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Probiotics have been applied extensively in aquaculture and demonstrated a range of benefits, but the mechanisms mediating such responses remain largely unknown. A clear illustration of the effect of probiotics on the autochthonous gut microbiota is the first step in understanding the underlying mechanisms. In this study, the autochthonous microbiota in the foregut, midgut and hindgut of juvenile grouper Epinephelus coioides following the dietary administration of probiotic Enterococcus faecium MM4 for 60 days were assessed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) with subsequent sequencing analysis. Generally similar DGGE patterns, with 15 common bands, were observed in the foregut, midgut and hindgut of fish fed the probiotic diet or the control diet, while more visible bands were present in fish fed the probiotic diet. The similarity dendrogram showed that the foregut samples formed an independent cluster distinctly different from the midgut and hindgut samples, but a high similarity (81.4%) was observed among the three gut sections. Significantly increased species richness and Shannon index were observed in the midgut and hindgut samples in the probiotic group compared with the control group, which suggested that probiotic E. faecium could elevate the autochthonous microbial diversity in the midgut and hindgut. Sequences analysis showed that probiotic E. faecium stimulated the growth of some unidentified bacteria and potentially beneficial bacteria, while exerted no apparent effect on potentially harmful Staphylococcus saprophyticus.

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