What will our open research platform publish and how will it advance microbiology?

Posted on June 22, 2021   by Justin Clark and Alex Howat

The Microbiology Society’s sound science and open access journal, Access Microbiology, will be converting into an open research platform in October 2021. This blog examines the benefits of publishing sound science and details the broad range of article types we are aiming to publish on the platform. 

This is the third in a series of blogs about this project, which is being funded by a Learned Society Curation Award by the Wellcome Trust and the Howard Hughes Medical Institute. In our previous blogs, we introduced our initial ideas and research behind the project and the manuscript review tools selected for inclusion in the platform. Here we examine the importance of publishing all scientific research, who benefits from this and the types of articles we will be welcoming on the platform. 

What is sound science in microbiology? 

Very simply – any work that is technically correct. In microbiology, this can be incredibly varied and might include the analysis of original research in the lab, descriptions of large datasets, the treatment of a patient from initial presentation to completion of treatment, a new tool or code used to help researchers in their research, or even the description of a useful technique used in microbiology teaching or outreach. Too many valuable research outputs are lost because they are not seen as ‘high impact’, or indeed, because the experiment was completely unsuccessful. Access Microbiology aims to reduce this kind of research waste by basing its publication criteria on methodological rigour rather than novelty. 

Why is it important and who can benefit from it? 

Publishing sound science reduces scientific waste and, vitally, early-career researchers’ precious time. Most experiments based on big ideas do not yield perfect results immediately. It can take time to come up with the right question and develop appropriate techniques to test a hypothesis. Much of the data generated along the way does not end up revealing what researchers were expecting (i.e. null) and is thus, not considered worthy of publication. Researchers, generally at PhD or post-doc level, can spend significant amounts of time testing hypotheses that other labs have already investigated. Publishing these experimental research outputs means that others do not have to repeat the same experiments, and future researchers may be able to iterate on that study design in ways we cannot yet conceive! 

Publishing one confirmatory study does not mean this is the end of the story – research initially considered to be high impact can be debunked by null studies. Many advancements in the medical and clinical arena rely on vast amounts of data to confirm that a hypothesis is true before it can be considered a viable option for further study. The more studies are done, the more likely it is to be true. Microbiology Society member Professor Lindsay Hall explains this clearly: 

“We need to share negative or results that confirm previous findings, which is really important in the context of microbiome research, to ensure we are not overhyping different associations, but also to make sure what we are seeing is a really strong association so we can potentially move forward into the clinic. The open research platform is the ideal place to deposit these findings and this data so it can be widely accessed by the wider research community and can make positive strides in the microbiome research space.” 

Work considered to lack novelty can shed light on existing or even new questions when new data comes to light. Ensuring this research and data is preserved in the scientific record allows other researchers to use it to address their own research interests not previously considered in their current study.  

Importantly, publication of sound science puts a paper to an early-career researcher’s name and provides evidence that they have done vast amounts of research during their post – a vital part of their career progression. 

What will the open research platform publish? 

If it relates to microbiology and the science is sound, Access Microbiology will consider it for publication. In the recent survey, carried out by the Society in April and May, it became clear that there is a demand for a wide variety of article types that are not typically seen in traditional journals (see Figure 1).  

Figure 1. Types of research that survey respondents would like our open research platform to publish, from a recent survey conducted by the Microbiology Society. Responses shown are to the question, ‘What type of research would you like the open research platform to publish? (please select all that apply)’. Total responses are indicated above each bar. 

Below is a summary of the article types that will be published by the open research platform. 

Research Articles and Methods 

Research Articles (and Short Communications, for shorter articles) will present any original research from the lab and, importantly, may include negative, null and replication studies, as well as novel and impactful findings. Methods are similar in nature but specifically describe novel procedures, methodologies and techniques. 

Study Protocols 

Study Protocols provide a detailed report on planned or ongoing research studies. Publishing these articles ensures greater transparency in the research process, promotes collaboration and will help improve the standard of research. By enabling more information to be available on current studies, Study Protocols help to prevent unnecessary duplication of work. A researcher may subsequently publish the results, and any adjustments required to the protocol, in a future Research Article or equivalent. In addition to publishing Protocols, we are currently investigating how to incorporate Registered Reports into the platform. 

Software Tool articles 

With large datasets now underpinning much of microbiology research, more researchers are developing their own tools to answer key questions to this data, either by automating an established process or to analyse the data in a novel way. We encourage authors to report the development, code and key use cases of these tools so that others may adopt them in their own work, and to ensure the authors receive recognition for this advancement. Authors will be encouraged to deposit the software in a repository with as open a license as possible. 

Data Papers 

As noted above, there is a huge amount of data generated from research, but much of it is quietly deposited in repositories and remains largely untouched because it is unknown to the wider microbiology community. Publishing a Data Paper containing these datasets, including where and why it was generated, promotes it across the community, increasing the likelihood of its re-use and therefore, further discoveries.  

Case Reports 

Case Reports describe interesting diagnoses, investigation and/or treatment of infectious diseases in an individual or animal, that are of educational value to the community and critical to practising clinicians. 

Reviews  

Reviews provide an authoritative and balanced subject overview, suitable for a wide audience. According to Hulland and colleagues, they should ‘identify and synthesisze relevant literature to evaluate a specific research question, substantive domain, theoretical approach, or methodology, and thereby provide readers with a state-of-the-art understanding of the research topic’.  

Pedagogy articles 

The Microbiology Society believes that effective microbiology education is vitally important to advancing the discipline. Our open research platform will publish pedagogy articles to assist educators in teaching the subject with clarity and authority, promoting the exchange of microbiology knowledge. This could also include effective and unique outreach programmes or tools.  

We will continue to monitor research and publishing trends, and listen to our authors and Society members, in implementing or devising further article types in future. Access Microbiology will respond to the needs of our community.  

We believe that the publication of sound science makes for a more robust scientific ecosystem and benefits the researchers working within it, and we are committed to providing an avenue for these varied research outputs. Keep an eye on the open research platform blog series on Microbe Post as next month we will be publishing a blog on the subject of preprints vs. published articles – what exactly do we mean by the two terms, and how will we highlight the differences on the platform?  

If you have previous experience of, or comments on anything you have read here, we would love to hear from you. Please contact Alex Howat at [email protected].