Novel Systems Biology Techniques
Research Article | Novel Systems Biology TechniquesControlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing ExperimentsThe 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...
Special Issue Perspective | Novel Systems Biology TechniquesStrengthening Insights in Microbial Ecological Networks from Theory to ApplicationsNetworks 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.
Research Article | Novel Systems Biology TechniquesNetwork Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and VirulenceKlebsiella 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...
Research Article | Novel Systems Biology TechniquesResistance Gene-Directed Genome Mining of 50 Aspergillus SpeciesSpecies 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...
Research Article | Novel Systems Biology TechniquesPseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma PatientsWhile 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....
Research Article | Novel Systems Biology TechniquesMetabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen DominanceCystic 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...
Editor's Pick Research Article | Novel Systems Biology TechniquesDesigning Metabolic Division of Labor in Microbial CommunitiesUnderstanding 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...
Methods and Protocols | Novel Systems Biology TechniquesCurated BLAST for GenomesGiven 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...
Methods and Protocols | Novel Systems Biology TechniquesImpact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota ProfilingLarge-scale human microbiota studies require specimens collected from multiple sites and/or time points to maximize detection of the small effects in microbe-host interactions. However, batch biases caused by experimental protocols, such as sample collection, massively parallel sequencing, and bioinformatics analyses, remain critical and should be minimized. This work evaluated the effects of preservation solutions and bacterial 16S...
Editor's Pick Research Article | Novel Systems Biology TechniquesPerformance of Microbiome Sequence Inference Methods in Environments with Varying BiomassMicrobial communities have important ramifications for human health, but determining their impact requires accurate characterization. Current technology makes microbiome sequence data more accessible than ever. However, popular software methods for analyzing these data are based on algorithms developed alongside older sequencing technology and smaller data sets and thus may not be adequate for modern, high-throughput data sets....