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Publishing Fundamentals




Our “Publishing Fundamentals” are targeted to an early career audience and to those who want to better understand how academic publishing works and get involved with our journals as authors, editors or reviewers.

This page is the first step in our mission to assist you in your journey through publishing. Soon we will be expanding this with further resources and workshops focusing on specific topics to provide you with the tools to confidently navigate the publishing process and understand how we can work together to produce research to advance the understanding of microbiology. If you would like to suggest topics for our future resources, please fill in this form.


The publishing process can be broken down into different stages as shown in the diagram above. As an author, you will be responsible for the stages in green, that is conducting the research and writing and revising your paper. The stages in dark blue are a collaboration between the authors and the Society staff and you can find more details about those stages in the How to prepare your submission and Your article has been accepted, now what? How to promote your article sections of this page. The stages in light blue are the responsibility of the Society staff alongside our editors and reviewers.

When you submit your manuscript to one of our journals, it undergoes technical and ethics checks to ensure that it is compliant with our policies. Once these are complete, the manuscript is assigned to an editor whose role is to assess whether it is suitable for further consideration in the journal by ensuring it is in scope, scientifically sound and reasonably interesting.

If the editor is satisfied that your manuscript meets the journal’s criteria, they will invite peer reviewers to evaluate its scientific rigour and validity. Peer reviewers are experts in the field or the techniques you have utilised and they will use their expertise to consider if the science is robust and well communicated. Peer reviewers play a critical role in ensuring that high-quality science is published, allowing us to further advance the understanding of microbiology. More information around peer review can be found here: https://www.microbiologyresearch.org/information-for-reviewers.

Once the peer reviewers have submitted their comments, the editor will assess the manuscript once more taking into account the peer reviewers’ feedback and they will make a decision based on scientific soundness, appropriateness of method, analyses, validity of results as well as the novelty of your findings.

Once a manuscript has been accepted, it will go into production, a process by which the accepted manuscript is typeset and turned into a final html and pdf versions for publication.

Tip: Upon publication, we strongly encourage you to share your work with others and we will help to promote your paper to the wider community to increase its reach and advance the understanding of microbiology.

When preparing to submit your manuscript it is important that you ensure it is ready to be peer viewed. For example, we require that manuscripts are structured in a certain way and contain a conflict of interest statement and ethical approval. Our guidelines on how to prepare an article include a checklist to help you with this, and our Publishing Operations team will ensure all is in order by performing a number of checks before assigning your submission to an editor. This includes chekcing that the research is broadly in scope and satisfies any ethical and data requirements mandated by the journal you are submitting to.

If a manuscript does not meet the minimum criteria set out by the journal it will be returned by our office. We understand that this step may seem tedious, but these criteria are there to ensure that research can be adequately assessed by editors and reviewers. This will help speed up the process at the peer review and publication stages.

Most of the information that our editorial office requires will be captured by an online submission form, which is specific to the journal you are submitting to. We also ask you to upload a cover letter outlining your work and your reason for submitting to the journal, as well as any information you think would be important for journal staff and editors

Tip: Our Publishing Operations Editors are there to assist you from submission to publication: if you have questions or are unsure about any of these steps, feel free to email us at [email protected] and we will be happy to advise you.

Titles are the very first things editors, reviewers and readers will come across. Therefore, it is important that your title accurately summarise the key findings of your study while also being concise. Where possible, including appropriate keywords in your title will make your article more discoverable and will help your work reach the right audience and increase its dissemination. Use abbreviations sparingly and only for well-established and widely used abbreviations and acronyms.

Editors may recommend change to your title to better fit the style of the journal, so we suggest looking up some of the most recently published articles in your chosen journal to see if your title aligns with their style.

Tip: We suggest that you avoid using puns or making your title “funny”: while it could be attention-grabbing to the public, it is less likely to reach the correct audience for your work.

Requirements for abstracts vary across journals, though word counts tend to be 150-300 words. Abstracts should provide a concise, self-contained summary of your work, without abbreviations or references.

