Editor's Pick
Editor's Pick Research Article | Ecological and Evolutionary ScienceRegime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its ControlPhage-microbe communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history...
Editor's Pick Research Article | Applied and Environmental ScienceWide Distribution of Phage That Infect Freshwater SAR11 BacteriaFonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect ...
Editor's Pick Research Article | Clinical Science and EpidemiologyUsing DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of ConceptCurrent methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods,...
Editor's Pick Methods and Protocols | Applied and Environmental ScienceIntroducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry DataEstimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage...
Editor's Pick Research Article | Ecological and Evolutionary ScienceA Genome-Based Species Taxonomy of the Lactobacillus Genus ComplexThe Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy...
Editor's Pick Research Article | Novel Systems Biology TechniquesA Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human MicrobiotaExperimental advances have enabled the acquisition of tandem mass spectrometry and metagenomics sequencing data from tens of thousands of environmental/host-oriented microbial communities. Each of these communities contains hundreds of microbial features (corresponding to microbial species) and thousands of molecular features (corresponding to microbial natural products). However, with the current technology, it is very difficult to...
Editor's Pick Research Article | Ecological and Evolutionary ScienceStrategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME WorkshopHigh-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A weeklong workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional...
Editor's Pick Research Article | Host-Microbe BiologyDual RNA-seq in Streptococcus pneumoniae Infection Reveals Compartmentalized Neutrophil Responses in Lung and Pleural SpaceThe factors that regulate the passage of bacteria between different anatomical compartments are unclear. We have used an experimental model of infection with Streptococcus pneumoniae to examine the host and bacterial factors involved in the passage of bacteria from the lung to the pleural space. The transcriptional profile of host and bacterial cells within the...
Editor's Pick Research Article | Host-Microbe BiologyA Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian CentenariansThe gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment...
Editor's Pick Research Article | Molecular Biology and PhysiologyAlteration of Proteomes in First-Generation Cultures of Bacillus pumilus Spores Exposed to Outer SpaceSpore-forming bacteria are well known for their resistance to harsh environments and are of concern for spreading contamination to extraterrestrial bodies during future life detection missions. Bacillus pumilus has been regularly isolated from spacecraft-associated surfaces and exhibited unusual resistance to ultraviolet light and other sterilization techniques. A...