Building on basic metagenomics with complementary technologies

Metagenomics, the application of random shotgun sequencing to environmental samples, is a powerful approach for characterizing microbial communities. However, this method only represents the cornerstone of what can be achieved using a range of complementary technologies such as transcriptomics, proteomics, cell sorting and microfluidics. Together, these approaches hold great promise for the study of microbial ecology and evolution.

[1]  G. Church,et al.  Sequencing genomes from single cells by polymerase cloning , 2006, Nature Biotechnology.

[2]  Stephen R. Quake,et al.  Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria , 2006, Science.

[3]  T. Urich,et al.  Archaea predominate among ammonia-oxidizing prokaryotes in soils , 2006, Nature.

[4]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[5]  R. Stepanauskas,et al.  Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time , 2007, Proceedings of the National Academy of Sciences.

[6]  Byron F. Brehm-Stecher,et al.  Single-Cell Microbiology: Tools, Technologies, and Applications , 2004, Microbiology and Molecular Biology Reviews.

[7]  Yehia M. Ibrahim,et al.  Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface , 2006, Journal of the American Society for Mass Spectrometry.

[8]  C. Hutchison,et al.  Cell-free cloning using φ29 DNA polymerase , 2005 .

[9]  Natalia Ivanova,et al.  Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities , 2006, Nature Biotechnology.

[10]  Philip L. F. Johnson,et al.  Inference of population genetic parameters in metagenomics: a clean look at messy data. , 2006, Genome research.

[11]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.

[12]  J. Derisi,et al.  Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise , 2006, Nature.

[13]  C. Mathew.  Encyclopedia of genetics, genomics, proteomics and bioinformatics. , 2005 .

[14]  Manfred Auer,et al.  High-pressure freezing, cellular tomography, and structural cell biology. , 2006, BioTechniques.

[15]  Marcy Yann,et al.  ヒト口腔からの微量の培養されないTM7微生物の単一細胞遺伝分析による生物学的「不明な物体」の詳細な分析 , 2007 .

[16]  G. Whitesides,et al.  Microfabrication meets microbiology , 2007, Nature Reviews Microbiology.

[17]  R. Amann,et al.  Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. , 2000, Environmental microbiology.

[18]  M. Hecker,et al.  From genomics via proteomics to cellular physiology of the Gram‐positive model organism Bacillus subtilis , 2005, Cellular microbiology.

[19]  Florent E. Angly,et al.  The Marine Viromes of Four Oceanic Regions , 2006, PLoS biology.

[20]  Jillian F Banfield,et al.  Population genomics in natural microbial communities. , 2006, Trends in ecology & evolution.

[21]  A. Thompson,et al.  Salmonella transcriptomics: relating regulons, stimulons and regulatory networks to the process of infection. , 2006, Current opinion in microbiology.

[22]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[23]  Dieter Söll,et al.  The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[25]  A. L. Koch,et al.  Determination of the Biomasses of Small Bacteria at Low Concentrations in a Mixture of Species with Forward Light Scatter Measurements by Flow Cytometry , 1998, Applied and Environmental Microbiology.

[26]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[27]  A. Salamov,et al.  Use of simulated data sets to evaluate the fidelity of metagenomic processing methods , 2007, Nature Methods.

[28]  Douglas Benson,et al.  High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry , 2006, Journal of biology.

[29]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[30]  M. Hahn.  Isolation of Strains Belonging to the Cosmopolitan Polynucleobacter necessarius Cluster from Freshwater Habitats Located in Three Climatic Zones , 2003, Applied and Environmental Microbiology.

[31]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[32]  M. Moran,et al.  Analysis of Microbial Gene Transcripts in Environmental Samples , 2005, Applied and Environmental Microbiology.

[33]  Natalia N. Ivanova,et al.  Symbiosis insights through metagenomic analysis of a microbial consortium. , 2006, Nature Reviews Microbiology.

[34]  S. Giovannoni,et al.  The uncultured microbial majority. , 2003, Annual review of microbiology.

[35]  Philip Hugenholtz,et al.  Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis , 2006, Science.

[36]  M. Dumont,et al.  Stable isotope probing — linking microbial identity to function , 2005, Nature Reviews Microbiology.

[37]  P. Hugenholtz,et al.  Environmental shotgun sequencing , 2005 .

[38]  Karsten Zengler,et al.  Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities , 2007, Applied and Environmental Microbiology.

[39]  Eoin L. Brodie,et al.  Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments , 2006, Applied and Environmental Microbiology.

[40]  J. Banfield,et al.  Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community , 2005, Applied and Environmental Microbiology.

[41]  S. Giovannoni,et al.  Cultivation of the ubiquitous SAR11 marine bacterioplankton clade , 2002, Nature.

[42]  S. Quake,et al.  Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth , 2007, Proceedings of the National Academy of Sciences.

[43]  K. Lewis,et al.  Isolating "Uncultivable" Microorganisms in Pure Culture in a Simulated Natural Environment , 2002, Science.

[44]  Harald Huber,et al.  A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont , 2002, Nature.

[45]  Natalia N. Ivanova,et al.  Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite , 2007, Nature.

[46]  P. Hugenholtz.  Exploring prokaryotic diversity in the genomic era , 2002, Genome Biology.

[47]  E. Delong,et al.  Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior , 2006, Science.

[48]  Vincent J. Denef,et al.  Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria , 2007, Nature.

[49]  J. Banfield,et al.  Community Proteomics of a Natural Microbial Biofilm , 2005, Science.

[50]  Roger S Lasken,et al.  Unbiased whole-genome amplification directly from clinical samples. , 2003, Genome Research.

[51]  Rudolf Amann,et al.  Flow Sorting of Marine Bacterioplankton after Fluorescence In Situ Hybridization , 2004, Applied and Environmental Microbiology.