Your introductory sentences should give the wider background to your research which should be followed by a couple of sentences outlining your goal or aim in carrying out your study and a top-level summary of the methods used. Then, you should provide an overview your results and findings, briefly discussing any future research or implications for the field. Finally, remember that references should not be included in the abstract and that you should define any abbreviations you are introducing.

You should also keep in mind that journals may have specific requirement or optional features. For example, the Journal of Medical Microbiology requires structured abstracts (more information on what this means can be found here). Microbiology encourages the use of graphical abstracts, which are author-created diagrams summarising your research and which are becoming increasingly popular in scientific journals. In order to speed up the process and avoid having the manuscript sent back to you for changes, make sure you check our Information for authors page.

Tip: Use the same keywords in your initial submission form to the journal, the title and the abstract to increase discoverability of your work.

The first thing to consider is scope. Editors will reject out-of-scope papers before peer review and by making sure your work is within scope before submitting. Identifying the most suitable journal for your manuscript will help you avoid submitting to a less appropriate journal, being rejected and having to start again. If you aren’t sure, get in touch with the journal office and we will be happy to help. All journals have an ‘About’ page detailing their scope. Reading this will help you determine if your work is a good fit. Here is a top-line overview of the journals' scopes:

Access Microbiology 

An open research platform publishing sound science across the breadth of microbiology, including replication studies, negative results and case reports 

International Journal of Systematic and Evolutionary Microbiology 

The official publication of the ICSP and the BAM division of the IUMS. The official journal of record for the International Committee on Systematics of Prokaryotes. 

Journal of General Virology 

The journal at the forefront of virology research and home to ICTV Virus Taxonomy Profiles. 

Journal of Medical Microbiology 

The go-to interdisciplinary journal for medical, dental and veterinary microbiology at the bench and in the clinic. 

Microbial Genomics 

The Open Access journal of choice for pioneering research in genomics, fully supported by innovative, collaborative services. 

Microbiology 

The home of high-quality research from across the breadth of microbiology since 1947. 


Tip: If you are not sure about which is the most appropriate journals for your research, don’t hesitate to ask us at [email protected].

With the rise in the number of predatory journals and dubious ethical and peer review practices in recent years, it is more important than ever to ensure your research is published in reputable and ethical journals with rigorous peer review practices.

You need to be confident your chosen journal has a suitable profile among your peers and consider, for example, if your colleagues and network publish in or read that journal. When you are thinking about the profile of a journal, it’s easy to just look for the highest impact factor you can achieve. However, a good quality community journal in your specialist area might often be a more appropriate home for your manuscript and we recommend that you consider a variety of metrics collectively instead. The Microbiology Society is a signatory of the Declaration on Research Assessment (DORA) which has been signed by hundreds of institutions, funders, societies, and publishers worldwide. This is a commitment to use a variety of metrics to measure the performance of our portfolio not just the impact factor.

Tip: You can read more about our ethics policies here: https://www.microbiologyresearch.org/ethics-policies

Publishing Open Access simply means that anyone with access to the internet, located anywhere in the world, is able to view, read and download your article free of charge.

Traditionally, journals operated on a subscription basis meaning librarians at institutions take out a subscription with a journal or publisher, and pay for access to all the content for those based at the institution. If your institution does not have a subscription, then you are unable to read the published content. This can create difficulties for researchers - for example, you would not be able to access articles relevant to your study if your institution does not have access to that specific journal.

Open Access aims to provide more equitable access to research, allowing individuals, the public, and those at institutions with less available funding to access published research. This ensures that everyone has equal access to science research, which is particularly pertinent for research that affects human health and research that is publicly funded. In this model, authors pay a fee, also known as an Article Processing Charge (APC), once their manuscript has been accepted in order to finalise their Open Access publication. The cost of this fee to publish will sometimes be incorporated into a grant proposal or covered by institutional funding.

