CUNY SPH researchers develop reporting guidelines for human microbiome research

Nov. 23, 2021
3D rendering of human intestine villi and microbiome

The interdisciplinary nature of human microbiome research makes organization and reporting of results a challenge, while inconsistent reporting can make it difficult to replicate results and determine the comparability of independent studies. To address this problem, CUNY SPH Associate Professors Heidi Jones and Levi Waldron, along with doctoral candidate Chloe Mirzayi, led the development of a checklist to guide the preparation and review of manuscripts in human microbiome studies.

For the study, which was published last week in Nature Medicine, the researchers built a consortium of 101 authors from 89 institutions in 17 countries to refine and agree on the Strengthening The Organization and Reporting of Microbiome Studies (STORMS) checklist and develop a consensus statement on the need for it. The consortium authors included nine faculty, staff, students, and alumni from CUNY SPH and the Institute for Implementation Science in Population Health (ISPH). Use of the checklist has been adopted by the Nature family of journals as a requirement of publication.

“I’m thrilled to see the field recognize that inconsistency of reporting in publication is a barrier to progress, and to see us take this first step towards improving that,” says Dr. Waldron. “This project actually started as a result of another ongoing project at our school to create a standardized database of the published literature on relationships between the human microbiome and disease. I’ve supervised dozens of students who have reviewed and standardized the information from more than 500 published papers, and we’ve been forced to appreciate the difficulty often in understanding even the most basic elements of Methods and Results from published manuscripts. Once you get past the Abstract and Conclusions, it can be like the Wild West.”

Lead author Chloe Mirzayi reflected on how much work it was to develop consensus and publish the consensus statement.

“It took more than 10 years after the start of the modern sequencing-based field of human microbiome research for a consensus set of reporting guidelines to be published, and I can understand why—it was not easy to develop,” she says. “I had to synthesize feedback from dozens of researchers from many different fields while maintaining a coherent and manageable checklist, and communicate back to everyone how all feedback had been incorporated or not. Working with more than 100 authors and managing every small detail with respect to publication was a lot of work.”

Co-senior author Dr. Jones says the next step will be working to convince the rest of the journals in the field to adopt the 17-item, 69-sub-item checklist.

“Most epidemiology journals use existing reporting checklists, but they don’t provide one on microbiome studies,” she says. “We maintained the relevant elements from other widely-adopted checklists, which should ease the transition to using STORMS for epidemiological studies of the human microbiome.”

Mirzayi, C., Renson, A., Genomic Standards Consortium. et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med 27, 1885–1892 (2021).