BMC Genomic Data is calling for submissions to our Collection, Genomics of antibiotic producing microorganisms. The study of antibiotic-producing microorganisms, including bacteria and fungi, has been a cornerstone of biomedical research, leading to the discovery of numerous natural products with bactericidal activity. Understanding the genomics of these microorganisms is key to unraveling the molecular mechanisms underlying antibiotic production, secondary metabolism, and the evolution of antibiotic resistance. This Collection aims to gather research that explores the genomics of antibiotic-producing microorganisms, including the identification of antibiotic biosynthesis gene clusters, the role of secondary metabolism, and the application of synthetic biology in harnessing the potential of these microorganisms for drug discovery.

The growing availability of microbial genome sequences, coupled with advancements in sequencing technologies and annotation tools, has expanded the reservoir of genomic data available, providing unprecedented opportunities to mine for new antibiotic-producing gene clusters or microorganisms. For instance, the recent identification of the Acyldepsipeptide (ADEP) class, which targets bacterial protease ClpP, underscores the bactericidal potential of newly characterized natural products. Such discoveries highlight the importance of integrating genomic data with functional studies to understand the regulatory mechanisms governing secondary metabolism and explore engineering strategies for the production of novel antibiotics.

Advancing our collective understanding in this area is essential to address the growing need for alternative solutions in response to the increasing threat posed by multi-resistant organisms such as MRSA (Methicillin-resistant Staphylococcus aureus) and XDR-TB (Extensively Drug-Resistant Mycobacterium tuberculosis). By leveraging advances in genomic sequencing and bioinformatics, researchers can identify previously unknown antibiotic biosynthesis gene clusters, engineer microorganisms for enhanced natural product biosynthesis, and apply synthetic biology tools to develop novel antimicrobial compounds.

The current focus on genomics has greatly enhanced our ability to study natural products and antibiotic biosynthesis gene clusters. The integration of large-scale genomic data with functional analyses enables researchers to uncover biosynthetic pathways and better understand the molecular mechanisms behind antibiotic production. Advances in sequencing technologies and genome mining strategies are opening new possibilities for the discovery of novel antimicrobial agents.

These genomic insights enable us to isolate new gene clusters and target the pathways involved in antibiotic production. Mining microbial genomes from underexplored environments, such as deep-sea ecosystems and unique soil habitats, has significantly expanded the scope for discovering previously unrecognized organisms capable of producing novel compounds. Moreover, combining genome mining with synthetic biology approaches has facilitated the reconstruction and modification of antibiotic biosynthetic pathways, pushing the boundaries of natural product discovery.

For decades, researchers have focused on traditional antibiotic-producing microorganisms, primarily within well-known groups like Actinobacteria and fungi. However, recent strategies have shifted toward exploring more diverse ecological niches, sequencing an increasing variety of microbial genomes, and using bioinformatics tools to predict and validate the function of new biosynthetic gene clusters. This broader approach, combined with innovative synthetic biology techniques, aims to boost the discovery of new antimicrobial agents with clinical relevance.

We welcome submissions that address a wide range of topics related to the genomics of antibiotic-producing microorganisms, including but not limited to:

Bacteria and fungi as antibiotic producers

Natural products and secondary metabolism

Antibiotic biosynthesis gene clusters

Synthetic biology in antibiotic discovery

Data notes of newly sequenced genomes

Mining underexplored environments for novel microorganisms and antibiotics

Evolutionary analysis of antibiotic resistance mechanisms

Functional genomics and transcriptomics to uncover regulatory networks in secondary metabolism

All manuscripts submitted to this journal, including those submitted to collections and special issues, are assessed in line with our editorial policies and the journal’s peer-review process. Reviewers and editors are required to declare competing interests and can be excluded from the peer review process if a competing interest exists.

BMC Genomic Data is calling for submission to our Collection, Bacterial data notes. Bacterial genomic data plays a crucial role in advancing our understanding of microbial diversity, evolution, and pathogenicity. As we explore the complexity of the genetic makeup of bacteria, we uncover insights that inform public health initiatives, environmental monitoring, and biotechnological applications. The wealth of data generated through high-throughput sequencing technologies presents both opportunities and challenges, necessitating standardized methods for data sharing and interpretation. This Collection seeks to provide a platform for sharing valuable bacterial genomic data notes that contribute to the collective knowledge in this rapidly evolving field.

The significance of bacterial genomic data cannot be overstated in the context of global health, particularly in addressing antibiotic resistance (AMR) and the potential of biotechnology, especially through genome editing technologies like CRISPR-Cas9, which are derived from bacterial systems. Recent advances in genomics have led to breakthroughs in identifying antibiotic resistance genes, tracking infectious disease outbreaks, and exploring bacteria for bioremediation and bioengineering. For example, whole-genome sequencing has uncovered new resistance mechanisms in E. coli and Klebsiella pneumoniae, while CRISPR-based tools allow rapid detection of resistance genes like blaNDM-1. Genomic sequencing has also been instrumental in tracking the spread of antibiotic-resistant Mycobacterium tuberculosis strains. In bioremediation, bacteria like Pseudomonas putida are being harnessed to degrade pollutants, and synthetic biology is enabling the production of biofuels and bioplastics through engineered bacteria, such as genetically modified E. coli strains or other bacterial species that have been engineered to mimic E. coli's characteristics, making them more efficient in industrial processes. Moreover, we welcome contributions that explore bacterial pathogens of veterinary relevance within a One Health framework, including genomic investigations of zoonotic potential, antimicrobial resistance surveillance across human–animal–environment interfaces, and genome-based diagnostic innovations in veterinary microbiology. Data notes focusing on comparative genomics of emerging veterinary pathogens, mobile genetic elements facilitating host adaptation, or high-throughput approaches for resistance gene detection in clinical and environmental settings are also encouraged.

The rapid dissemination of bacterial genomes through data notes is important for quickly sharing information and thus enabling collaboration. By publishing unpolished sequences and facilitating fast data exchange, these notes help create a more connected research community. Looking ahead, continued documentation of bacterial genomic data may lead to advancements in understanding genetic mechanisms behind bacterial resilience, developing new treatments, and responding to emerging infectious diseases. Advances in machine learning and artificial intelligence could also refine how we analyze the data, offering new perspectives and insights into microbial ecology and evolution.

We invite contributions that examine a wide range of topics relating to bacterial data notes, including but not limited to:

Novel methods for bacterial genome annotation

New bacterial genomes

Comparative genomics of pathogenic and non-pathogenic strains

Bacterial responses to environmental stressors

Characterization of antibiotic resistance genes

Identification and functional analysis of virulence factors in pathogens

Genomic insights into bacterial symbiosis and mutualism

Metagenomic approaches to studying bacterial communities in diverse environments

Advances in synthetic biology for bacterial applications in biotechnology

Phage-bacteria interactions and their genomic basis

Plasmidome and mobile genetic elements

Bacterial epigenomics and gene regulation

Genomics-informed approaches in veterinary microbiology and infectious disease surveillance

One Health-focused bacterial genome data integrating animal, human, and environmental sources

Genomic characterization of emerging zoonotic and veterinary pathogens

Data notes on antimicrobial resistance genes in veterinary clinical isolates

Whole-genome based taxonomic re-evaluation of bacterial species and subspecies

Genomic delineation and proposal of novel bacterial taxa

Phylogenomic approaches to resolve taxonomic ambiguities among closely related bacterial strains

All manuscripts submitted to this journal, including those submitted to collections and special issues, are assessed in line with our editorial policies and the journal’s peer-review process. Reviewers and editors are required to declare competing interests and can be excluded from the peer review process if a competing interest exists.