Latest Articles
Research Article | Applied and Environmental ScienceTime Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated SludgeDisturbance is a key determinant of community assembly and dynamics in natural and engineered ecosystems. Microbiome response to disturbance is thought to be influenced by bacterial growth traits and life history strategies. In this time series observational study, the response to disturbance of microbial communities in a full-scale activated sludge wastewater treatment plant was assessed by computing specific cellular traits of genomes...
Commentary | Applied and Environmental ScienceA Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence AnalysesDNA sequence-based microbiome studies can be impacted by a range of different methodological artefacts. Contamination originating from laboratory kits and reagents can lead to erroneous results, particularly in samples containing a low microbial biomass.
Observation | Novel Systems Biology Techniquesredbiom: a Rapid Sample Discovery and Feature Characterization SystemAlthough analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify...
Research Article | Novel Systems Biology TechniquesQuantifying and Understanding Well-to-Well Contamination in Microbiome ResearchMicrobiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating...
Research Article | Ecological and Evolutionary ScienceProteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic AlphaproteobacteriumAmmonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have...
Research Article | Host-Microbe BiologyMultipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial PerspectiveThe symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own...
Research Article | Molecular Biology and PhysiologyGenomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic PathwaysMycobacterium tuberculosis causes 10 million cases of tuberculosis (TB), resulting in over 1 million deaths each year. TB therapy is challenging because it requires a minimum of 6 months of treatment with multiple drugs. Protracted treatment times and the emergent spread of drug-resistant M. tuberculosis...
Research Article | Host-Microbe BiologyPorcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed IntakeInterest in the role of intestinal microbiota in determining FE in pigs has increased in recent years. However, it is not known if the same FE-associated bacteria are found across different rearing environments. In this study, geographic location and intestinal sampling site had a greater influence on the pig gut microbiome than FE. This presents challenges when aiming to identify consistent reliable microbial biomarkers for FE....
Research Article | Applied and Environmental ScienceFunctional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex CommunitiesThe rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly...
Research Article | Molecular Biology and PhysiologyA Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reeseiIn this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression of these genes in...