Metagenomics and metabonomics of calcium oxalate nephrolithiasis rats

Clostridium butyricum (CB), as a probiotic, has shown potential in improving renal function in kidney diseases. Here, we aimed to explore the role and mechanism of CB in calcium oxalate (CaOx) nephrolithiasis. Sprague-Dawley (SD) rats (4-6 weeks old, male) were acclimatized for one week before the experiments commenced. First, 18 rats were randomly assigned to three equal groups: Control (Con) group, CaOx group and CB group. The rats in Con group had access to sterile tap water, whereas the rats in CaOx group received 1% ethylene glycol (EG) and 0.5% ammonium chloride (AC) in their drinking water for four weeks. The biotherapeutic strain of Clostridium butyricum was purchased from MIYARISAN Pharmaceutical Co., Ltd. (Tokyo, Japan) and was resuspended at a concentration of approximately 1×109 CFU/ml for further use. The CB group received drinking water supplemented with 1% EG + 0.5% AC and was co‑treated daily with 1 ml (1x109 CFU) of CB solution via gavage. The rats in Con and CaOx groups received 1 ml of normal saline via gavage. The stool of the rats among the three groups were conducted 16S sequencing and untargeted metabolomics. Then, the stool, serum, and kidneys of the rats among the three groups were conducted targeted bile acid metabolomics. This dataset contains the data of the metabolomics and microbiome.