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Objective:To investigate the effect of decocted Coptis chinensis Franch.(Huanglian Jianji,黄连煎剂,HLJJ) and berbenne on the gut microbiota of the rats with metabolic syndrome (MS) induced by high-fat diet (HFD).Methods:Sixty Sprague Dawley rats were randomly divided into normal diet (ND) group (n =15)and HFD group (n =45).After 8 weeks of feeding,the HFD group was further divided into three groups:a group provided with a combination of HLJJ and HFD for 4 weeks,a group provided with a combination of berberine and HFD for 4 weeks,and a group supplied only with HFD for 4 consecutive weeks.Epididymal fat weight,serum high-density lipoproteincholesterohC (HDL-C),lowdensity lipoproteincholesterol-C (LDL-C) and irisin levels were measured.In addition,the V3-V4 region of the cecum microbiota 16S rRNA gene amplicon was sequenced on the Illumina MiSeq platform.Results:MS was successfully induced in the rats with HFD for 8 weeks.After 12 weeks,serum irisin levels in the HFD + berberine group were significantly increased compared with those in the HFD group (P ＜.05).The high-quality tags were delineated into 1149 operational taxonomic units at a 97％ similarity level.Furthermore,at the genus level,Akkermansia muciniphila (A.muciniphila),Bacteroides,and Ruminococcus were markedly increased,whereas Candidatus arthromitus,Prevotella,Phascolarctobacterium were in great decrease in the HLJJ group and the berberine group,compared with the HFD group.The abundance of A.muciniphila,Ruminococcus gnavus and Bacteroides was significantly higher in the berberine group,whereas,the abundance of Oscillospira was lower in the berberine group,compared with the HLJJ group.Conclusion:HLJJ and berberine changed the gut microbiota in rats with MS.The mechanism underlying the treatments of berberine and HLJJ on HFD-induced MS is partly different.