ABSTRACT
Studies of inflammatory bowel disease (IBD) have been inconclusive in relating microbiota with distribution of inflammation. We report microbiota, host transcriptomics, epigenomics and genetics from matched inflamed and non-inflamed colonic mucosa [50 Crohn's disease (CD); 80 ulcerative colitis (UC); 31 controls]. Changes in community-wide and within-patient microbiota are linked with inflammation, but we find no evidence for a distinct microbial diagnostic signature, probably due to heterogeneous host-microbe interactions, and show only marginal microbiota associations with habitual diet. Epithelial DNA methylation improves disease classification and is associated with both inflammation and microbiota composition. Microbiota sub-groups are driven by dominant Enterbacteriaceae and Bacteroides species, representative strains of which are pro-inflammatory in vitro, are also associated with immune-related epigenetic markers. In conclusion, inflamed and non-inflamed colonic segments in both CD and UC differ in microbiota composition and epigenetic profiles.
Subject(s)
Colitis, Ulcerative/immunology , Crohn Disease/immunology , Epigenesis, Genetic/immunology , Gastrointestinal Microbiome/immunology , Host Microbial Interactions/immunology , Adult , Aged , Bacteroides/genetics , Bacteroides/immunology , Bacteroides/isolation & purification , Biopsy , Caco-2 Cells , Case-Control Studies , Cohort Studies , Colitis, Ulcerative/genetics , Colitis, Ulcerative/microbiology , Colitis, Ulcerative/pathology , Colon/diagnostic imaging , Colon/immunology , Colon/microbiology , Colon/pathology , Colonoscopy , Crohn Disease/genetics , Crohn Disease/microbiology , Crohn Disease/pathology , DNA, Bacterial/isolation & purification , Enterobacteriaceae/genetics , Enterobacteriaceae/immunology , Enterobacteriaceae/isolation & purification , Epigenomics , Female , Gastrointestinal Microbiome/genetics , Host Microbial Interactions/genetics , Humans , Intestinal Mucosa/diagnostic imaging , Intestinal Mucosa/immunology , Intestinal Mucosa/microbiology , Intestinal Mucosa/pathology , Male , Middle Aged , RNA, Ribosomal, 16S/genetics , RNA-Seq , Young AdultABSTRACT
AIMS: To evaluate the diversity and antimicrobial activity of bacteria from the marine sponges Suberites carnosus and Leucosolenia sp. METHODS AND RESULTS: Two hundred and thirty-seven bacteria were isolated from the sponges S. carnosus (Demospongiae) and Leucosolenia sp. (Calcarea). Isolates from the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria were obtained. Isolates of the genus Pseudovibrio were dominant among the bacteria from S. carnosus, whereas Pseudoalteromonas and Vibrio were the dominant genera isolated from Leucosolenia sp. Approximately 50% of the isolates from S. carnosus displayed antibacterial activity, and c. 15% of the isolates from Leucosolenia sp. demonstrated activity against the test fungal strains. The antibacterial activity observed was mostly from Pseudovibrio and Spongiobacter isolates, while the majority of the antifungal activity was observed from the Pseudoalteromonas, Bacillus and Vibrio isolates. CONCLUSIONS: Both sponges possess a diverse range of bioactive and potentially novel bacteria. Differences observed from the sponge-derived groups of isolates in terms of bioactivity suggest that S. carnosus isolates may be a better source of antibacterial compounds, while Leucosolenia sp. isolates appear to be a better source of antifungal compounds. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study in which cultured bacterial isolates from the marine sponges S. carnosus and a Leucosolenia sp. have been evaluated for their antibacterial activity. The high percentage of antibacterial isolates from S. carnosus and of antifungal isolates from Leucosolenia sp. suggests that these two sponges may be good sources for potentially novel marine natural products.
