In this month’s issue, we launch a new Series on best practices: an evolving collection of articles that will expand over time to highlight tools, frameworks and resources that push us towards better microbiology research.

Good microbiological research depends on good practice. Many of us probably remember diving into the pages of textbooks to learn how to correctly prepare culture media or being taught how to do that first streak on an agar plate, as a foundation for further experimental work. However, the nature of microbiological research is constantly evolving. As technologies and research questions develop, so do the issues of how to best plan, execute and report experiments. Where and how we sample, what we do with the resulting data, and how we make sure that research is ethical and representative needs continuous reappraisal.

Best practices take many forms, and their main aim is to foster robust, reproducible, representative and relevant research. Across the Nature Portfolio we have guidelines for reporting, research ethics, and data and code availability. Although many of these span scientific disciplines, for example, the use of animal models in line with the ARRIVE guidelines1, others are more discipline specific, such as dual use research of concern (DURC), which is particularly relevant to microbiology. These guidelines aim to facilitate best practice and are complemented by research communities arriving at a consensus in response to emerging issues.

At Nature Microbiology, we are committed to publishing the best microbiology research and to supporting best practices. In this issue, we introduce a new Series curated with articles from the Nature Microbiology archives to provide a central resource covering field-specific and more general issues across the spectrum of microbiology. We hope that the Series will provide a ‘living textbook’ for experienced microbiologists and newcomers alike, with room to grow alongside evolving better practices in microbiology. Here, we present three Perspectives included in the Series that cover best practices in microbiome research. Given the complexity of microbiomes, tools are needed to dissect the cellular and molecular interactions that govern host–microbe interactions or ecosystem functioning. Much as model organisms such as Escherichia coli were adopted to facilitate the study of fundamental bacteriology, model systems comprising groups of selected microbial species, known as synthetic microbial communities (SynComs), are gaining traction as tools to understand the biology of microbiomes. Working with SynComs requires its own set of best practices, however, as laid out in two Perspectives in this issue.

Koskella and colleagues provide a primer discussing SynCom design, implementation and evaluation. They outline strategies to decide which strains to include depending on the research question and how this can be validated. Ethical considerations also come into play, with the authors emphasizing the need for representative SynComs and assessments to determine any potential risk, for example, community invasion, propensity for horizontal gene transfer or pathogenic potential. In a complementary Perspective, Northen, Garrido-Oter and colleagues highlight the need for community standards for SynComs in plant–microbiome research. These microbes have the potential to boost agricultural efficiency while promoting ecosystem health. To effectively understand and reap the benefits of this across the globe, the authors argue that reference SynComs, accompanied by a minimum standard of metadata describing each community, should be developed alongside standardized protocols and benchmarking approaches. Essentially, infrastructure must be developed and funding provided to enable strain and data sharing in a fully accessible manner. These recommendations somewhat mirror the FAIR principles2 for data management and sharing, which set out that data should be findable, accessible, interoperable and reusable. Such efforts ensure reproducibility, foster collaboration and encourage pooling or reusing of data and resources to make for a more inclusive and sustainable research environment — a key facet of best practice.

Planning is also a bedrock of best practice. Defining the research question and planning experiments to answer that question is essential. This is particularly true for clinical trials, which require extensive registration and reporting ahead of participant enrolment. There has been increasing interest in assessing whether probiotics, bacteria with health benefits, or prebiotics, substrates that promote the growth of such bacteria, can improve outcomes for infectious and non-infectious diseases. In their Perspective, Whelan and co-authors highlight how results from clinical trials involving prebiotics or probiotics are often variable and that this is probably due to the effect of diet on the gut microbiome. They discuss evidence supporting diet-driven effects on intervention efficacy and how diet needs to be recorded and considered in such trials, and most importantly, they propose ten recommendations for future trials to be implemented alongside existing clinical guidelines. These include thorough reporting of prebiotic or probiotic composition (structure, source and strain) and intake (dosage, timing and whether consumption is with food), and considering whether to include participants whose diet drastically changes, for example due to religious holidays or festivals, as this will ultimately impact substrate availability in the gut and thus the microbiome. The role of habitual diet in these studies requires further investigation, but more thorough reporting and robust study design will improve our understanding of these complex interactions and ultimately clinical practice.

Accompanying these Perspectives is a collection of papers from the archives spanning experimental best practices, data sharing and management, ethics, and nomenclature and taxonomy. We share resources and strategies to support open science including journal guidelines for data availability and community guidelines for sharing microbiome data and analyses3. Alongside SynComs, other experimental models for microbiology research are discussed. We highlight a framework for inclusive microbiome research with Indigenous communities4 and considerations for the Nagoya Protocol in microbiology research5. Finally, we include community consensus statements for taxonomy and nomenclature, which constantly evolve with the discovery of previously undescribed microbial life.

We hope this collection of articles provides a resource for the community. We will continue to grow the Series over the coming months and years as we seek to publish content that strives to develop and define best practices in microbiology, with the ultimate goal of ensuring robust, reproducible, representative and relevant research.