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bioinformatics

  • Open Access
    BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities
    Methods and Protocols
    BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities

    The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on “in-house” reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time expensive, error- and bias-prone process lacks standardization, cripples the potential for...

    Brendan A. Daisley, Gregor Reid
  • Open Access
    GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses
    Research Article
    GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses

    GEO archives transcriptomic data from over 5,800 microbial experiments and allows researchers to answer questions not directly addressed in published papers. However, less than 4% of the microbial data sets include the sample group annotations required for high-throughput reanalysis.

    Zhongyou Li, Katja Koeppen, Victoria I. Holden, Samuel L. Neff, Liviu Cengher, Elora G. Demers, Dallas L. Mould, Bruce A. Stanton, Thomas H. Hampton
  • Open Access
    EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
    Research Article
    EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

    Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research.

    Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight
  • Open Access
    Computational Analysis of Microbial Flow Cytometry Data
    Minireview | Applied and Environmental Science
    Computational Analysis of Microbial Flow Cytometry Data

    Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution.

    Peter Rubbens, Ruben Props
  • Open Access
    A Simplified and Efficient Method for Himar-1 Transposon Sequencing in Bacteria, Demonstrated by Creation and Analysis of a Saturated Transposon-Mutant Library in <span class="named-content genus-species" id="named-content-1">Mycobacterium abscessus</span>
    Research Article | Novel Systems Biology Techniques
    A Simplified and Efficient Method for Himar-1 Transposon Sequencing in Bacteria, Demonstrated by Creation and Analysis of a Saturated Transposon-Mutant Library in Mycobacterium abscessus

    Transposon insertion sequencing is a powerful tool, but many researchers are discouraged by the apparent technical complexity of preparing the genomic library for deep sequencing and by the complicated computational analysis needed for insertion site identification. Our proposed method makes the preparation of the library easy and straightforward, relying on well-known molecular biology techniques. In addition, the results obtained from...

    Mark Foreman, Moran Gershoni, Daniel Barkan
  • Open Access
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
    Research Article | Novel Systems Biology Techniques
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

    Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary...

    Alexander M. Kloosterman, Kyle E. Shelton, Gilles P. van Wezel, Marnix H. Medema, Douglas A. Mitchell
  • Open Access
    Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations
    Methods and Protocols | Molecular Biology and Physiology
    Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations

    The correct mapping of promoter elements is a crucial step in microbial genomics. Also, when combining new DNA elements into synthetic sequences, predicting the potential generation of new promoter sequences is critical. Over the last years, many bioinformatics tools have been created to allow users to predict promoter elements in a sequence or genome of interest. Here, we assess the predictive power of some of the main prediction tools...

    Murilo Henrique Anzolini Cassiano, Rafael Silva-Rocha
  • Open Access
    Computational Basis for On-Demand Production of Diversified Therapeutic Phage Cocktails
    Research Article | Therapeutics and Prevention
    Computational Basis for On-Demand Production of Diversified Therapeutic Phage Cocktails

    The antibiotic resistance crisis has led to renewed interest in phage therapy as an alternative means of treating infection. However, conventional methods for isolating pathogen-specific phage are slow, labor-intensive, and frequently unsuccessful. We have demonstrated that computationally identified prophages carried by near-neighbor bacteria can serve as starting material for production of engineered phages that kill the target...

    Catherine M. Mageeney, Anupama Sinha, Richard A. Mosesso, Douglas L. Medlin, Britney Y. Lau, Alecia B. Rokes, Todd W. Lane, Steven S. Branda, Kelly P. Williams
  • Open Access
    manta: a Clustering Algorithm for Weighted Ecological Networks
    Methods and Protocols | Novel Systems Biology Techniques
    manta: a Clustering Algorithm for Weighted Ecological Networks

    manta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.

    Lisa Röttjers, Karoline Faust
  • Open Access
    A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination
    Editor's Pick Editorial
    A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination
    Chase M. Clark, Brian T. Murphy, Laura M. Sanchez

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