Core Gut Microbiome in Patients with Staghorn Calculi in Malaysia

Globally, staghorn calculi stone prevalence is 3–5% annually, with a lifetime prevalence of up to 25%. Recurrence rates are 10% within the first year, 50% within 5–10 years, and 75% over 20 years, despite improvements in treatment. This study aimed to profile the gut microbiota in 77 participants, including 37 staghorn calculi patients and 40 healthy individuals, to identify biomarkers linked to staghorn calculi formation. At the phylum level, Firmicutes A and Proteobacteria were more abundant in the staghorn group, comprising 52.86% and 13.65%, respectively. At the species level, staghorn patients had lower levels of Bifidobacterium adolescentis and higher Escherichia and Megamonas funifomis abundances compared to controls. Core microbiome analysis identified Blautia A as the most abundant species in healthy individuals, whereas Megamonas funiformis was exclusive to staghorn patients, suggesting its potential as a disease biomarker. LEfSe analysis confirmed Megamonas funiformis as significantly enriched in staghorn patients (LDA score: -4.46). These findings highlight critical gut microbiome differences that may contribute to staghorn calculi development.