Fig. 5: VFG analysis of the PUMCH dataset.

The violin plot shows the total abundance (A) and diversity (B) of VFGs in HMP (Human Microbiome project, n = 350), HC (Healthy control, n = 50), T2D (Type 2 diabetes, n = 50), and T2D-CVD (T2D patients with cardiovascular disease, n = 50) (centre line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers). Statistical significance between HMP, HC, T2D, and T2D-CVD was determined via a two-sided Kruskal‒Wallis test, and correction for multiple comparisons was performed via Benjamini‒Hochberg adjustment (***p < 0.001, **p < 0.01, *p < 0.05; ns, p > 0.05). VFGs with more than 5 mapped reads were identified. The abundance of VFGs in the sample is represented by log10(TPM). 0 was replaced with 0.0001 for log calculation. C VFs that were significantly enriched between HCs and T2D patients, HCs and T2D-CVD patients, and T2D patients and T2D-CVD patients (>10% prevalence and >50% coverage, p < 0.05). Statistical significance was determined by a two-sided Kruskal‒Wallis test, and correction for multiple comparisons was performed via Benjamini‒Hochberg adjustment. The colour of the bubble represents the category of VFs. The solid circles represent common features among diseases (enriched in at least 2 types of disease), whereas the solid circles with squares represent disease-specific VF features. The y-axis labels coloured in black are species-specific VFs, and those coloured in grey are non-species-specific VFs. * represents “plasmid-borne only” VFs; ** represents “alternate” VFs. D Spearman correlation between the abundance of VFs and clinical indices (two-sided). Correction for multiple comparisons was performed via Benjamini‒Hochberg adjustment. The results with R > 0.35 and p < 0.05 are shown. FBG fasting blood glucose, HbA1c haemoglobin A1c, HOMA_IR homeostatic model assessment for insulin resistance. Source data are provided as a source data file.