Latest Articles
Research Article | Therapeutics and PreventionIdentification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community AssemblyAntibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C...
Research Article | Molecular Biology and PhysiologyRegulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial CommunityMicroorganisms in the natural world are found in communities, communicating and interacting with each other; therefore, it is essential that microbial regulatory mechanisms, such as gene regulation affected by small RNAs (sRNAs), be investigated at the community level. This work demonstrates that metatranscriptomic field experiments can link environmental variation with changes in RNA pools and have the potential to provide new insights...
Research Article | Ecological and Evolutionary ScienceAdaptation of Lactobacillus plantarum to Ampicillin Involves Mechanisms That Maintain Protein HomeostasisAntibiotic resistance acquired by adaptation to certain antibiotics has led to growing public concerns. Here, a long-term evolution experiment was used together with proteomic analysis to identify genes/proteins responsible for the adaptive phenotype. This work has provided novel insights into the biosafety of new probiotics with high tolerance to antibiotics.
Research Article | Ecological and Evolutionary ScienceHorizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasilienseIn this study, we examine the impact of transcriptional network rearrangements driven by horizontal gene acquisition in PhoP and SlyA regulons using as a case study a phytopathosystem comprised of potato tubers and the soft-rot pathogen Pectobacterium brasiliense 1692 (Pb1692).
Research Article | Novel Systems Biology TechniquesTransfer Learning for Toxoplasma gondii RecognitionToxoplasma gondii, one of the world’s most common parasites, can infect all types of warm-blooded animals, including one-third of the world’s human population. Artificial intelligence (AI) could provide accurate and rapid diagnosis in fighting Toxoplasma. So far, none of the previously reported deep learning methods have attempted to explore the advantages of...
Research Article | Therapeutics and PreventionEffects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In VitroPatients with gastrointestinal disorders often exhibit derangements in their gut microbiota, which can exacerbate their symptoms. Replenishing these ecosystems with beneficial bacteria through fecal microbiota transplantation is thus a proposedly useful therapeutic; however, clinical success has varied, necessitating research into strategies to improve outcomes. Antibiotic pretreatment has been suggested as one such approach, but...
Editor's Pick Research Article | Therapeutics and PreventionStable Neutralization of a Virulence Factor in Bacteria Using Temperate Phage in the Mammalian GutWith the increasing frequency of antibiotic resistance, it is critical to explore new therapeutic strategies for treating bacterial infections. Here, we use a temperate phage, i.e., one that integrates itself into the bacterial genome, to neutralize the expression of a virulence factor by modifying bacterial function at the genetic level. We show that Shiga toxin production can be significantly reduced in vitro and in the...
Research Article | Novel Systems Biology TechniquesExtreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting TranslationBacterial persistence is a fascinating phenomenon in which a small subpopulation of bacteria becomes phenotypically tolerant to lethal antibiotic exposure. There is growing evidence that populations of bacteria in chronic clinical infections develop a hyperpersistent phenotype, enabling a substantially larger subpopulation to survive repeated antibiotic treatment. The mechanisms of persistence and modes of increasing persistence rates...
Research Article | Clinical Science and EpidemiologyPrediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural NetworksMachine learning is a proven method to predict AMR; however, the performance of any machine learning model depends on the quality of the input data. Therefore, we evaluated different methods of representing information about mutations as well as mobilizable genes, so that the information can serve as input for a robust model. We combined data from multiple bacterial species in order to develop species-independent machine learning models...
Research Article | Molecular Biology and PhysiologyA Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in MethylobacterHere, we describe a novel and complex hypoxia response system in a methanotrophic bacterium that involves modules of central carbon metabolism, denitrification, quorum sensing, and a secondary metabolite, tundrenone. This intricate stress response system, so far unique to Methylobacter species, may be responsible for the persistence and activity of these species across gradients of dioxygen tensions and for the cosmopolitan...