关键词: 益生菌剂, 肠道疾病, 菌群丰度, Ion Torrent PGM测序技术, 生物信息学

Abstract: The aim of the present study was to explore the regulatory effect of probiotics on the intestinal microbial diversity and abundance in patient populations with intestinal diseases. A probiotic preparation (PPr) was regularly consumed at a constant amount for 6 weeks by healthy, constipated, diarrheal, abdominal bloating, irritable bowel syndrome and irregular defecation populations. Before, during and after the experiment, fecal samples were collected for bacterial genomic DNA extraction. The sequencing of 16S rRNA V3 region was performed with the Personal Genome Machine (PGM, Ion Torrent). The sequencing data were used for diversity analysis by bioinformatics and multivariate statistical analysis. When the sequencing depth was satisfactory, the effect of the probiotics in correcting gut microbiota imbalance in the subjects was evaluated at the four levels of phylum, family, genus and even species. All sequencing reads were divided into 2 320 operational taxonomic units at a 97% similarity level. Bacteroidestes, Firmicutes, Proteobacteria and Actinobacteria were the dominant phyla, accounting for 99.81% of the total number of sequences. For all the subjects, the probiotics had a longlasting positive impact on Lachnospiraceae whereas Alcaligenaceae, Rikenellaceae, Bifidobacteria (Bifidobacteriaceae) and other dominant bacteria returned to the pre-intervention level when the intervention was withdrawn. The effects of probiotics on gut microbiota were different among all patient populations, and both Cyanobacteria and Fusobacteria were detected in the constipation group after consumption of the priobiotics. Principal component analysis (PCA) analysis showed that the regulatory effect of the probiotics in the diarrheal group was superior to that in two other groups during the first to the fourth week of intervention. The diversity and abundance of 10 genera including Faecalibacterium, Acinetobacter, Blautia, Clostridium, Dialister, Eggerthella, Granulicatella, Lactobacillus, Oxalobacter, Pyramidobacter were significantly increased in the diarrheal group, while only three genera: Prevotella, Megamonas and Collinsella in the constipation group changed. Moreover, the other groups exhibited a change in the abundance of Adlercreutzia, Collinsella, Klebsiella, Parabacteroides, and Sutterella. PCA analysis also revealed obvious differences in the regulatory effect of the probiotics among different gut microbial populations and that the probiotics had different effects in improving and treating different intestinal diseases. In addition, Bacteroides and Odoribacter in the constipation group tended to decrease to normal levels. Heatmap analysis showed that several key functional fungi, such as Akkermansia muciniphila, Bacteroides fragilis and Faecalibacterium prausnitzii, were found to appear only at some stages, but disappear after the intervention was withdrawn. At this time, the original Bacteroides ovatus began to decrease. The appearance of these bacteria was beneficial to host health. In summary, probiotic intervention can play a role in altering the diversity and abundance of gut microbes and inhibit the growth of harmful microorganisms in the gut. More importantly, the appearance of beneficial bacteria manifests the physiological effectiveness of the probiotics. Therefore, the probiotics have promising applications in maintaining a healthy state of intestinal microflora.

Key words: probiotics, intestinal disease, flora abundance, Ion Torrent PGM sequencing technology, bioinformatics