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Novel Systems Biology Techniques

  • Open Access
    Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
    Research Article | Novel Systems Biology Techniques
    Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

    Microbiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating...

    Jeremiah J. Minich, Jon G. Sanders, Amnon Amir, Greg Humphrey, Jack A. Gilbert, Rob Knight
  • Open Access
    Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions
    Special Issue Perspective | Novel Systems Biology Techniques
    Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions

    Integrated omics applied to microbial communities offers a great opportunity to analyze the niche breadths (i.e., resource and condition ranges usable by a species) of constituent populations, ranging from generalists, with a broad niche breadth, to specialists, with a narrow one. In this context, extracellular metabolomics measurements describe resource spaces available to microbial populations; dedicated analyses of metagenomics data...

    Emilie E. L. Muller
  • Open Access
    Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments
    Research Article | Novel Systems Biology Techniques
    Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

    The relative scarcity of microbes in low-microbial-biomass environments makes accurate determination of community composition challenging. Identifying and controlling for contaminant bacterial DNA are critical steps in understanding microbial communities from these low-biomass environments. Our study introduces the use of a mock community dilution series as a positive control and evaluates four computational strategies that can identify...

    Lisa Karstens, Mark Asquith, Sean Davin, Damien Fair, W. Thomas Gregory, Alan J. Wolfe, Jonathan Braun, Shannon McWeeney
  • Open Access
    Strengthening Insights in Microbial Ecological Networks from Theory to Applications
    Special Issue Perspective | Novel Systems Biology Techniques
    Strengthening Insights in Microbial Ecological Networks from Theory to Applications

    Networks encode the interactions between the components in complex systems and play an essential role in understanding complex systems. Microbial ecological networks provide a system-level insight for comprehensively understanding complex microbial interactions, which play important roles in microbial community assembly.

    Xiaofei Lv, Kankan Zhao, Ran Xue, Yuanhui Liu, Jianming Xu, Bin Ma
  • Open Access
    Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Strains Identifies Genes for Antibiotic Resistance and Virulence
    Research Article | Novel Systems Biology Techniques
    Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence

    Klebsiella pneumoniae is a major bacterial pathogen that causes pneumonia and urinary tract infections in human. K. pneumoniae infections are treated with carbapenem, but carbapenem-resistant K. pneumoniae has been spreading...

    Muyoung Lee, Naina Adren Pinto, Chan Yeong Kim, Sunmo Yang, Roshan D’Souza, Dongeun Yong, Insuk Lee
  • Open Access
    Resistance Gene-Directed Genome Mining of 50 <em>Aspergillus</em> Species
    Research Article | Novel Systems Biology Techniques
    Resistance Gene-Directed Genome Mining of 50 Aspergillus Species

    Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites; some of these compounds are used as pharmaceuticals, such as penicillin, cyclosporine, and statin. With whole-genome sequencing, it became apparent that the genetic potential for secondary metabolite production is much larger than expected. As an increasing number of species are whole-genome sequenced, thousands of secondary...

    Inge Kjærbølling, Tammi Vesth, Mikael R. Andersen
  • Open Access
    <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients
    Research Article | Novel Systems Biology Techniques
    Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients

    While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P....

    Moamen M. Elmassry, Nithya S. Mudaliar, Kameswara Rao Kottapalli, Sharmila Dissanaike, John A. Griswold, Michael J. San Francisco, Jane A. Colmer-Hamood, Abdul N. Hamood
  • Open Access
    Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance
    Research Article | Novel Systems Biology Techniques
    Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance

    Cystic fibrosis (CF) is a genetic disease in which chronic airway infections and lung inflammation result in respiratory failure. CF airway infections are usually caused by bacterial communities that are difficult to eradicate with available antibiotics. Using species abundance data for clinically stable adult CF patients assimilated from three published studies, we developed a metabolic model of CF airway communities to better...

    Michael A. Henson, Giulia Orazi, Poonam Phalak, George A. O’Toole
  • Open Access
    Designing Metabolic Division of Labor in Microbial Communities
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Designing Metabolic Division of Labor in Microbial Communities

    Understanding how microbes assemble into communities is a fundamental open issue in biology, relevant to human health, metabolic engineering, and environmental sustainability. A possible mechanism for interactions of microbes is through cross-feeding, i.e., the exchange of small molecules. These metabolic exchanges may allow different microbes to specialize in distinct tasks and evolve division of labor. To systematically explore the...

    Meghan Thommes, Taiyao Wang, Qi Zhao, Ioannis C. Paschalidis, Daniel Segrè
  • Open Access
    Curated BLAST for Genomes
    Methods and Protocols | Novel Systems Biology Techniques
    Curated BLAST for Genomes

    Given a microbe’s genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without...

    Morgan N. Price, Adam P. Arkin

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