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Bacteria produce antibacterials that drive competition and regulate community composition. While diverse examples have been found, few families of antibacterial agents appear to be widespread across phylogenetically divergent bacteria. Here, we show that what appeared to be a limited, niche class of Gram-negative bacteriocins, called class II microcins, is in fact a highly abundant, sequence- and function-diverse class of secreted bacteriocins. Based on systematic investigations in the Enterobacteriaceae and gut microbiomes, we demonstrate that class II microcins encompass diverse sequence space, bacterial strains of origin, spectra of activity, and mechanisms of action. Importantly, we show microcins discovered here are active against pathogenic E. coli during mouse gut colonization, supporting important roles for these unrecognized antibacterials in vivo. Our study reveals the overlooked abundance and diversity of microcins found dispersed throughout Bacteria and opens opportunities to uncover and exploit mechanisms of competition to modulate microbial communities.
Pubmed ID: 40595659
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Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.
View all literature mentionsCommercial organization for research and development genomics services and technical support to researchers.
View all literature mentionsCentral repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.
View all literature mentionsSoftware program for phylogenetic analyses of large datasets under maximum likelihood.
View all literature mentionsData repository of bacteriocin natural antimicrobial peptides and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. New bacteriocin submissions are welcome. Various tools have been incorporated for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser. BACTIBASE should be a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE contains calculated or predicted physicochemical properties of 218 bacteriocins produced by both Gram-positive (194) and Gram-negative bacteria (19). They also note the presence of three bacteriocins from the Archaea domain. The database now comprises 31 genera (2009).
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsA commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
View all literature mentionsSoftware package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentionsOpen source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsFull service sequencing core that provides both Sanger and Next Generation Sequencing services, in addition to library prep and quality check services, open access to equipment and training. Works directly with the bioinformatics core who can provide assist in any of your analysis needs to data storage solutions.
View all literature mentionsBiomedical Research Computing Facility as core for Biomedical Research Support. Provides small, centrally managed compute clusters and storage, suitable for local, interactive computing, to biomedical research groups.
View all literature mentionsProteomics and Metabolomics services and collaborative efforts are provided at Biological Mass Spectrometry Facility. We use high resolution Orbitrap mass spectrometers with UPLC at high flow for metabolomics and nanoUPLC for proteomics work. We have Bruker Autoflex for self service MALDI. Our proteomics services are protein ID, quantitation, and modification analysis, with fractionation for deeper coverage and de novo sequencing of mAbs available. We collaborate for customized projects. We have untargeted metabolomics for quantitative or qualitative analysis of extracted metabolites using C18 column.
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