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Aims and 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

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)

Metagenomics and Microbiomes

  • Amplicon sequencing, metagenomics, metatranscriptomics, and single-cell genomics
  • Host, plant and environmental-associated microbiomes, commensal communities, microbiome disturbances and microbiome-targeting therapies
  • Technological innovations from method development to cutting-edge computational pipelines
  • 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 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

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Indexing and metrics

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.

Visit our Impact and metrics page to learn more about the metrics for Microbial Genomics.

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Information for authors

Preparing a submission? Check out our new submission checklist for a guide to what you will need.

For more information about submitting to Microbial Genomics, please see our Article typesPrepare an article and Submission and peer review pages. 

Microbial Genomics is a Gold Open Access journal. Microbiology Society journals offer two routes for Gold Open Access publishing: Publish and Read and Article Processing Charges. More information can be found on our Open Access costs page.

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Contact us

Email the journal Editorial Office at [email protected]

For the sales and marketing team, please contact [email protected]

Social media:

Twitter – @MicrobioSoc

Facebook – www.facebook.com/MicrobiologySociety

LinkedIn – www.linkedin.com/company/microbiology-society

By phone: 

Call +44 (0)20 3034 4870

By post or in person:

Microbiology Society

14–16 Meredith Street



United Kingdom

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