AbstractObjectiveTo study the distribution of fecal microbiota in diarrhea‐predominant irritable bowel syndrome (IBS‐D) patients of spleen–kidney‐yang deficiency and liver depression and spleen deficiency, to make an objective foundation for dialectics of different type of IBS‐D. And to provide the clinical doctors an experimental basis for medication by regulating dysbacteriosis.MethodsWe collected feces from the control group, spleen–kidney‐yang deficiency IBS‐D group, and liver‐depression and spleen‐deficiency IBS‐D group. After the extraction of fecal DNA, global DNA was isolated from every sample, and 16S ribosomal RNA was sequenced, and then we analyzed the results for bacteria such as Alpha diversity, community composition, LEfSe, and partial least squares discriminant analysis.ResultsWe compared the changes among the fecal bacteria in the intestine of the IBS‐D patients and healthy controls and found the specificity of spleen–kidney‐yang deficiency syndrome and liver‐depression and spleen‐deficiency syndrome. The control group has the highest flora diversity (control group > liver‐depression and spleen‐deficiency > spleen–kidney‐yang deficiency group). The control group, spleen–kidney‐yang deficiency group, and liver‐depression and spleen‐deficiency group are different in phylum (Actinobacteria, Fusobacteria), class (Actinobacteria, Fusobacteria), order (Enterobacteriales, Bifidobacteriales, Fusobacteriales), and family (Bifidobacteriaceae, Ruminococcaceae, Enterobacteriaceae, Acidaminococcaceae, Veillonellaceae, Fusobacteriaceae). Bifidobacteriaceae and Ruminococcaceae in the control group, Enterobacteriales, Fusobacteriales, Acidaminococcaceae, and Phascolarctobacterium in the spleen–kidney‐yang deficiency group, and streptococcus are the specific bacteria in the liver‐depression and spleen‐deficiency group. Intestinal flora disturbance is closely related to IBS‐D.ConclusionsThere is a correlation between traditional Chinese medicine syndrome type and intestinal flora. The control group, the spleen–kidney‐yang deficiency group, and the liver‐depression and spleen‐deficiency group have specific bacteria.