Latest Articles
Methods and Protocols | Novel Systems Biology TechniquesMicrobiome Helper: a Custom and Streamlined Workflow for Microbiome ResearchAs the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results....
Research Article | Molecular Biology and PhysiologyTranscriptional Profiling of the Oral Pathogen Streptococcus mutans in Response to Competence Signaling Peptide XIPGenetic competence provides bacteria with an opportunity to increase genetic diversity or acquire novel traits conferring a survival advantage. In the cariogenic pathogen Streptococcus mutans, DNA transformation is regulated by the competence stimulating peptide XIP (ComX-inducing p...
Methods and Protocols | Molecular Biology and PhysiologyFrom Genomes to Phenotypes: Traitar, the Microbial Trait AnalyzerBacteria are ubiquitous in our ecosystem and have a major impact on human health, e.g., by supporting digestion in the human gut. Bacterial communities can also aid in biotechnological processes such as wastewater treatment or decontamination of polluted soils. Diverse bacteria contribute with their unique capabilities to the functioning of such ecosystems, but lab experiments to investigate those capabilities are labor-intensive. Major...
Editor's Pick Research Article | Novel Systems Biology TechniquesSpatial Molecular Architecture of the Microbial Community of a Peltigera LichenMicrobial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and...
Research Article | Ecological and Evolutionary ScienceSSUnique: Detecting Sequence Novelty in Microbiome SurveysExtensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain many unclassified sequences, many representing organisms with novel taxonomy (taxonomic “blind spots”) and potentially unique ecology. This novelty is poorly explored in standard workflows, which narrows the breadth and discovery potential of such studies. Here we present the SSUnique analysis pipeline,...
Research Article | Molecular Biology and PhysiologyGenomewide Dam Methylation in Escherichia coli during Long-Term Stationary PhaseWhile it has been shown that methylation remains relatively constant into early stationary phase of E. coli, this study goes further through death phase and long-term stationary phase, a unique time in the bacterial life cycle due to nutrient limitation and strong selection for mutants with increased fitness. The absence of methylation at GATC sites can influence the...
Research Article | Applied and Environmental ScienceIonic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide HydrolysisPretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a...
Research Article | Molecular Biology and PhysiologyA Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putidaThe regulatory nodes that govern metabolic traffic in bacteria often show connectivities that could be deemed unnecessarily complex at a first glance. Being a soil dweller and plant colonizer, Pseudomonas putida frequently encounters fructose in the niches that it inhabits. As is the case with many other sugars, fructose is internalized by a dedicated...
Research Article | Molecular Biology and PhysiologyGlobal Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus BiofilmsProkaryotes are thought to regulate their proteomes largely at the level of transcription. However, the results from this first set of global transcriptomic and proteomic analyses of paired microbial samples presented here show that this assumption is false for the majority of genes and their products in S. pyogenes. In addition, the tenuousness of the link between...
Editor's Pick Research Article | Host-Microbe BiologyIntegrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus MonkeysProbiotics are becoming increasingly popular due to their perceived effects on health, despite a lack of mechanistic information on how they impart these benefits. Infant formula and complementary foods are common targets for supplementation with probiotics. However, different probiotic strains have different properties, and there is a lack of data on long-term health effects on the consumer. Given the increasing interest in...