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Novel Systems Biology Techniques

  • Open Access
    On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore
    Editor's Pick Minireview | Novel Systems Biology Techniques
    On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore

    For decades, microbiologists have considered uncertainties as an undesired side effect of experimental protocols. As a consequence, standard microbial system modeling strives to hide uncertainties for the sake of deterministic understanding.

    Benoit Delahaye, Damien Eveillard, Nicholas Bouskill
  • Open Access
    Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
    Methods and Protocols | Novel Systems Biology Techniques
    Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes

    The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA...

    Elin Videvall, Maria Strandh, Anel Engelbrecht, Schalk Cloete, Charlie K. Cornwallis
  • Open Access
    Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes
    Research Article | Novel Systems Biology Techniques
    Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes

    DS-FDR can achieve higher statistical power to detect significant findings in sparse and noisy microbiome data compared to the commonly used Benjamini-Hochberg procedure and other FDR-controlling procedures.

    Lingjing Jiang, Amnon Amir, James T. Morton, Ruth Heller, Ery Arias-Castro, Rob Knight
  • Open Access
    A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites
    Editor's Pick Methods and Protocols | Novel Systems Biology Techniques
    A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

    Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion a range of research to investigate how the diversity of a microbiome and interactions among its members impact its function, where function can be measured as exometabolites. The system allows for community exometabolite profiling to be coupled with genome mining, transcript...

    John L. Chodkowski, Ashley Shade
  • Open Access
    Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis
    Research Article | Novel Systems Biology Techniques
    Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis

    To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, salinity, and pH and under other conditions. In order to understand the cause-effect relationships between the dynamic function of the stress network and ultimate physiological consequences, this...

    Cynthia L. Darnell, Peter D. Tonner, Jordan G. Gulli, Scott C. Schmidler, Amy K. Schmid
  • Open Access
    Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota
    Research Article | Novel Systems Biology Techniques
    Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota

    The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples...

    Eric J. de Muinck, Knut E. A. Lundin, Pål Trosvik
  • Open Access
    Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI

    The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require...

    Joshua J. Hamilton, Sarahi L. Garcia, Brittany S. Brown, Ben O. Oyserman, Francisco Moya-Flores, Stefan Bertilsson, Rex R. Malmstrom, Katrina T. Forest, Katherine D. McMahon
  • Open Access
    PaperBLAST: Text Mining Papers for Information about Homologs
    Methods and Protocols | Novel Systems Biology Techniques
    PaperBLAST: Text Mining Papers for Information about Homologs

    With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about...

    Morgan N. Price, Adam P. Arkin
  • Open Access
    Pathovar Transcriptomes
    Commentary | Novel Systems Biology Techniques
    Pathovar Transcriptomes

    Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-...

    Amy Platenkamp, Jay L. Mellies
  • Open Access
    Transcriptional Variation of Diverse Enteropathogenic <em>Escherichia coli</em> Isolates under Virulence-Inducing Conditions
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions

    Recent studies have demonstrated that there is considerable genomic diversity among EPEC isolates; however, it is unknown if this genomic diversity leads to differences in their global transcription. This study used RNA-Seq to compare the global transcriptomes of EPEC isolates from diverse phylogenomic lineages. We demonstrate that there are lineage- and isolate-specific differences in the transcriptomes of genomically diverse EPEC...

    Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko

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