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PMID: 25091868 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Review

Recent advances in genomic DNA sequencing of microbial species from single cells.

Nature reviews. Genetics ·Vol. 15 ·No. 9 ·2014-09-00 ·Pages 577-84

Lasken RS, McLean JS

Abstract

The vast majority of microbial species remain uncultivated and, until recently, about half of all known bacterial phyla were identified only from their 16S ribosomal RNA gene sequence. With the advent of single-cell sequencing, genomes of uncultivated species are rapidly filling in unsequenced branches of the microbial phylogenetic tree. The wealth of new insights gained from these previously inaccessible groups is providing a deeper understanding of their basic biology, taxonomy and evolution, as well as their diverse roles in environmental ecosystems and human health.

MeSH Terms
Bacteria/classification,genetics DNA, Bacterial/chemistry,genetics DNA, Ribosomal/chemistry,genetics Evolution, Molecular Genetic Variation Genome, Bacterial/genetics Genomics Microbiota Phylogeny RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA/methods
Chemicals
DNA, Bacterial DNA, Ribosomal RNA, Ribosomal, 16S
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Lasken Roger S
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, USA.
McLean Jeffrey S
1] J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, USA. [2] School of Dentistry, Department of Periodontics, University of Washington, Seattle, Washington 98195, USA.
References (44)
44 references, click to expand
  1. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.
    Science. 2012 Sep 28;337(6102):1661-5 PMID: 23019650
  2. Genomic DNA amplification from a single bacterium.
    Appl Environ Microbiol. 2005 Jun;71(6):3342-7 PMID: 15933038
  3. Insights into the phylogeny and coding potential of microbial dark matter.
    Nature. 2013 Jul 25;499(7459):431-7 PMID: 23851394
  4. Unexplored reservoirs of pathogenic bacteria: protozoa and biofilms.
    Trends Microbiol. 1999 Jan;7(1):46-50 PMID: 10068997
  5. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
    Bioinformatics. 2012 Jun 1;28(11):1420-8 PMID: 22495754
  6. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
    J Comput Biol. 2012 May;19(5):455-77 PMID: 22506599
  7. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.
    Nat Commun. 2013;4:1854 PMID: 23673639
  8. Comprehensive human genome amplification using multiple displacement amplification.
    Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6 PMID: 11959976
  9. Sequencing genomes from single cells by polymerase cloning.
    Nat Biotechnol. 2006 Jun;24(6):680-6 PMID: 16732271
  10. Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics.
    Nat Protoc. 2014 May;9(5):1038-48 PMID: 24722403
  11. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla.
    mBio. 2013 Oct 22;4(5):e00708-13 PMID: 24149512
  12. Singled out for sequencing.
    Nat Methods. 2014 Jan;11(1):13-7 PMID: 24524130
  13. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
    Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9 PMID: 23754396
  14. Frequent loss of Shiga-like toxin genes in clinical isolates of Escherichia coli upon subcultivation.
    Infect Immun. 1992 Aug;60(8):3464-7 PMID: 1639518
  15. The "most wanted" taxa from the human microbiome for whole genome sequencing.
    PLoS One. 2012;7(7):e41294 PMID: 22848458
  16. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
    Genome Res. 2013 May;23(5):878-88 PMID: 23493677
  17. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
    Genome Res. 2013 May;23(5):867-77 PMID: 23564253
  18. Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).
    Appl Environ Microbiol. 2011 Nov;77(21):7804-14 PMID: 21908640
  19. An environmental bacterial taxon with a large and distinct metabolic repertoire.
    Nature. 2014 Feb 6;506(7486):58-62 PMID: 24476823
  20. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments.
    PLoS Biol. 2007 Sep;5(9):e230 PMID: 17760503
  21. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.
    ISME J. 2011 Jan;5(1):61-70 PMID: 20613790
  22. Formation of a novel phagosome by the Legionnaires' disease bacterium (Legionella pneumophila) in human monocytes.
    J Exp Med. 1983 Oct 1;158(4):1319-31 PMID: 6619736
  23. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.
    Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5540-5 PMID: 23509275
  24. Nanoliter reactors improve multiple displacement amplification of genomes from single cells.
    PLoS Genet. 2007 Sep;3(9):1702-8 PMID: 17892324
  25. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.
    Nat Biotechnol. 2011 Sep 18;29(10):915-21 PMID: 21926975
  26. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells.
    Nat Biotechnol. 2013 Dec;31(12):1126-32 PMID: 24213699
  27. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.
    Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11889-94 PMID: 17620602
  28. Targeted access to the genomes of low-abundance organisms in complex microbial communities.
    Appl Environ Microbiol. 2007 May;73(10):3205-14 PMID: 17369337
  29. Biofilms: the environmental playground of Legionella pneumophila.
    Environ Microbiol. 2010 Mar;12(3):557-66 PMID: 19678829
  30. Mosaic copy number variation in human neurons.
    Science. 2013 Nov 1;342(6158):632-7 PMID: 24179226
  31. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges.
    ISME J. 2013 Dec;7(12):2287-300 PMID: 23842652
  32. Unbiased whole-genome amplification directly from clinical samples.
    Genome Res. 2003 May;13(5):954-64 PMID: 12695328
  33. Genomic sequencing of uncultured microorganisms from single cells.
    Nat Rev Microbiol. 2012 Sep;10(9):631-40 PMID: 22890147
  34. Mechanism of chimera formation during the Multiple Displacement Amplification reaction.
    BMC Biotechnol. 2007 Apr 12;7:19 PMID: 17430586
  35. Marine biofilms on submerged surfaces are a reservoir for Escherichia coli and Vibrio cholerae.
    Biofouling. 2010 Jan;26(1):39-46 PMID: 20390555
  36. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.
    ISME J. 2012 Sep;6(9):1715-27 PMID: 22717885
  37. Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa.
    J Bacteriol. 2009 Jan;191(1):210-9 PMID: 18952788
  38. Single-cell sequencing-based technologies will revolutionize whole-organism science.
    Nat Rev Genet. 2013 Sep;14(9):618-30 PMID: 23897237
  39. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.
    J Comput Biol. 2013 Oct;20(10):714-37 PMID: 24093227
  40. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification.
    Genome Res. 2001 Jun;11(6):1095-9 PMID: 11381035
  41. Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.
    Genome Res. 2013 May;23(5):855-66 PMID: 23525359
  42. Transmission of Helicobacter pylori and the role of water and biofilms.
    J Water Health. 2009 Sep;7(3):469-77 PMID: 19491497
  43. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
    Nat Biotechnol. 2013 Jun;31(6):533-8 PMID: 23707974
  44. Artificial polyploidy improves bacterial single cell genome recovery.
    PLoS One. 2012;7(5):e37387 PMID: 22666352
Article Info
Journal
Nature reviews. Genetics
Abbr.
Nat Rev Genet
ISSN
1471-0064
DOI
10.1038/nrg3785
Published
2014-09-00
Epub
2014-00-05
Pages
577-84
Language
English
Region
England
NLM ID
100962779
PMCID
PMC4454502
Subset
IM
Grants
NIGMS NIH HHS · R01 GM095373 · United States
NHGRI NIH HHS · 2R01 HG003647 · United States
NIAID NIH HHS · HHSN272200900007C · United States
NIGMS NIH HHS · 1R01GM095373 · United States
External Links
PubMed source DOI: 10.1038/nrg3785 PMC Full Text View journal details
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