LOOKING FOR THE MOST USEFUL TAXA AS MICROBIAL BIOMARKERS TO DECIPHER IBD MICROBIOTA: A PILOT STUDY

INTRODUCTION AND AIM: The existing literature on human intestinal microbiota in IBDdoes not reveal uniform alterations in microbiota composition among all patients and mostof studies have been conducted on fecal microbiota. The aim of the present study was toevaluate the mucosal and fecal microbiota composition in healthy controls (CTRLs) andIBD patients, in a case-control study exploited by 16S rRNA targeted metagenomics-basedapproach. METHODS: Fecal specimens were collected from 14 IBD patients [10 Crohn'sdisease (CD), 4 ulcerative colitis (UC)], and from 11 healthy subjects, undergone colonoscopyfor screening. Mucosal specimens were obtained during colonoscopy from the terminalileum, and descending colon. All patients were in wash-out from antibiotics, probiotics andcorticosteroids. PH was assessed by pyrosequencing as follows: Genomic DNA was isolatedfrom the entire set of samples. The V1-V3 region of 16S rRNA locus was amplified on a454-Junior Genome Sequencer. Reads were analyzed by Quantitative Insights into MicrobialEcology, grouped into operational taxonomic units (OTUs) at a sequence similarity level of97% for taxonomic assignment, and aligned for OTUs matching against Greengenes database.RESULTS: In adult IBD patients colonic biopsies showed a statistically significant increaseof Proteobacteria and decrease of butyrate producing bacteria (Roseburia, Faecalibacteriumprausnitzii, Ruminococcus) compared to CTRLs. The microbiota analysis of stool samplesshowed only a predominant presence of Enterobacteriaceae in IBD compared to CTRLs(P<0.05). Stratifying patients findings, according to intestinal sampling site, only in colonbiopsies a significant reduction of butyrate producing bacteria was observed. At phylum level,a significant decrease of Proteobacteria and Firmicutes togheter with a reduced abundanceof Bacteroidetes was evident in IBD biopsies compared to fecal samples. Finally, in activedisease status, a decrease of Ruminococcus, Peptostreptococcus and Paraprevotella and anincrease in Enterococcus was found(P<0.05). CONCLUSION: In IBD patients there is areduction of butyrate-producing bacteria, more pronounced in mucosal- than in faecalassociatedmicrobiota. It appears that microbiota adhering to the gut mucosa better discriminatespatients from controls especially at family/species level. Our data suggest to go intothe direction of diagnostic pipeline to improve microbiota profiling with special referenceto mucosal biosystem: disease bacterial biomarker searching and characterization