Home LiteratureArticle Details
PMID: 20687950 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.

BMC genomics ·Vol. 11 ·2010-08-05 ·Pages 461

Stark M, Berger SA, Stamatakis A, von Mering C

Abstract

Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information. We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.

MeSH Terms
Algorithms DNA/analysis,classification,genetics Internet Likelihood Functions Phylogeny Sequence Analysis, DNA/methods Software Design
Chemicals
DNA
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Stark Manuel
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
Berger Simon A
Stamatakis Alexandros
von Mering Christian
References (68)
68 references, click to expand
  1. Molecular phylogenetics: state-of-the-art methods for looking into the past.
    Trends Genet. 2001 May;17(5):262-72 PMID: 11335036
  2. Signature genes as a phylogenomic tool.
    Mol Biol Evol. 2008 Aug;25(8):1659-67 PMID: 18492663
  3. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes.
    PLoS Biol. 2007 Mar;5(3):e82 PMID: 17355177
  4. Phylogenetic classification of short environmental DNA fragments.
    Nucleic Acids Res. 2008 Apr;36(7):2230-9 PMID: 18285365
  5. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.
    DNA Res. 2005;12(5):281-90 PMID: 16769690
  6. Prediction of effective genome size in metagenomic samples.
    Genome Biol. 2007;8(1):R10 PMID: 17224063
  7. Cultivating previously uncultured soil bacteria using a soil substrate membrane system.
    Nat Protoc. 2008;3(8):1261-9 PMID: 18714294
  8. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
    Syst Biol. 2007 Aug;56(4):564-77 PMID: 17654362
  9. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO.
    Science. 2003 Oct 10;302(5643):286-90 PMID: 14551435
  10. A rapid bootstrap algorithm for the RAxML Web servers.
    Syst Biol. 2008 Oct;57(5):758-71 PMID: 18853362
  11. Get the most out of your metagenome: computational analysis of environmental sequence data.
    Curr Opin Microbiol. 2007 Oct;10(5):490-8 PMID: 17936679
  12. Treephyler: fast taxonomic profiling of metagenomes.
    Bioinformatics. 2010 Apr 1;26(7):960-1 PMID: 20172941
  13. Functional marker genes for identification of sulfate-reducing prokaryotes.
    Methods Enzymol. 2005;397:469-89 PMID: 16260310
  14. Evolutionary trees from DNA sequences: a maximum likelihood approach.
    J Mol Evol. 1981;17(6):368-76 PMID: 7288891
  15. Metagenomics: DNA sequencing of environmental samples.
    Nat Rev Genet. 2005 Nov;6(11):805-14 PMID: 16304596
  16. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.
    BMC Bioinformatics. 2004 Oct 26;5:163 PMID: 15507136
  17. Central role of the cell in microbial ecology.
    Microbiol Mol Biol Rev. 2009 Dec;73(4):712-29 PMID: 19946138
  18. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D346-54 PMID: 19914934
  19. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities.
    Appl Environ Microbiol. 2000 May;66(5):2096-104 PMID: 10788387
  20. Bias in template-to-product ratios in multitemplate PCR.
    Appl Environ Microbiol. 1998 Oct;64(10):3724-30 PMID: 9758791
  21. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.
    Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16428-33 PMID: 19805315
  22. Cultivating the uncultured: limits, advances and future challenges.
    Extremophiles. 2009 Jul;13(4):583-94 PMID: 19548063
  23. NCBI Reference Sequences: current status, policy and new initiatives.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D32-6 PMID: 18927115
  24. GeneWise and Genomewise.
    Genome Res. 2004 May;14(5):988-95 PMID: 15123596
  25. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
    Nat Methods. 2007 Jun;4(6):495-500 PMID: 17468765
  26. The airborne metagenome in an indoor urban environment.
    PLoS One. 2008 Apr 02;3(4):e1862 PMID: 18382653
  27. Metagenomics: application of genomics to uncultured microorganisms.
    Microbiol Mol Biol Rev. 2004 Dec;68(4):669-85 PMID: 15590779
  28. Exploring prokaryotic diversity in the genomic era.
    Genome Biol. 2002;3(2):REVIEWS0003 PMID: 11864374
  29. SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences.
    Bioinformatics. 2009 Jul 15;25(14):1722-30 PMID: 19439565
  30. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
    Bioinformatics. 2002 Mar;18(3):502-4 PMID: 11934758
  31. IMG/M: a data management and analysis system for metagenomes.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D534-8 PMID: 17932063
  32. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria.
    Science. 2006 Dec 1;314(5804):1464-7 PMID: 17138901
  33. A bioinformatician's guide to metagenomics.
