1887

About the journal: Microbial Genomics

Contents

  1. Overview
  2. Journal scope
  3. Subject categories
  4. Article categories
  5. Submitting an article
  6. Contact information

1. Overview

Microbial Genomics is a fully open access, mandatory open data and double-blind peer reviewed journal publishing high-profile original research on archaea, bacteria, microbial eukaryotes and viruses.

Co-Editors-in-Chief:

Professor Nicholas Thomson, Wellcome Trust, Sanger Institute, UK

Professor Stephen Bentley, Wellcome Trust, Sanger Institute, UK

Microbial Genomics at a glance

Key Features:

✔  Fully open access: article processing charges (APCs) currently waived

✔  Mandatory open data policy

✔  Continuous publishing

✔  Microbial Genomics is a double-blind peer review journal

✔  Expert international Editorial Board

✔  All articles published under a default CC-BY-NC 4.0 licence, with optional CC-BY 4.0 available

✔  Pre-print policy

✔  Post-print policy: a six-month embargo

✔  Adheres to COPE guidelines on publishing ethics

✔  Partners with Microreact, a free data visualisation and sharing platform

✔  Microbial Genomics is published by the Microbiology Society, a not-for-profit publisher

✔  Published on a modern journal platform that offers altmetrics and support for multimedia content

Back to contents list


2. Journal scope

Microbial Genomics is a fully open access, open data and peer reviewed journal that publishes high quality, original research on archaea, bacteria, microbial eukaryotes and viruses.

Microbial Genomics welcomes articles that use genomic approaches to understand microbial evolution, population genomics and phylogeography, outbreaks and epidemiological investigations, impact of climate or changing niche, metagenomic and whole transcriptome studies, and bioinformatic analysis covering the breadth of microbiology, from clinically important pathogens to microbial life in diverse ecosystems.

Our aim is to publish articles communicating novel insights gained from using genomic data, exciting new applications and innovative analysis approaches. Publications will be targeted towards a better understanding of subjects ranging from long term and contemporary evolution to insights of immediate clinical and/or environmental relevance.

Examples range from fundamental insights into microbial evolution, host/interactions/adaptation, to new diagnostics and methods to track microbes to advance understanding of the spread and evolution of antimicrobial resistance or the impact of vaccines, and further to inform the development of antimicrobial agents. Other examples include the development of new approaches to industrial microbiology and bioremediation informed by new knowledge of genomics and metagenomics of environmental microbes and their communities. We will seek to include bioinformatics papers that apply existing or novel methods to provide ground-breaking insights or to guide the interpretation of biological characteristics, particularly those where the bioinformatics analysis were key for the conclusions of the paper.

Microbial Genomics is a mandatory open data journal and authors are required to submit supporting data, protocols, and/or bioinformatics programmes and software to relevant depositories. Article processing charges (APCs) are currently waived.

Microbial Genomics is part of the journal catalogue of the Microbiology Society, a registered charity, which returns publication profits into the development of the journal, for fostering research in microbiology and virology, the organisation of international scientific conferences, or for education and outreach purposes.

Back to contents list


3. Subject categories

Microbial Genomics will publish articles under the following subject categories:

1. Microbial evolution and epidemiology

Genomic studies of microbes through the lenses of evolution and epidemiology. Includes: studies of microbial population genetic/genomic structures; phylogeographic and phylodynamic investigations; microbial evolution and adaptation; and genomic investigation of communicable diseases, including outbreak investigations and emerging infectious diseases of humans and non-humans.

1.1 Population genomics

1.2 Phylogeography

1.3 Mechanisms of evolution

1.4 Communicable disease genomics

1.5 Zoonosis/anthroponosis

2. Microbial communities

Studies employing marker gene, full metagenomic or metatranscriptomic data to characterise and understand the structure, function and dynamics of natural communities of microbes. Includes: studies in animal/plant-associated niches, including links between microbial communities and host health; studies of environmental microbial niches such as soil and water; response of microbial communities to perturbations.

2.1 Human

2.2 Environmental

2.3 Other: animals, insects, plants

3. Microbe-niche interactions

Studies where analysis of genomic/transcriptomic/proteomic data is employed to identify genes/proteins that play a specific role in interactions between microbes and their niche. Includes: host-pathogen interactions; persistent mutualism, commensalism and parasitic relationship; adaptation to changing environmental niches; adaptation to changing hosts.

3.1 Mutualism, commensalism and parasitism

3.2 Pathogenesis

3.3 Host adaptation

3.4 Environmental niche adaptation

4. Genomic methodologies

New models and computational methods which enable important biological insight from microbial genome data. Includes: phylogenetic methods; genome analysis tools; models for population and genome evolution; methods for sequence analysis.

4.1 Genome variation detection

4.2 Data clustering methods

4.3 Novel phylogenetic methods

4.4 Genome-phenotype association

5. Responses to human interventions

Genomic studies of microbial responses to human interventions including clinical interventions such as antibiotic therapy, vaccines or infection control measures; as well as agriculture and environmental changes such as climate change or pollution. Microbial responses may include functional responses or adaptive evolution; however, evolutionary studies that do not measure interventions directly may be more suited to the "Microbial Evolution and epidemiology" category.

