Consensus among a large array of stakeholders was assessed via five separate two-rounds Delphi surveys (formal processes designed to build international consensus on key questions among experts). For each survey, a publication with recommendations is in preparation or was submitted. Delphi Survey 1: Minimal requirement for clinical metadata and sample processing in microbiome clinical studies (72 & 61 respondents in rounds 1 & 2). Delphi Survey 2: Microbiome for medical doctors and clinicians (54 & 49 respondents). Delphi Survey 3: Preclinical models in microbiome research: How to prove causality & therapeutic inference (107 & 87 respondents). Delphi Survey 4: Faecal Microbiota Transplantation trials: What is the minimum set of outcomes to measure when assessing the effect on the microbiome (51 & 37 respondents). Delphi Survey 5: Consensus on Microbiome-based biomarkers validation process (114 & 93 respondents) ; Publication in revision for Lancet Microbes.
The work performed within IHMCSA was set within 2 Pillars on 1) Standards for microbiome research and applications and 2) Healthy microbiome, causality and confounders to which were added transversal actions on Ethics of microbiome science and Inception of the European Microbiome Centres Consortium. We outline below the work performed and key achievements and outcomes.
Pillar 1. Standards for microbiome research and applications. Concerning Metadata and sample processing in microbiome-based clinical trials, the key outcome of several workshops and a Delphi survey is a publication with recommendations (in preparation). Concerning Data production and data repositories, consensus workshops on human microbiome data and inter-operability, including GDPR considerations, will lead to a publication with recommendations on shareable/interoperable microbiome data (in preparation). Specifically on Data analysis, the achievement of consensus workshops on human microbiome analysis standards, including integration of multi-omics data will be a publication with recommendations on secondary analysis, including multi-omics data integration (in preparation).
Pillar 2. Healthy microbiome, causality and confounders. Work towards defining the Healthy microbiome and virome, accounting for confounders involved an international consensus workshop on the futures of microbiome and virome research - towards Roadmaps to defining microbiome and virome health. Outcomes are a white paper with recommendations ‘The human microbiome as a reporter and predictor of health’ and a publication ‘Clarifying the concept of healthy microbiome through an epidemiological lens’ (submitted to Nat Rev Microbio). Specifically on Assessing causality, a workshops on in vitro and in vivo models to assess causality of microbiome alteration in diseases, and two Delphi surveys secured consensus. Outcomes include recommendations for a Roadmap of Strategic Research and Innovation Agenda and a consensus opinion paper ‘New approaches for fecal microbiota transfer trial design’ (in preparation). Concerning the Design, validation and verification of microbiome-based biomarkers, two workshops were held on regulatory mechanisms for biomarker development and on recommendations on reference materials for microbiome research and translation. A comparative assessment of six different microbiome testing kits and services available in Europe and the USA was also performed. A correspondence article on ‘microbiome testing kits and services – recommendations and associated regulatory matters’ is in preparation for Microbiome. In addition, this work led to the definition of a consensus roadmap for a novel initiative : the European Microbiome-Dedicated Surveillance Network (EMDSN).
Transversal actions. Concerning Ethics of microbiome science, two consensus workshops on microbiome self-monitoring and ethical implications, and on Consortium Authorship were held. Following the publication Zwart. 2022. “Love is a microbe too”: microbiome dialectics’. Endeavour, two publications ‘Consortium Authorship: ethical implications of emerging authorship practices in team science’ and ‘Awareness of Human Microbiome may Promote Healthier Lifestyle and More Positive Environmental Attitudes’ were submitted.
Concerning the Inception of the European Microbiome Centres Consortium, a task-force was established and met monthly over a semester to work on defining membership criteria, timing of inception, roadmap to initiation of activities, and to determine Working Groups (standardization; analytics; public health; roadmap; regulatory; communication). These gathered involvement from more than 50 partners and stakeholders. A framework agreement was signed by the 5 co-founders (INRAE, EMBL, UCC, UniTrento, UniCopenhagen). A publication ‘inception of the European Microbiome Centres Consortium’ is in preparation.
