A systematic review of the applications of Mendelian randomization assessing the causal relevance of the gut microbiome in human health and disease

Objectives To investigate the current application of Mendelian randomization (MR) in assessing the causal relevance of the gut microbiome in human health and evaluate the quality of these studies. Design Systematic review Data sources Ovid MEDLINE, Embase, Web of Science, bioRxiv and medRxiv were searched from inception to the 12th of January 2023. Eligibility criteria Full-texts and conference abstracts of studies that conducted MR analyses to investigate the causal role of the gut microbiome on any outcome.

and analysis Two independent reviewers screened titles and abstracts, assessed full texts for eligibility, extracted data and assessed study quality. Extracted data included information on authors, hypothesis/rationale, methodology used (including genetic instrumentation decisions and analyses), results and limitations. As no quality assessment tool currently exists for MR studies, the quality of each study was assessed using a series of questions adapted from two previous systematic reviews of MR studies and a comparison with the STROBE-MR guidelines. Results were narratively synthesized, and meta-analyses were conducted, where possible, if the exposure and outcome were comparable (including definition and units) and data sources were appropriately independent across studies.

Of the 463 records identified, 66 were eligible for inclusion. We identified 48,082 individual MR estimates of the relationship between 612 gut microbial traits (defined by relative abundance, presence vs. absence or functional pathway) and 905 health outcomes including those categorized into autoimmunity, behaviour, cancer, prescription drug usage, immunity, inflammation, longevity, medical procedures, metabolic health, nutrition, pain, sexual and reproductive health, and diseases of several organs and systems. According to the quality assessment, all studies were judged to be of poor quality, due to the inappropriate application of MR – specifically, instrument selection, exposure and outcome definition, choice of analytical methodology, assessment of reverse causation and replication – and lack of transparent reporting of findings. Therefore, meta-analysis across studies was largely impossible.

Whilst there has been growth in the application of MR to understand the causal role of the microbiome in human health, these studies fail to appropriately apply the method and transparently report findings. Further, our systematic review provides evidence of an unmet requirement for careful examination and interpretation of derived causal estimates. Here, we make recommendations for the improvement of applications of MR to the microbiome going forward. Study registration https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=314055 What is already known on this topic Mendelian randomization (MR) is increasingly used to assess the causal relevance of the gut microbiome in human health. Concerns exist regarding the methodological quality, validity of MR studies in this context and, thus, the level of misinformation entering the public domain. There is a requirement to evaluate the application and reporting quality of these studies. What this study adds Our findings show that most MR studies investigating the gut microbiome and health outcomes are of poor quality due to methodological flaws and inadequate reporting. Our study highlights the urgent need for improved study design, rigorous Competing Interest Statement The authors have declared no competing interest. Clinical Protocols https://www.crd.york.ac.uk/PROSPERO/view/314055 Funding Statement A Cancer Research UK (CRUK) Population Research Postdoctoral Fellowship [grant number RCCPDF\100007; awarded to KHW in 2022] funded both CH and AD. KHW is supported by the University of Bristol. AM is supported by a CRUK PhD studentship [grant number C18281/A30905]. AB was supported by the University of the West of England (UWE) during a BSc industry placement at the University of Bristol. LJG is funded by the CRUK Integrative Cancer Epidemiology Programme (C18281/A29019) and FS is funded by the National Institute for Health and Care Research (NIHR: NIHR153861). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This research is a review of existing studies on humans and only used information from publicly available studies. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability The data produced as part of this review are presented in the paper supplement and online at https://github.com/KaitlinHazelWade/Microbiome_MR_review/.