    Microbiol Mol Biol Rev. 2008 Dec;72(4):557-78, Table of Contents PMID: 19052320
  34. Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum.
    Biochemistry. 2008 Oct 28;47(43):11171-3 PMID: 18826254
  35. Quantitative phylogenetic assessment of microbial communities in diverse environments.
    Science. 2007 Feb 23;315(5815):1126-30 PMID: 17272687
  36. What's in the mix: phylogenetic classification of metagenome sequence samples.
    Curr Opin Microbiol. 2007 Oct;10(5):499-503 PMID: 17933580
  37. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis.
    FEMS Microbiol Ecol. 2007 May;60(2):341-50 PMID: 17343679
  38. A simple, fast, and accurate method of phylogenomic inference.
    Genome Biol. 2008 Oct 13;9(10):R151 PMID: 18851752
  39. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.
    Nat Methods. 2009 Sep;6(9):673-6 PMID: 19648916
  40. A core gut microbiome in obese and lean twins.
    Nature. 2009 Jan 22;457(7228):480-4 PMID: 19043404
  41. Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
    Mol Syst Biol. 2008;4:198 PMID: 18523433
  42. The natural history of nitrogen fixation.
    Mol Biol Evol. 2004 Mar;21(3):541-54 PMID: 14694078
  43. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.
    PLoS Comput Biol. 2009 Dec;5(12):e1000593 PMID: 20011103
  44. A computational screen for type I polyketide synthases in metagenomics shotgun data.
    PLoS One. 2008;3(10):e3515 PMID: 18953415
  45. Community-wide analysis of microbial genome sequence signatures.
    Genome Biol. 2009;10(8):R85 PMID: 19698104
  46. Comparative metagenomics of microbial communities.
    Science. 2005 Apr 22;308(5721):554-7 PMID: 15845853
  47. Genomic sequencing of single microbial cells from environmental samples.
    Curr Opin Microbiol. 2008 Jun;11(3):198-204 PMID: 18550420
  48. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment.
    Microb Ecol. 2007 Apr;53(3):371-83 PMID: 17334858
  49. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products.
    Chem Biol. 1998 Oct;5(10):R245-9 PMID: 9818143
  50. Phylogenetic diversity of nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites.
    Appl Environ Microbiol. 1999 Nov;65(11):4926-34 PMID: 10543805
  51. MEGAN analysis of metagenomic data.
    Genome Res. 2007 Mar;17(3):377-86 PMID: 17255551
  52. Inference of microbial recombination rates from metagenomic data.
    PLoS Genet. 2009 Oct;5(10):e1000674 PMID: 19798447
  53. CAMERA: a community resource for metagenomics.
    PLoS Biol. 2007 Mar;5(3):e75 PMID: 17355175
  54. Toward automatic reconstruction of a highly resolved tree of life.
    Science. 2006 Mar 3;311(5765):1283-7 PMID: 16513982
  55. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
    Bioinformatics. 2006 Nov 1;22(21):2688-90 PMID: 16928733
  56. Sequencing genomes from single cells by polymerase cloning.
    Nat Biotechnol. 2006 Jun;24(6):680-6 PMID: 16732271
  57. KEGG for linking genomes to life and the environment.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4 PMID: 18077471
  58. Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark.
    Environ Microbiol. 2008 Oct;10(10):2527-36 PMID: 18557770
  59. High-resolution metagenomics targets specific functional types in complex microbial communities.
    Nat Biotechnol. 2008 Sep;26(9):1029-34 PMID: 18711340
  60. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
    Nature. 2009 Dec 24;462(7276):1056-60 PMID: 20033048
  61. Review and re-analysis of domain-specific 16S primers.
    J Microbiol Methods. 2003 Dec;55(3):541-55 PMID: 14607398
  62. The NIH Human Microbiome Project.
    Genome Res. 2009 Dec;19(12):2317-23 PMID: 19819907
  63. Metagenomic marine nitrogen fixation--feast or famine?
    Trends Microbiol. 2005 Sep;13(9):416-20 PMID: 16043354
  64. Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment.
    Appl Microbiol Biotechnol. 2010 Jan;85(3):425-40 PMID: 19830422
  65. Accurate phylogenetic classification of variable-length DNA fragments.
    Nat Methods. 2007 Jan;4(1):63-72 PMID: 17179938
  66. Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism?
    Res Microbiol. 2005 Jun-Jul;156(5-6):611-8 PMID: 15950120
  67. Phylogeny estimation: traditional and Bayesian approaches.
    Nat Rev Genet. 2003 Apr;4(4):275-84 PMID: 12671658
  68. STRING 8--a global view on proteins and their functional interactions in 630 organisms.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6 PMID: 18940858
Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-11-461
Published
2010-08-05
Epub
2010-00-05
Pages
461
Language
English
Region
England
NLM ID
100965258
PMCID
PMC3091657
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-11-461 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2