Novel Systems Biology Techniques
Special Issue Perspective | Novel Systems Biology TechniquesComputational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome EcologyMicrobial and plant specialized metabolites, also known as natural products, are key mediators of microbe-microbe and host-microbe interactions and constitute a rich resource for drug development. In the past decade, genome mining has emerged as a prominent strategy for natural product discovery.
Research Article | Novel Systems Biology TechniquesMagic Pools: Parallel Assessment of Transposon Delivery Vectors in BacteriaMolecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The...
Editor's Pick Minireview | Novel Systems Biology TechniquesOn the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them AnymoreFor 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.
Research Article | Novel Systems Biology TechniquesDiscrete False-Discovery Rate Improves Identification of Differentially Abundant MicrobesDS-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.
Methods and Protocols | Novel Systems Biology TechniquesDirect PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut MicrobiomesThe 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...
Editor's Pick Methods and Protocols | Novel Systems Biology TechniquesA Synthetic Community System for Probing Microbial Interactions Driven by ExometabolitesUnderstanding 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...
Research Article | Novel Systems Biology TechniquesSystematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping AnalysisTo 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...
Research Article | Novel Systems Biology TechniquesLinking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal MicrobiotaThe 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...
Editor's Pick Research Article | Novel Systems Biology TechniquesMetabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acIThe 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...
Methods and Protocols | Novel Systems Biology TechniquesPaperBLAST: Text Mining Papers for Information about HomologsWith 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...