BackgroundMounting evidence indicates that the gut microbiome (GMB) plays an essential role in kidney stone (KS) formation. In this study, we conducted a systematic review and meta-analysis to compare the composition of gut microbiota in kidney stone patients and healthy individuals, and further understand the role of gut microbiota in nephrolithiasis.ResultsSix databases were searched to find taxonomy-based comparison studies on the GMB until September 2022. Meta-analyses were performed using RevMan 5.3 to estimate the overall relative abundance of gut microbiota in KS patients and healthy subjects. Eight studies were included with 356 nephrolithiasis patients and 347 healthy subjects. The meta-analysis suggested that KS patients had a higher abundance ofBacteroides(35.11% vs 21.25%, Z = 3.56,P= 0.0004) andEscherichia_Shigella(4.39% vs 1.78%, Z = 3.23,P= 0.001), and a lower abundance ofPrevotella_9(8.41% vs 10.65%, Z = 4.49,P< 0.00001). Qualitative analysis revealed that beta-diversity was different between the two groups (P< 0.05); Ten taxa (Bacteroides,Phascolarctobacterium,Faecalibacterium,Flavobacterium,Akkermansia, Lactobacillus, Escherichia coli, RhodobacterandGordonia) helped the detection of kidney stones (P< 0.05); Genes or protein families of the GMB involved in oxalate degradation, glycan synthesis, and energy metabolism were altered in patients (P< 0.05).ConclusionsThere is a characteristic gut microbiota dysbiosis in kidney stone patients. Individualized therapies like microbial supplementation, probiotic or synbiotic preparations and adjusted diet patterns based on individual gut microbial characteristics of patients may be more effective in preventing stone formation and recurrence.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-023-02891-0.