Standardization of microbiome studies for urolithiasis: an international consensus agreement

Abstract

Numerous metagenome-wide association studies (MWAS) for urolithiasis have been published, leading to the discovery of potential interactions between the microbiome and urolithiasis. However, questions remain about the reproducibility, applicability and physiological relevance of these data owing to discrepancies in experimental technique and a lack of standardization in the field. One barrier to interpreting MWAS is that experimental biases can be introduced at every step of the experimental pipeline, including sample collection, preservation, storage, processing, sequencing, data analysis and validation. Thus, the introduction of standardized protocols that maintain the flexibility to achieve study-specific objectives is urgently required. To address this need, the first international consortium for microbiome in urinary stone disease — MICROCOSM — was created and consensus panel members were asked to participate in a consensus meeting to develop standardized protocols for microbiome studies if they had published an MWAS on urolithiasis. Study-specific protocols were revised until a consensus was reached. This consensus group generated standardized protocols, which are publicly available via a secure online server, for each step in the typical clinical microbiome–urolithiasis study pipeline. This standardization creates the benchmark for future studies to facilitate consistent interpretation of results and, collectively, to lead to effective interventions to prevent the onset of urolithiasis, and will also be useful for investigators interested in microbiome research in other urological diseases.

Urinary Microbial and Metabolomic Profiles in Kidney Stone Disease

“…Consistent with their reports, we found that E. coli also accounted for a greater proportion of the microbiomes in nephrolithiasis patients than in healthy individuals. Additionally, previous studies have determined that the genus Staphylococcus was overrepresented, while Lactobacillus was less abundant in nephrolithiasis patients than in healthy controls (Zampini et al, 2019;Liu et al, 2020a;Kachroo et al, 2021); again, our findings support these reports. It has been shown that Staphylococcus promotes the formation of kidney stones by producing the enzyme urease, which increases pH, while Lactobacilli exerts an inhibitory action by degrading oxalate (Lewanika et al, 2007;Torzewska et al, 2019).…”

Enterobacter cloacae: a villain in CaOx stone disease?

“…Samples were immediately frozen in liquid nitrogen, and subsequently stored under – 80 ℃. The whole process maintained sterility via the instruction of MICROCOSM (an international consortium for microbiome in urinary stone disease) [ 15 ]. After stone composition analysis, we selected urine samples of patients with a definite diagnosis of CaOx stones and applied 16S rRNA gene sequencing.…”

Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions

“…Importantly, metadata does not only refer to sample attributes, but also to sample preparation and processing [128]. The variability of metadata can limit the conclusions, since the observed patterns might not be attributable to a certain factor(s) [129,130] that should also be considered when selecting study subjects. In this context, we call attention to the necessity of validating metadata submitted to public repositories by providing immediate and informative feedback to the submitting researchers [128].…”