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Advances in the biology of Actinomycetes

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Advances in the biology of Actinomycetes
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The Actinomycetota are amongst the most diverse bacterial phyla with representatives found globally in a wide range of ecological niches. To reflect this biological diversity, the 20th International Symposium on the Biology of Actinomycetes brings together state-of-the-art science on the biology of these remarkable organisms. To celebrate the symposium, we are creating a cross-journal collection of articles within the Microbiology Society suite of journals to reflect the diversity of subjects covered in the symposium from growth and development, phylogenomics and taxonomy, synthetic biology and genetics, genomics, regulation, natural product biosynthesis and discovery, metabolism, industrial applications of Actinomycetes and biotechnology, Actinomycete interactions and ecology.

This cross-journal collection will feature new primary research, opinion pieces, and review articles arising from the “20th International Symposium on the Biology of Actinomycetes” meeting held in Egmond aan Zee, the Netherlands, 15-19 June 2025.

The collection is also open for new submissions from all researchers working across the breadth of Actinomycetes research. The collection is open for submissions across Microbiology, Microbial Genomics, Journal of Medical Microbiology, Access Microbiology and International Journal of Systematic and Evolutionary Microbiology. Please indicate within your submission that it is intended for the collection.

Guest Editors: Paul Hoskisson (University of Strathclyde, UK), Francisco Barona-Gómez (Leiden University, Netherlands), Katherine Duncan (University of Newcastle, UK), Lorena Fernández-Martínez (University of Glasgow, UK,) Matt Hutchings (John Innes Centre, UK), John Munnoch (University of Strathclyde, UK), Martha Trujillo (University of Salamanca, Spain)

Deadline for submissions: 31st December 2025

Journals submission links:

Image credit: Paul Hoskisson

Collection Contents

4 results

    • An integrated multi-omic approach for discovery and dereplication of bioactive microbial natural products

      Soil bacteria are a major source of clinically useful antibiotics, yet the majority of soil-dwelling micro-organisms remain uncultivable by standard laboratory methods. To access this untapped microbial diversity, we employed microbial diffusion chambers to isolate bacteria from ten Australian soil samples. A total of 1,218 bacterial isolates were recovered, representing a diverse collection spanning 61 genera from 32 families, covering the major known phyla of soil bacteria. Antibiotic activity screening revealed that 16% of isolates inhibited the growth of at least 1 of or , with 120 isolates displaying activity against multidrug-resistant pathogens including methicillin-resistant and vancomycin-resistant . Mass spectrometry-based dereplication using GNPS identified known antibiotics in 33% of bioactive strains, including actinomycin D, nonactins and valinomycin. Genomic analysis confirmed the presence of corresponding biosynthetic gene clusters, while targeted analysis of selected strains uncovered production of additional antibiotics such as nigericin and streptothricin that were not initially detected by MS. Our results demonstrate that diffusion chambers enhance bacterial recovery from soil and show the benefits of a combined pipeline including bioactivity screening, MS and genomics for effective antibiotic dereplication and discovery.

    • Biodiscovery of through metabolo-genomics reveals functional diversity across contrasting Mexican ecosystems

      Discovery of novel bioactive natural products from has decreased, motivating the exploration of rare ecosystems. In this work, we integrated genomics and untargeted metabolomics to profile the biosynthetic capacity of and strains isolated from two contrasting, Ramsar-listed Mexican biomes with well-defined ecological features: Cuatro Ciénegas, a semi-arid, oligotrophic karst basin with high microbial endemism, and Calakmul, a tropical rainforest characterized by high biodiversity, seasonal wetlands and limestone-derived alkaline soils. We hypothesized that bacteria isolated from contrasting environments would encode for novel and distinctive subsets of secondary metabolites. Using different metabolo-genomic approaches, a diverse collection of and strains was identified, including several potentially novel species. Genome mining revealed a large repertoire of biosynthetic gene clusters (BGCs), many without matches to known metabolites, while molecular networking and dereplication (GNPS, SNAP-MS) exposed extensive chemical diversity within the isolates. Targeted synteny/ortholog analyses (CORASON) linked subsets of metabolites to BGCs, confirming actinomycin and collismycin and identifying komodoquinone-, nocardiopsistin- and rubiginone-like clusters. Notably, bioactivity assays of crude extracts demonstrated effective antifungal effects against SC5314 biofilms and planktonic growth, suggesting their potential therapeutic use. These findings reveal a significant untapped chemical space encoded by from Ramsar sites, while reinforcing the need for improved tools to connect genomic and metabolomic data for natural product discovery.

    • Enhanced prediction of expression control in bacterial biosynthetic gene clusters via genomic and functional data integration

      Accurate identification of transcription factor binding sites (TFBSs) is fundamental to understanding gene regulation. Traditional position weight matrix (PWM) motif-based methods scan genomes to predict potential TFBSs based on sequence similarity. However, these approaches struggle to detect degenerate or low-affinity sites, which are common in bacterial biosynthetic gene clusters (BGCs). BGCs, which encode proteins and enzymes for production, export, resistance and regulation of specialized bioactive compounds, are typically regulated by multiple transcription factors acting on weakly conserved binding sites. This complexity and regulatory specificity limit the effectiveness of standard motif-scanning tools, impeding efforts to activate silent cryptic clusters and discover novel natural products. To overcome these limitations, we developed COnditions for Microbial Metabolite Activated Transcription (COMMBAT), a scoring method designed to improve TFBS prediction in BGCs. COMMBAT integrates two complementary components: an , derived from PWM-based motif matching, and a , which incorporates both the genomic context () and gene function () within the transcriptional unit associated with the TFBS. These components are normalized and combined to generate a final that more accurately reflects biological relevance, prioritizing TFBSs neighbouring promoter regions and regulating functionally important BGC genes (such as regulatory and core biosynthetic genes). Evaluations demonstrate that COMMBAT substantially outperforms sequence-only methods in identifying already experimentally validated TFBS, offering a powerful tool to accelerate the discovery of transcriptional elicitors of microbial natural product biosynthesis. The COMMBAT website is available at

    • Assessing the effect of temperature on metabolite production

      Rare actinomycetes are increasingly recognised as a valuable yet underexplored source of bioactive compounds with significant biomedical potential. While it is well established that bacteria have evolved adaptive mechanisms to withstand environmental stressors, such as variations in temperature, salinity or pH, our understanding of how these abiotic parameters influence bacterial metabolism remains limited. This has important implications not only for laboratory cultivation but also for predicting microbial behaviour in natural ecosystems. In this study, we investigated the effect of temperature on specialized metabolite production by the genus . Seven strains isolated from marine sediments in three regions – Scotland, the sub-Arctic and Antarctica – were cultured at 20, 25 and 30 °C. Strain-specific growth curves were generated to normalize metabolite extraction at equivalent growth stages, resulting in a total of 54 metabolite extracts. Liquid chromatography-high-resolution mass spectrometry analysis combined with molecular networking revealed that lower cultivation temperatures reduced bacterial biomass and delayed the onset of the stationary phase, and strain KRD197 exhibited temperature shifts in metabolism that were associated with alterations in carbohydrate and fatty acid metabolism, potentially linked to osmotic regulation and cell membrane adaptation. These findings highlight the impact of temperature on -specialized metabolism and support the potential of rare actinomycetes from extreme environments for expanding chemistry from these understudied genera.

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