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Microbial Genomics – Scope

Published by the Microbiology Society, Microbial Genomics is a Gold Open Access, peer-reviewed journal publishing cutting edge, pioneering research into genomic approaches to microbiology, fully supported by Open Data and innovative collaborative services. We cover topics including, but not limited to:

Functional Genomics and Microbe–Niche Interactions

  • Studies of in situ function, gene regulation and expression
  • Gene interactions and the functional effects of genomic variation
  • Understanding gene and genome function in the natural environment

Populations, Pathogens and Epidemiology

  • Microbial population genomics and ecology, including environments, interactions, transmission, and the generation and maintenance of diversity
  • Population structure and phylogeography
  • Outbreaks and epidemiological investigations
  • Genomics of pathogen emergence, persistence, transmission and virulence (including antimicrobial resistance)

Microbial Communities

  • Metagenomic, marker gene and transcriptome-based studies
  • Host and environmental-associated microbiomes, commensal communities, dysbiosis and microbial therapy 
  • Ecosystems, community and niche interactions and the dynamics of change
  • Microbial genomics and diversity of natural habitats (terrestrial and aquatic)

Evolution and Responses to Interventions

  • The genome evolution of complex traits
  • Evolutionary mechanisms of speciation, adaptation, and genomic diversity.
  • Timescale of molecular evolution 
  • Genomics and experimental evolution
  • Responses to human interventions (e.g. clinical, agricultural)

Genomic Methodologies

  • New models and computational methods including sequencing tools, algorithms and protocols
  • Theoretical and practical advances in bioinformatics, including sequence analysis, alignment, phylogenetics and understanding the basis for phenotypic traits 
  • Novel ‘-omics’ approaches investigating microbes from single-cells to microbial communities

We welcome articles showing novel insights, exciting new applications, or innovative approaches to analysis using genomic data, as well as articles developing our understanding of microbial genomics, from large, long-term studies on microbial evolution and epidemiology to studies that have immediate clinical or environmental relevance. We welcome a range of article types including Research Articles, Reviews and Mini Reviews, and Methods; please see the guidance on article types and structures for more information. We are particularly keen to encourage:

  • BioResource articles: research that is recognised as a significant resource with potential long-term impact.
  • Outbreak reports: genomic investigations of disease outbreaks (viral, fungal and bacterial)
  • Genomics of archaea and fungi
  • Host-microbiota interactions, with a particular emphasis on studies where sequence data provides real biological insights into the role that microbial communities play in host health.
  • Experimental evolution studies that focus on evolutionary responses to antimicrobial stresses, as well as those with longitudinal genomic data sets examining evolution in response to treatment and host-associated stresses.
  • High-throughput imaging and metabolomics analysis of host-microbe interactions and influences in both directions between microbe and host.
  • New methods of microbial sequence analysis that can scale to large datasets including thousands of genomes
  • Studies in which genomic variation is robustly linked with important biological phenotypes or consequences

Microbial Genomics is indexed in Medline (PubMed), PubMed Central, Web of Science (Science Citation Index Expanded, Biological Abstracts and BIOSIS Previews), and Scopus, as well as on Google Scholar and ScienceOpen, ensuring maximum discoverability of your research.

Please contact [email protected] with any queries about Microbial Genomics. All pre-submission enquiries are reviewed by the Editor-in-Chief without reference to previously submitted articles.

For more information about Microbial Genomics, please see our Information for authors or our Open Access rates page for information on the article processing charges.


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