Predicting diabetic kidney disease with serum metabolomics and gut microbiota
Authors: Hu Yuyun , Ni Xue , Chen Qinghuo , Qu Yihui , Chen Kanan , Zhu Gaohui , Zhang Minqiao , Xu Ningjie , Bai Xu , Wang Jing , Ma Yanhong , Luo Qun , Cai Kedan 
Published: October 2024

Objective: This study aims to identify biomarkers for reliably predicting diabetic kidney disease (DKD), systematically characterize serum metabolites and gut microbiota in DKD patients, and investigate the correlation between differential serum metabolites and gut microbiota.
Methods: From September 2021 to January 2023, 90 subjects were recruited: 30 with DKD, 30 with type 2 diabetes mellitus (T2DM), and 30 normal controls (NCs). Serum metabolites, including 180 different metabolites, were analyzed using targeted metabolomics UPLC-MS/MS, and gut microbiota were assessed via 16S rRNA sequencing. Differential metabolites were identified through univariate (t-test or Mann-Whitney U-test, P < 0.05) and multivariate analyses (OPLS-DA model, VIP > 1, P < 0.05), followed by selection using the least absolute shrinkage and selection operator (LASSO). The selected overlapping serum metabolites, along with DKD-associated differential gut microbiota, were used to develop a logistic regression prediction model for DKD based on six markers.
Results: In the DKD group compared to the DM and NC groups, 39 and 60 differential serum metabolites were identified, respectively (VIP > 1, P < 0.01). Among these, 36 serum metabolites, including alpha-Hydroxyisobutyric acid, were significantly elevated in DKD patients compared to those with DM. Of these, 28 metabolites showed a negative correlation with estimated glomerular filtration rate (eGFR), while 29 showed a positive correlation with urine albumin creatinine ratio (UACR). Patients with DKD were further categorized into subgroups (DKD middle and DKD early) based on eGFR (eGFR < 90 ml/min/1.73m², eGFR ≥ 90 ml/min/1.73m²), revealing 23 differential metabolites. Dysbiosis of the gut microbiota was evident in DKD patients, with lower relative abundances of g_Prevotella and g_Faecalibacteriumcompared to the DM and NC groups. Subgroup analysis indicated decreased relative abundances of g_Prevotella and g_Faecalibacterium in the DKD middle group, along with a decrease in g_Klebsiella compared to the DKD early group, which correlated positively with DKD patients' eGFR. There were 11 common metabolites among the three groups of differential metabolites. Among these, three serum metabolites—imidazolepropionic acid, adipoylcarnitine, and 1-methylhistidine—were identified as predictive serum metabolic markers. Disease prediction models (logistic regression models) were constructed based on these three metabolites combined with three genera of bacteria. These models demonstrated strong discriminatory power for diagnosing patients with DKD compared to patients with DM (area under the receiver operating characteristic curve (AUROC) =0.939 and precision-recall curve (AUPR) = 0.940). The models also effectively discriminated between patients with DKD and NCs (0.976, 0.973).
Conclusions: This study revealed distinctive serum metabolites and gut microbiota in patients with DKD. It demonstrated the potential utility of three specific serum metabolites and three genera of bacteria in diagnosing patients with DKD and assessing their renal dysfunction.