Guidelines for microbiome studies in renal physiology

Abstract

Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and faecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animal and clinical studies assessing renal function, many which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatisation, baseline microbiota and its normalisation, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardising study designs, methods and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.

The Influence of Angiotensin II on the Gut Microbiome of Mice: Findings from a Retrospective Study

“…The findings support guidelines for gut microbiome studies in hypertension and renal function, where appropriate control for these factors has been suggested. 35,36 In our study, we investigated the bacterial component of the gut microbiome as a proof-of-concept. However, how signatures of other members of the gut microbiome such as phages and fungi are affected by external factors remain unclear.…”

Prospects for Leveraging the Microbiota as Medicine for Hypertension

“…In addition, available guidelines and checklists for human studies could be better utilized. [57][58][59]140…”

“…However, there exists a disparity in the standards used in these studies, despite the availability of guidelines for their conduct. 58,59 To effectively identify the effects of the gut microbiota on hypertension as a phenotype, large, well-characterized clinical cohorts are imperative. For instance, to date, few studies have used 24-hour ambulatory BP measurement as a diagnostic tool.…”

Unravelling the Link between the Gut Microbiome and Autoimmune and Inflammatory Kidney Diseases: A Potential New Therapeutic Approach

“…Experimentation in animal models requires controlled experimental conditions, allowing for standardized protocols and reproducibility of results. However, factors such as housing, age, sample collection site, littermate effect, bedding, supplier effect may influence consistency and reproducibility of experiments [152].…”