Background: Coptidis rhizoma extracts (CREs) have been used widely for their anti-diabetic and anti-microbial activities, and
berberine/
jatrorrhizine/
coptisine/
palmatine are the primary bioactive components. Although guidelines have adopted content analyses of these components as a quality control method for CREs, it is difficult to differentiate the CREs from different sources using this method because of the lack of indications for their related pharmacological activities. Purpose: To explore the effect of CREs (CREA/CREB/CREC) with different compositions of major components on the gut microbiota and
blood glucose levels in db/db mice. Methods: Degradation of
berberine/
jatrorrhizine/
coptisine/
palmatine from CREA/CREB/CREC in rat/mouse intestinal contents and their impact on nine common gastrointestinal bacteria were investigated. In addition, the effects of
oral administration of CREA/CREB/CREC for 2 weeks on the gut microbiota and
blood glucose levels in db/db mice were monitored via
insulin/
glucose tolerance test (ITT/GTT),
insulin concentration, homeostatic model assessment of
insulin resistance and fecal
16S rRNA sequencing. Results and Conclusion: The total amount of
berberine/
jatrorrhizine/
coptisine/
palmatine was highest in CREA. Clostridium perfringens was strongly inhibited by all three CREs, with CREA demonstrating the most significant inhibitory effects on minimum inhibitory concentration, time-kill kinetics, and
ATP production. In db/db mice, CREA resulted in the most significant decrease in ITT/GTT and depicted different changes in the microbiota from CREB/CREC. Thus, CREs with different compositions of
berberine/
jatrorrhizine/
coptisine/
palmatine differed in terms of time-kill kinetics and
ATP production assays on C. perfringens. CREA revealed the potent bacterial inhibitory effects and
glucose-lowering activity.