The Microbiology Society is committed to the benefits of Open Access, but recognises that it can create barriers to publication for authors - for example, those without funding to cover the APC fee. In order to foster a truly inclusive publishing environment, the Society offers several ways to assist authors with these fees. Our Publish and Read agreements enabe correspodign authors at institutions that sign up to benefit rom uncapped Open Access publishing across our whole portfolio and unlimited access to the entire archive of Society publications. We also operates a waiver policy based on the Hinari programme. If the corresponding author of an article is based within a country in Group A or B of the HINARI list, their paper is automatically entitled to 100% APC waiver.

Tip: Make sure you check any Open Access policies your institution or funder may have and whether your funder or institution has specific Open Access requirements.

Open data encompasses a wide range of processes and principles, but at its core ensures that all relevant data for an article is freely and immediately available to anyone to reanalyse, reuse and build on. This includes generated and supporting raw data, and images, code or software; essentially, any information that has led to the conclusions presented in the research and that would allow the experimental processes described in the research to be fully reproduced by a reader.

Open data aims to increase reproducibility in the scientific literature and maintain transparency wherever possible. It ensures authors get credit for conducting the research and collecting the data first, and can generate further citations as the datasets are iterated in future work. However, there are concerns and limitations to consider. For example, sharing fully raw data at individual patient level may compromise a patient’s right to anonymity. These considerations should be balanced with the benefits of open data.

The Microbiology Society supports the aims of open data and encourages all authors submitting to any of the journals to make their supporting data fully open by depositing it with recognised and public archiving repositories, such as Figshare, Dryad, Zenodo and CodeOcean. Other methods of making supporting data available include presenting them in the main manuscript or within additional supplementary material, where appropriate. When doing so, it is important to keep in mind that when patients are involved, the data must be anonymised and not compromise patient confidentiality.

Microbial Genomics and Access Microbiology have mandatory open data policies, and authors are required to deposit and provide access to all data related to their submission. Microbial Genomics requires all sequencing data to be deposited and publicly available at submission; all other supporting data can be made privately available at point of submission for peer review, and then must be made publicly available at acceptance. Owing to the preprint stage and nature of the platform, Access Microbiology requires supporting data to be deposited and be publicly available at time of submission.

A preprint is an early version of your manuscript which you can make available online before submitting your work to a journal for publication. The key differences between preprints and published articles is that preprints do not go through editorial assessment or peer review and are simply posted in online repositories by the authors.

Sharing your research with the community as soon as possible can be valuable for your study and for the field; therefore, we encourage authors to post on preprint servers such as bioRxiv prior to submission. Once your paper has been published, make sure that the preprint is updated to indicate a Version of Record has been published by adding a link to the published paper reading '© [name of Author(s), year]. The definitive peer reviewed, edited version of this article is published in [name of Journal, volume, issue, year, DOI]”.

Access Microbiology, operates as an open research platform. When you submit an article for consideration, your manuscript will by default be posted online as a preprint in PDF format with a citable DOI, meaning you can gain credit for your work immediately and start receiving community feedback.

Tip: If you have deposited a preprint of your article in bioRxiv, you will be able to submit it directly to one of our journals from the bioRxiv server. However, if you chose to submit it direclty to us, please ensure to provide a link to the preprint in the submission form.

Open research is the term used to capture the broader movement towards accessibility, transparency, and reproducibility within scientific research. This evolution in the scientific publishing landscape has made it increasingly important for researchers to disseminate their research as quickly as possible whilst still maintaining the high quality ensured by the peer review process. Access Microbiology is what we call an ‘open research platform’ and it provides a new approach to publishing that supports researchers in producing sound, reproducible science whilst providing real recognition for the scholarly work of reviewers and editors.

Open Access and open data are key parts of the open research discourse, as is transparency of the peer review process. On an open research platform, submissions are initially published as preprints following a series of initial technical checks. Peer review then takes place transparently with the reviewers’ reports, editor’s comments and author's responses posted alongside the preprint as citable scholarly outputs. This aims to demystify how the quality of scientific research is assessed through open and transparent editorial and peer review processes.

