Introduction: The gut microbiota is increasingly recognized as a critical component in the control of host health. Dysbiosis and chronic kidney disease (CKD) have a bidirectional link. Butyrate- producing bacteria have recently gained attention and is a poorly understood faecal state in CKD children.
 Aim: to study the variations in butyrate generating species (Roseburia spp. and F. prausnitzii) in the faeces of children with CKD at different stages.
 Methods: A case-control study with 52 CKD children and 26 healthy subjects was conducted. To verify the alterations in these species, the quantitative real-time polymerase chain reaction (qPCR) was performed.
 Results: Roseburia spp. and F. prausnitzii were considerably lower in CKD children compared to controls and were significantly lower in CKD stage5 (p <0.001). The best cutoff of F. prausnitzii ratio for association with end stage renal disease is ≤15.205 with area under curve 0.928 with (p<0.001).  Roseburia spp., F. prausnitzii ratio were statistically significantly lower in CKD patients with thrombosis than cases without evidence of thrombosis (p=0.011, p=0.009) respectively.
Conclusion: The depletion of Roseburia spp. and F. prausnitzii can be considered microbiomarkers of CKD inflammation, thrombosis, and progression in CKD children.