OBJECTIVE: To investigate the fecal microbiota changes in patients with spleen(Pi)-deficiency(SPD), a common Chinese medicine syndrome with digestive and absorptive disturbances and to provide insight into the relationship between Chinese medicine syndrome and gut dysbiosis.METHODS: Fecal microbiotas from the stool samples of 53 SPD patients and 35 healthy subjects were analyzed via 16 S r RNA gene polymerase chain reaction(PCR)-denaturation gradient gel electrophoresis(DGGE). SPD-related marker genes from20 SPD patients and 20 healthy subjects were identified through gene sequencing, while some genes were quantified using quantitative PCR(q PCR). Discriminant analysis was conducted using SPSS software, and the canonical discriminant function formula for Pi-deficiency was established.RESULTS: Alterations in microbiota diversity and composition between the SPD and healthy groups were demonstrated via 16 S r RNA gene PCR-DGGE combined with multivariate statistical analysis. Fecal microbiota changes were also observed among different SPD-subtype patients. Eight SPD-related markers were found, and putative species corresponding to these markers were identified through gene sequencing, which may have potential associations with the common digestive dysfunctions in SPD patients. q PCR methods were established for two of these markers, which were significantly altered in the SPD patients. The canonical discriminant function formula was calculated for SPD, and the validity rates of these markers were over 85%.CONCLUSION: Fecal microbiotas are altered in patients with SPD, which may provide insight for further studies on clinically diagnosing and treating SPD. The results may also provide data to gain a better understanding of Traditional Chinese Medicine syndrome and gut dysbiosis.