Abstract Background and Aims The gut microbiota plays a crucial role in a variety of diseases, including chronic kidney disease (CKD). The gut-kidney axis is mediated through metabolism dependent pathways. The relationship between CKD and the dietary consumption of live microbes has not been explicitly studied. Probiotic food intake may play a beneficial role in human health including the gut microbiota. However, in addition to probiotic foods, live micro-organisms are also found in other food products, such as raw vegetables and fruits. In this study, we adjusted for the potential association between dietary live microbiome intake and chronic kidney disease (CKD) in different baseline characteristics, including kidney function status. Method A total of 22,039 subjects were included in the study. We used data from the US National Health and Nutrition Examination Survey 2011-2018. Based on a 2-day 24-hour dietary recall, the dietary intake of the live microbiome was adjusted and the participants were categorized into three groups: low (<104 CFU/g), medium (104–107 CFU/g), or high (>107 CFU/g) dietary intake of live microbes, according to the classification system for the dietary intake of live microbes and participants’ 24-hour dietary recall data. Low intake was used as a reference. Stage 3 CKD with high risk of progression was defined by a combination of estimated glomerular filtration rate (GFR-EPI <60 mL/min/1.73 m2) and urinary albumin-to-creatinine ratio (uACR >30 mg/g was defined as microalbuminuria). CKD was defined by a combination of GFR-EPI <60 mL/min/1.73 m2 or uACR, >30 mg/g. Albuminuria was defined as uACR >300 mg/g. The analyses used weighted logistic regression models (crude model and first, adjusted for age, gender, race, education and second, adjusted for hypertension, diabetes, total cholesterol level, BMI, hemoglobin level, total calorie intake, GFR and serum creatinine level). Results After model adjustment (Model 2, p< 0.0001), women in the medium dietary live microbe intake group had a low prevalence of stage 3 CKD with high risk of progression in contrast to those in the low dietary live microbiome intake group (OR: 0.913, 95% Cl: 0.63-1.32, p< 0.01), between high and low group (OR: 0.333, 95% Cl: 0.13-0.86, p< 0.01). However there was no significant association in men. In model 2, patients in the medium dietary live microbiome intake group had a low prevalence of microalbuminuria in contrast to those in the low dietary live microbiome intake group (OR: 0.789, 95% Cl: 0.63-0.98, p< 0.05). In model 2, we also found the significant association with albuminuria between high and low (OR 0.784, 95% Cl: 0.63-0.98, p< 0.05), medium and low (OR: 0.572, 95% Cl: 0.33-0.98, p< 0.05) dietary live microbiome intake patient groups. In model 2, those in the medium dietary live microbe intake group had a low prevalence of CKD in contrast to those in the low dietary live microbiome intake group (OR: 0.896, 95% Cl: 0.82-0.98) p< 0.01), but there was no significant association between the high and low dietary live microbiome intake groups. Conclusion In this study, a medium or high dietary live microbiome intake was associated with a low prevalence of stage 3 CKD with ahigh risk of progression in women. A medium dietary live microbiome intake was associated with a low prevalence of chronic kidney disease or microalbuminuria in the population. A medium or high dietary live microbiome intake was associated with a low prevalence of albuminuria. A medium dietary live microbiome intake was associated with a low prevalence of microalbuminuria.