Guidelines and checklists exist for various areas of research. In microbiology, this is particularly evident for clinical research. For example, the Consolidated Standards of Reporting Trials (CONSORT) checklist provides reporting guidance for randomized trials and the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement is available for observational studies including cohort and cross-sectional epidemiological studies. These community-led checklists were created with the aim of ensuring ethical, robust and reproducible clinical research. They guide authors in their planning, execution and reporting of a study, while also supporting reviewers and editors when assessing the work, thus ensuring patient safety, scientific integrity and the potential translation of the work into clinical practice.

Research guidelines are not limited to clinical research. Advances in sequencing technologies, making them cheaper, faster and consequently more accessible, led to a sudden surge in the generation of genomic data. It was soon clear that standards were urgently needed to ensure that sequencing datasets were handled and reported appropriately to enable reproducibility and use in further analyses. In response, a group of researchers formed the Genomic Standards Consortium. This led to the publication of the minimum information about a genome sequence (MIGS) specification in 20081. MIGS provides a set of core descriptors for genomes (or minimum information about a metagenome sequence (MIMS)), which includes relevant metadata such as the environmental context of a sequence and the sequencing method used. In 2011, the Genomic Standards Consortium extended MIGS by proposing additional standards for reporting marker gene sequences, such as 16S rRNA gene sequences regularly used in microbiome studies2. These guidelines, called the minimum information about a marker gene sequence (MIMARKS), comprised ‘environmental packages’ to provide expanded guidelines for reporting the environment from which a sample was taken. Without this information, sequencing data lack context, limiting our ability to properly interpret them and make accurate conclusions. Together, these checklists form the minimum information about any (x) sequence (MIxS), which provides a single guide for any sequence data.

Over the next ten years, further microbiome-relevant guidelines were developed to keep pace with the increasing complexity of the field and exponential growth of multi-omics data, including an additional extension of MIxS for metagenome-assembled genomes3. As the human microbiome field grew, so did the similarities with the epidemiology field where studies involve large human cohorts. To safeguard the integrity of the field, a set of microbiome-specific reporting guidelines were needed.

In 2021, a diverse group of human microbiome researchers produced a checklist of 17 items to inform reporting of human microbiome research called Strengthening The Organization and Reporting of Microbiome Studies (STORMS)4. STORMS builds on existing MIxS guidelines as well as checklists for epidemiological studies, such as STROBE, due to shared features, while also encompassing the use of biological samples, culture-dependent analyses and microbiome-specific bioinformatics — elements common across human microbiome studies. The checklist is organized into six sections, following the structure of a research paper from abstract through to reporting of methods and results. The aim of this tool is similar to other scientific guidelines — to support authors reporting their work, editors and reviewers during peer review, and consequent interpretation by readers and reproducibility across studies in the field.

Although previous checklists have included guidance on detailed reporting, sequencing repositories still suffer from insufficient information alongside sequences, particularly environmental microbiome studies. While STORMS guided human microbiome researchers, reporting guidance was missing for environmental- and non-human-host-associated microbiomes, which have different considerations. Metadata considerations include details of field studies, specifics of sampling (for example, latitude and longitude, pH and depth) and the use of cross-disciplinary approaches that may not be widely used by other microbiologists. To address this, last year, a workshop brought together a diverse group of 50 participants comprising microbiome researchers, funders, editors and data repository representatives to reflect on existing standards and discuss how STORMS could be optimized and extended for environmental, non-human host and synthetic microbiomes5.

In this issue of Nature Microbiology, we present the outcomes of this workshop as a Consensus Statement on The Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies (STREAMS) guidelines. In addition to the workshop attendees, multiple rounds of feedback were provided by a wider group of microbiome researchers, totalling input from 248 researchers across 28 countries whose work spans a range of microbiomes. These community-led guidelines build upon the STORMS checklist to include 67 items and cover terrestrial, aquatic, atmospheric and engineered microbiomes, animal and plant microbiomes, as well as synthetic microbiomes. Key modifications include the environmental context of a sample, for example, the geographic location of the sample that encourages provision of geographic coordinates, as well as the relevant history of the sampling environment such as drought, and ethical considerations including the Nagoya Protocol6 or the CARE principles for work involving Indigenous lands or samples. To aid implementation, the authors included case study examples where they have applied the checklist to published studies spanning eight different microbiomes covered by the STREAMS guidelines.

While these guidelines do not provide specific guidance for the planning or execution of a microbiome study, the authors provide an additional version of the checklist via a data management plan tool. This can support researchers in the midst of a study to ensure relevant information is captured. These guidelines can also be used in conjunction with field-specific best practices, for example, those for low-biomass, plant or engineered microbiomes7,8,9.

As research fields grow and evolve, guidelines and standards must too. This is true for the STREAMS guidelines. The authors have incorporated mechanisms for regular updates so that the guidelines represent the communities they were designed to serve and support. Creating guidelines requires a balance of sufficient detail to ensure reproducibility and resource utility, without creating additional barriers or workloads. The involvement of a diverse group of researchers in an open and iterative process can help encourage broad uptake and limit barriers that could stifle discovery or collaboration. Involving additional groups of microbiome researchers, particularly those in lower- and middle-income countries who may have fewer resources to implement such checklists, will help create guidelines that can be feasibly adhered to across different settings, promoting broad uptake, which will ultimately benefit the field.

The STREAMS guidelines are just that — a guide. They are not mandatory but should be used as another tool in a microbiome researcher’s arsenal. However, like many tools, its application has the potential to advance the field. We therefore recommend that our microbiome authors use this tool for robust, reproducible and relevant research.