5.1 Agriculture

5.2 Antibiotics

5.3 Vaccines

5.4 Climate change

6. Systems microbiology

Large-scale analysis of microbial genome collections; comparative analysis of model organisms and metagenomics datasets; transcriptomics and proteomics, gene and protein interaction networks, systems microbiology; high-throughput annotation, metabolic reconstruction and pathway inference; ancestral state reconstruction, horizontal gene transfer and pangenomes; big-data approaches, databases and analysis systems.

6.1 Large-scale comparative genomics

6.2 Transcriptomics, proteomics, networks

6.3 Genome annotation, metabolic reconstructions

6.4 Pangenome analysis, big-data approaches

Back to contents list


4. Article categories

Microbial Genomics will publish the following articles:

Article category Description Structure (for guidance only) Submission template
Research Articles The study, results, and interpretations of original research
Re-analysis of published data, including meta-analyses and methods bringing together multiple datasets would also be considered, provided that novel insights are produced
6000 words max
8 figures and tables max
No limit on references or supplementary data
Author statements – funding information, acknowledgements, conflicts of interest, ethical statements
LINK
Reviews Insights into a specific research area that has seen significant development or progress; including evaluation, critical assessment, and perspectives on current topics within microbial genomics 6000 words max
8 figures and tables max
No limit on references or supplementary data
Author statements – funding information, acknowledgements, conflicts of interest, ethical statements
LINK
Methods Applying and validating novel experimental approaches or computational methods or procedures, highlighting the practical application to real data and the novel contribution / advance provided by the method. Also includes new approaches to data visualisation 2,000 words max.
4 figures and tables max
No limit on references or supplementary data
Author statements – funding information, acknowledgements, conflicts of interest, ethical statements
LINK
Short Paper Providing the flexibility to write concise reports of importance to the field of microbiology that highlight the power and resolution provided by 'omics' approaches. For example, small outbreak investigations,the creation of genomics resources (including new resources linking data with samples and improved reference data) of broad interest/utility, genomics initiatives, genomic reanalysis of established concepts and novel non-genomicdata (e.g. electron micrographs) which support earlier genomic-driven hypotheses. Rapid communications of highly topical matters such as infectious disease outbreak, drug development breakthrough and environmental/climate management are also encouraged 500-2000 words max
8 figures and tables max
No limit on references or supplementary data
Author statements – funding information, acknowledgements, conflicts of interest, ethical statements
LINK
Commentary Commentary is a very flexible format which does not usually contain
primary research data. It could be a comment, a response or rebuttal to be published with another article, or it may be published in direct response to an article already published. Commentaries will be mostly solicited, but may be submitted to Microbial Genomics independently
Up to 1000 words
Title should read ‘Response to: …’ or ‘Commentary: Title of Original Article’
There should be no abstract in this article type
1 figure or table
10 references max
Commentaries should cite the article on which it comments. Author statements – funding information, acknowledgements, conflicts of interest, ethical statements
LINK
BioResource Designed to highlight research that generates analyses and presents work that is recognised by a broad section of the research community as a significant BioResource with potential long-term impact
The principle focus of this format is an accurate description of the data and samples, with emphasis on its significance and accessibility. Data must be presented in a format and manner that maximises its utility to the research community for the purposes outlined in the article
6000 words max
8 figures and tables max
No limit on references or supplementary data
Author statements – funding information, acknowledgements, conflicts of interest, ethical statements
LINK
Outbreak Report All Outbreak Reports should provide a description of the outbreak’s basic epidemiology (case counts, demographics, etc); the genomics approach taken; results and an ‘Outcome’ box summarising the take-home points arising from the investigation, whether they be epidemiological or methodological. Analysis methods must be fully documented, including all parameters and reference sequences used (source code available or specify full details of commercial package) 6000 words max
8 figures and tables max
No limit on references or supplementary data.
Author statements – funding information, acknowledgements, conflicts of interest, ethical statements
LINK

It is not a conflict of interest to be an Editor as well as an author, as long as the Editor is not involved in any component of the peer review process.

Back to contents list


5. Submit an article

All articles must be submitted through our Editorial Manager online submission site using the relevant template, and accompanied by a cover letter summarising your reasons for submitting the article to the journal and how it meets the Aims and Scope of the journal.

Please visit the Submit an article page for further information including the pre-submission checklist. More detailed advice on the formatting of figures, tables and reference lists can be found in the Information for authors.

Back to contents list


6. Contact Information

Queries or comments about online submission should be sent via email from the submission site.

General enquiries should be sent to the Editorial Office:

Microbial Genomics, Editorial Office, Microbiology Society, Charles Darwin House, 12 Roger Street, London, WC1N 2JU

Tel: +44 (0)20 7685 2543 Email: mgen@microbiologysociety.org

Back to contents list


This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error