Novel Systems Biology Techniques
Research Article | Novel Systems Biology TechniquesMetabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic ModelingCombating antimicrobial resistance has been highlighted as a critical global health priority. Due to the drying drug discovery pipeline, polymyxins have been employed as the last-line therapy against Gram-negative “superbugs”; however, the detailed mechanisms of antibacterial killing remain largely unclear, hampering the improvement of polymyxin therapy. Our integrative modeling using the constructed genome-scale metabolic model i...
Methods and Protocols | Novel Systems Biology TechniquesCalour: an Interactive, Microbe-Centric Analysis ToolCalour allows us to identify interesting microbial patterns and generate novel biological hypotheses by interactively inspecting microbiome studies and incorporating annotation databases and convenient statistical tools. Calour can be used as a first-step tool for microbiome data exploration.
Editor's Pick Methods and Protocols | Novel Systems Biology Techniquesq2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome DataLongitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity. We describe q2-longitudinal, a software plugin for longitudinal analysis of microbiome data sets in QIIME 2. The availability of longitudinal statistics and visualizations in the QIIME 2 framework will make the analysis of longitudinal data more accessible to microbiome researchers.
Methods and Protocols | Novel Systems Biology TechniquesEvaluating the Information Content of Shallow Shotgun MetagenomicsA common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S...
Methods and Protocols | Novel Systems Biology TechniquesHigh-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome IntegrityReduced costs of sequencing have tremendously impacted the field of microbial ecology, allowing scientists to design more studies with larger sample sizes that often exceed 10,000 samples. Library preparation costs have not kept pace with sequencing prices, although automated liquid handling robots provide a unique opportunity to bridge this gap while also decreasing human error. Here, we take advantage of an acoustic liquid handling...
Research Article | Novel Systems Biology TechniquesRibosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon StarvationRibosome profiling accesses the translational step of gene expression via deep sequencing of ribosome-protected mRNA footprints. Pairing of ribosome profiling and transcriptomics data provides a translational efficiency for each gene. Here, the translatome and transcriptome of the model cyanobacterium Synechocystis were compared under carbon-replete and carbon starvation conditions. The latter may be experienced when...
Resource Report | Novel Systems Biology TechniquesComprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RFThe robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome...
Research Article | Novel Systems Biology TechniquesModeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of InformationBacteria sense and respond to their environments using a sophisticated array of sensors and regulatory networks to optimize their fitness and survival in a constantly changing environment. Understanding how these regulatory and sensory networks work will provide the capacity to predict bacterial behaviors and, potentially, to manipulate their interactions with an environment or host. Leveraging the information theory provides useful...
Methods and Protocols | Novel Systems Biology TechniquesSHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality ControlQuality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is...
Research Article | Novel Systems Biology TechniquesNonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence DiversityEstimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and...