Latest Articles
Research Article | Ecological and Evolutionary ScienceBioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer ApproachesAs a naturally occurring adaptive immune system, CRISPR-Cas (clustered regularly interspersed short palindromic repeats–CRISPR-associated genes) systems are widely found in bacteria and archaea to defend against viruses. Since 2013, the application of various bacterial CRISPR-Cas systems has become very popular due to their development into targeted and programmable genome engineering tools with the ability to edit almost any genome. As...
Research Article | Applied and Environmental ScienceProkaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other BiomesUnderstanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes...
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...
Research Article | Host-Microbe BiologyThe Formaldehyde Dehydrogenase SsFdh1 Is Regulated by and Functionally Cooperates with the GATA Transcription Factor SsNsd1 in Sclerotinia sclerotiorumS. sclerotiorum is a pathogenic fungus with sclerotium and infection cushion development, making S. sclerotiorum one of the most challenging agricultural pathogens with no effective control method. We identified important sclerotium and compound appressorium formation determinants, SsNsd1 and SsFdh1...
Research Article | Ecological and Evolutionary ScienceCharacteristics and Evolutionary Analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from Streamlined Plasmids to ChromidsThe evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic photoheterotrophic bacteria (AAPB) share physiological characteristics with chemoheterotrophs and represent an important group associated with bacteriochlorophyll-dependent phototrophy in the environment. Here, characterization and evolutionary analyses were conducted for 13 bacterial strains that contained...
Research Article | Host-Microbe BiologyTranscriptome Profiling Analysis of Bovine Vaginal Epithelial Cell Response to an Isolated Lactobacillus StrainBovine bacterial vaginitis causes infertility, abortion, and postpartum uterine diseases, causing serious economic loss to the dairy industry. The large-scale use of antibiotics destroys normal genital tract flora and hinders the defense mechanisms of the host. Recent research suggests that lactobacilli present in the vaginal microflora of healthy cows constitute the primary microbiological barrier to infection by genital pathogens,...
Research Article | Applied and Environmental ScienceRandomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow CytometryA major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are...
Research Article | Molecular Biology and PhysiologyComplex Responses to Hydrogen Peroxide and Hypochlorous Acid by the Probiotic Bacterium Lactobacillus reuteriReactive oxidants, including hydrogen peroxide and hypochlorous acid, are antimicrobial compounds produced by the immune system during inflammation. Little is known, however, about how many important types of bacteria present in the human microbiome respond to these oxidants, especially commensal and other health-associated species. We have now mapped the stress response to both H2O2 and HOCl in the intestinal...
Research Article | Clinical Science and EpidemiologyIdentification of Initial Colonizing Bacteria in Dental Plaques from Young Adults Using Full-Length 16S rRNA Gene SequencingSelective attachment of salivary bacteria to the tooth surface is an initial and repetitive phase in dental plaque development. We employed full-length 16S rRNA gene sequence analysis with a high taxonomic resolution using a third-generation sequencer, PacBio Sequel, to determine the bacterial composition during early plaque formation in 74 young adults accurately and in detail. The results revealed 21 bacterial taxa primarily involved...
Research Article | Host-Microbe BiologyGut Microbiota Has a Widespread and Modifiable Effect on Host Gene RegulationThe composition of the gut microbiome has been associated with various aspects of human health, but the mechanism of this interaction is still unclear. We utilized a cellular system to characterize the effect of the microbiome on human gene expression. We showed that some of these changes in expression may be mediated by changes in chromatin accessibility. Furthermore, we validate the role of a specific microbe and show that changes in...