman and 1 more. Proceedings of the National Academy of Sciences of the United States of America, 2007

627 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0525f469c8da6b53ca06b358dc06b5b412ac524e

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In Biomedical Engineering

Sergey I. Nikolenko

In Ecology

In Molecular Biology

Citations in the corpus

The core gut microbiome, energy balance and obesity (2009, methodology): “Additionally, methods designed to enrich microbial clades or lineages through selective culture and/or cell sorting, as well as methods that isolate single cells (Marcy et al. 2007), are needed to explore the potential niches (professions) of uncultured groups identified in the gut microbiota as a r”
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata (2007, neutral): “The development of novel methods that bypass the major restriction of culturing the organism for sequencing (23,24) will hopefully alleviate this bias.”
Single-cell RNA-seq: advances and future challenges (2014, positive): “…single-cell isolation to the biochemical steps of cDNA synthesis and detection, an example of which is shown in Figure 1C. Nano-liter microfluidic chambers have been used to isolate non-culturable cells from small-volume microbial community samples for individual genome amplification (64,67).”
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes (2013, neutral): “GC content [7].”
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes (2013, methodology): “Based on 16S data, OP1 was previously assessed as most closely related to Thermatoga; TM7 was closest to Chloroflexi (specifically Chloroflexus auranticus 43 ), and OP11 was very deep-branching 44 .”
A Bioinformatician's Guide to Metagenomics (2008, background): “ca/ Univ of British Columbia (23) Blast Marine viral communities from ocean environments SDSU (8) Blast Olavius algarvensis (gutless worm) microbiome from Mediterranean sea Max Planck Institute Joint Genome Institute (142) mORFind Oral TM7 microbial communities of Human healthy adults Joint Genome I”
Microbial Co-occurrence Relationships in the Human Microbiome (2012, background): “Phyla such as the TM7 and Synergistetes have only recently been characterized at the genetic level in the oral cavity [51,52], and little is yet known about their roles in this microbial ecosystem.”
Ecology and exploration of the rare biosphere (2015, methodology): “Supplementing HTS technolo gies with existing and developing methods — such as cell sorting 130 , 131 , genome recovery 132 , multiple displacement amplification 133 , stableisotope probing 134 , functional metagenomics 135 , targeted amplification of rare taxa 136 , cultivation 111 ,…”
The chicken gastrointestinal microbiome. (2014, background): “Single-cell microbiology has not yet achieved widespread adoption in the veterinary sciences, but already has demonstrated the potential for much more sophisticated queries than previously possible of the mechanisms underlying the ecology of complex microbial communities (Huang et al., 2007; Marcy e”