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James M Tiedje - One of the best experts on this subject based on the ideXlab platform.

  • microbial Community Analysis with ribosomal gene fragments from shotgun metagenomes
    Applied and Environmental Microbiology, 2016
    Co-Authors: Jiarong Guo, James R Cole, Qingpeng Zhang, Titus C Brown, James M Tiedje
    Abstract:

    Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised Community Analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised Community Analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon Analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the grouping of samples in ordination analyses. We applied this pipeline to soil samples with paired shotgun and amplicon data and confirmed bias against Verrucomicrobia in a commonly used V6-V8 primer set, as well as discovering likely bias against Actinobacteria and for Verrucomicrobia in a commonly used V4 primer set. This pipeline can utilize all variable regions in SSU rRNA and also can be applied to large-subunit (LSU) rRNA genes for confirmation of Community structure. The pipeline can scale to handle large amounts of soil metagenomic data (5 Gb memory and 5 central processing unit hours to process 38 Gb [1 lane] of trimmed Illumina HiSeq2500 data) and is freely available at https://github.com/dib-lab/SSUsearch under a BSD license.

  • terminal restriction fragment length polymorphism Analysis program a web based research tool for microbial Community Analysis
    Applied and Environmental Microbiology, 2000
    Co-Authors: Terence L. Marsh, Paul Saxman, James R Cole, James M Tiedje
    Abstract:

    Rapid Analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for Community Analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence Analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial Community Analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The Analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of Community Analysis with terminal restriction fragment length polymorphisms.

Mary Pat Fallon - One of the best experts on this subject based on the ideXlab platform.

James R Cole - One of the best experts on this subject based on the ideXlab platform.

  • microbial Community Analysis with ribosomal gene fragments from shotgun metagenomes
    Applied and Environmental Microbiology, 2016
    Co-Authors: Jiarong Guo, James R Cole, Qingpeng Zhang, Titus C Brown, James M Tiedje
    Abstract:

    Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised Community Analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised Community Analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon Analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the grouping of samples in ordination analyses. We applied this pipeline to soil samples with paired shotgun and amplicon data and confirmed bias against Verrucomicrobia in a commonly used V6-V8 primer set, as well as discovering likely bias against Actinobacteria and for Verrucomicrobia in a commonly used V4 primer set. This pipeline can utilize all variable regions in SSU rRNA and also can be applied to large-subunit (LSU) rRNA genes for confirmation of Community structure. The pipeline can scale to handle large amounts of soil metagenomic data (5 Gb memory and 5 central processing unit hours to process 38 Gb [1 lane] of trimmed Illumina HiSeq2500 data) and is freely available at https://github.com/dib-lab/SSUsearch under a BSD license.

  • terminal restriction fragment length polymorphism Analysis program a web based research tool for microbial Community Analysis
    Applied and Environmental Microbiology, 2000
    Co-Authors: Terence L. Marsh, Paul Saxman, James R Cole, James M Tiedje
    Abstract:

    Rapid Analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for Community Analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence Analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial Community Analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The Analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of Community Analysis with terminal restriction fragment length polymorphisms.

Terence L. Marsh - One of the best experts on this subject based on the ideXlab platform.

  • terminal restriction fragment length polymorphism Analysis program a web based research tool for microbial Community Analysis
    Applied and Environmental Microbiology, 2000
    Co-Authors: Terence L. Marsh, Paul Saxman, James R Cole, James M Tiedje
    Abstract:

    Rapid Analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for Community Analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence Analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial Community Analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The Analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of Community Analysis with terminal restriction fragment length polymorphisms.

Pascal Simonet - One of the best experts on this subject based on the ideXlab platform.

  • Molecular tools in rhizosphere microbiology—from single-cell to whole-Community Analysis
    Plant and Soil, 2009
    Co-Authors: Jan Sorensen, Mette Haubjerg Nicolaisen, Eliora Ron, Pascal Simonet
    Abstract:

    It is the aim of this chapter to present an overview of new, molecular tools that have been developed over recent years to study individual, single cells and composite, complex communities of microorganisms in the rhizosphere. We have carefully focused on culture-independent assays and selected methodologies that have already been or will soon be applicable for rhizosphere microbiology. Emphasis is placed on rhizosphere bacteria and the review first describes a number of the new methodologies developed for detection and localization of specific bacterial populations using modern electron and fluorescence microscopy combined with specific tagging techniques. First half of the chapter further comprises a thorough treatise of the recent development of reporter gene technology, i.e. using specific reporter bacteria to detect microscale distributions of rhizosphere compounds such as nutrients, metals and organic exudates or contaminants. Second half of the chapter devoted to microbial Community Analysis contains a thorough treatise of nucleotide- and PCR-based technologies to study composition and diversity of indigenous bacteria in the natural rhizosphere. Also included are the most recent developments of functional gene and gene expression analyses in the rhizosphere based on specific mRNA transcript or transcriptome Analysis, proteome Analysis and construction of metagenomic libraries.

  • Molecular tools in rhizosphere microbiology - from single-cell to whole-Community Analysis.
    Plant and Soil, 2009
    Co-Authors: Jan Tind Sørensen, Mette Haubjerg Nicolaisen, Eliora Z. Ron, Pascal Simonet
    Abstract:

    It is the aim of this chapter to present an overview of new, molecular tools that have been developed over recent years to study individual, single cells and composite, complex communities of microorganisms in the rhizosphere. We have carefully focused on culture-independent assays and selected methodologies that have already been or will soon be applicable for rhizosphere microbiology. Emphasis is placed on rhizosphere bacteria and the review first describes a number of the new methodologies developed for detection and localization of specific bacterial populations using modern electron and fluorescence microscopy combined with specific tagging techniques. First half of the chapter further comprises a thorough treatise of the recent development of reporter gene technology, i.e. using specific reporter bacteria to detect microscale distributions of rhizosphere compounds such as nutrients, metals and organic exudates or contaminants. Second half of the chapter devoted to microbial Community Analysis contains a thorough treatise of nucleotide- and PCR-based technologies to study composition and diversity of indigenous bacteria in the natural rhizosphere. Also included are the most recent developments of functional gene and gene expression analyses in the rhizosphere based on specific mRNA transcript or transcriptome Analysis, proteome Analysis and construction of metagenomic libraries.

  • Molecular tools in rhizosphere microbiology—from single-cell to whole-Community Analysis
    Plant and Soil, 2009
    Co-Authors: Jan Sorensen, Mette Haubjerg Nicolaisen, Eliora Ron, Pascal Simonet
    Abstract:

    International audienceIt is the aim of this chapter to present an overview of new, molecular tools that have been developed over recent years to study individual, single cells and composite, complex communities of microorganisms in the rhizosphere. We have carefully focused on culture-independent assays and selected methodologies that have already been or will soon be applicable for rhizosphere microbiology. Emphasis is placed on rhizosphere bacteria and the review first describes a number of the new methodologies developed for detection and localization of specific bacterial populations using modern electron and fluorescence microscopy combined with specific tagging techniques. First half of the chapter further comprises a thorough treatise of the recent development of reporter gene technology, i.e. using specific reporter bacteria to detect microscale distributions of rhizosphere compounds such as nutrients, metals and organic exudates or contaminants. Second half of the chapter devoted to microbial Community Analysis contains a thorough treatise of nucleotide- and PCR-based technologies to study composition and diversity of indigenous bacteria in the natural rhizosphere. Also included are the most recent developments of functional gene and gene expression analyses in the rhizosphere based on specific mRNA transcript or transcriptome Analysis, proteome Analysis and construction of metagenomic libraries