As in the traditional model, if an editor has decided that your manuscript requires some changes before it can be accepted, you will be invited to revise your submission. However, this revised manuscript will appear as an subsequent version of the original preprint with a new DOI. This means that updates and improvements of research are captured throughout the review process. Once a paper is accepted, the final version of a manuscript, also known as the Version of Record, is published and will be linked to and from the preprints.

Once an article is published it becomes part of the scientific record. Then there is the question of how are readers can find rsearch that's relevant to them. This is the role of scientific indexing and abstracting databases. These services standardise the metadata associated with articles and provide a search function to help users find exactly what they are looking for. In doing so, they increase the visibility and discoverability of research. Among the most prominent scientific indexing services are PubMed, a free resource funded by the US National Institutes of Health that contains over 36 million citations and abstracts of biomedical literature. Some funders may request that the full article text is available in indexes like PubMed Central so make sure to check the requirements of your funder when choosing where to submit your manuscript. More generalist indexers like Google Scholar crawl journals' content to build their indexes whilst also allowing authors to build profiles showcasing their research.

Once your research has been accepted and published, we encourage you to share it widely with others. Social media is a great way to tell people about your work and we recommend including the link to your article, tagging the Society and the journal and including relevant hashtags. This increases engagement with your work and allows others to share with their own networks. We can also support you in other ways to promote your research. If there is an interesting story behind your research, we may reach out asking you to share these stories on the  Microbe Post, our Society blog, or talk through your research on our Podcast, Microbe Talk. We can also assist you with press releases to get news outlets talking about your work and expand its reach.

Finally, our conferences and events are a fantastic place to present your research as a poster or talk, or just connect with people and use this as an opportunity to talk about your paper. These exchanges can be incredibly valuable and often result in future collaborations.

It can be disheartening to receive a reject decision; however, it is important to understand this is a normal part of the process, and it doesn’t mean that your work is without merit. Despite the effort put into developing a well-researched and meticulously written paper, manuscripts can be rejected for a number of reasons and it will happen to everyone. Whether the editors feel that the journal is not the right home for your manuscript or your research is not quite ready to be published yet, a reject decision should be seen as an opportunity to revise and expand your work, resulting in an improved article.

Revise and resubmit to the same journal. Our editors might reject your initial submission but encourage you to thoroughly revise it and resubmit it to the journal once you have performed more experiments or analyses taking into account the feedback from the reviewers and the editor. It is important to note that this is different from a major revision decision because the changes requested will result in a vastly different manuscript. This is often a great option if you are in a position to address the comments you have received and we recommend that you mention this in your cover letter when you submit again to ensure this is picked up by our Publishing Operations Editors. However, it is important to note that you should not resubmit your rejected manuscript unless you are confident you have addressed the advice from the editor.

Transfer to another journal. There will be occasions where the editors will reject your paper but will also recommend that you submit your work to another journal within our portfolio - either as it is or after revision. While our publications are editorially independent, our editors will be able to direct you to more suitable journals based on the aims, scope and the content of your work. When your results are not particularly novel, editors will recommend transferring your manuscript to Access Microbiology, the Microbiology Society’s sound science open research platform, which also publishes replication studies and negative results. When transferring your manuscript, remember to modify elements such as the cover letter and other journal-specific requirements as this will help speed up the process.

A key aspect of scientific research is ensuring that studies are accessible, discoverable and usable by the wider community to enable more research and further our understanding of microbiology. By publishing your research in our trusted portfolio, you can rely on our editors and peer reviewers to support your in improving your findings. They will help curate your manuscript to ensure that your research is shared with your peers and across their networks to inform and inspire new projects and discoveries, shape future research and help microbiology provide maximum benefit to society.

As a society publisher, we are not for profit and everything we offer our community happens thanks to the revenue generated by publishing. Our events, grants, policy work and professional development activities rely on our ability to capture content for publication and when you choose to publish with us, you are helping the beneficiaries of our grants, you are enabling professional development and career opportunities for your peers, and you are delivering events connecting researchers working on pressing global challenges. When you submit your manuscript to one of our titles, you are supporting your entire community.

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