Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease.

The global alteration of the gut microbial community (dysbiosis) plays an important role in the pathogenesis of inflammatory bowel diseases (IBDs). However, bacterial species that characterize dysbiosis in IBD remain unclear. In this study, we assessed the alteration of the fecal microbiota profile in patients with Crohn's disease (CD) using 16S rRNA sequencing. Fecal samples from 10 inactive CD patients and 10 healthy individuals were subjected to 16S rRNA sequencing. The V3-V4 hypervariable regions of 16S rRNA were sequenced by the Illumina MiSeq™II system. The average of 62,201 reads per CD sample was significantly lower than the average of 73,716 reads per control sample. The genera Bacteroides, Eubacterium, Faecalibacterium and Ruminococcus significantly decreased in CD patients as compared to healthy controls. In contrast, the genera Actinomyces and Bifidobacterium significantly increased in CD patients. At the species level, butyrate-producing bacterial species, such as Blautia faecis, Roseburia inulinivorans, Ruminococcus torques, Clostridium lavalense, Bacteroides uniformis and Faecalibacterium prausnitzii were significantly reduced in CD patients as compared to healthy individuals (p < 0.05). These results of 16S rRNA sequencing were confirmed in additional CD patients (n = 68) and in healthy controls (n = 46) using quantitative PCR. The abundance of Roseburia inulinivorans and Ruminococcus torques was significantly lower in C-reactive protein (CRP)-positive CD patients as compared to CRP-negative CD patients (p < 0.05). The dysbiosis of CD patients is characterized by reduced abundance of multiple butyrate-producing bacteria species.

Takahashi K ，Nishida A ，Fujimoto T ，Fujii M ，Shioya M ，Imaeda H ，Inatomi O ，Bamba S ，Sugimoto M ，Andoh A ... -  《-》

Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease.

Ma HQ ，Yu TT ，Zhao XJ ，Zhang Y ，Zhang HJ ... -  《-》

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.

Nishino K ，Nishida A ，Inoue R ，Kawada Y ，Ohno M ，Sakai S ，Inatomi O ，Bamba S ，Sugimoto M ，Kawahara M ，Naito Y ，Andoh A ... -  《-》

Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray.

A custom phylogenetic microarray composed of small subunit ribosomal RNA probes, representing ≈500 bacterial species from the human and animal gut, was developed and evaluated for analysis of gut microbial diversity using fecal samples from healthy subjects and Crohn's disease (CD) patients. Oligonucleotide probes (≈40 mer) used on the microarray were selected from published articles or designed with the "GoArray" microarray probe design program using selected bacterial 16S rRNA sequences. Fecal 16S rDNA from individual samples of six healthy subjects and six CD patients were used as template to generate fluorescently labeled cRNA that was hybridized to the microarray. Differences revealed by the microarray in relative abundance of microbial populations between healthy and diseased patients were verified using quantitative real-time polymerase chain reaction (PCR) with species-specific primer sets. The microarray analyses showed that Eubacterium rectale, Bacteroides fragilis group, B. vulgatus, Ruminococcus albus, R. callidus, R. bromii, and Faecalibacterium prausnitzii were 5-10-fold more abundant in the healthy subjects than in the CD patients, while Enterococcus sp., Clostridium difficile, Escherichia coli, Shigella flexneri, and Listeria sp. were more abundant in the CD group. The microarray detected differences in abundance of bacterial populations within the phylum Firmicutes that had been reported previously for the same samples based on phylogenetic analysis of metagenomic clone libraries. In addition, the microarray showed that Enterococcus sp. was in higher abundance in the CD patients. This microarray should be another useful tool to examine the diversity and abundance of human intestinal microbiota.

Kang S ，Denman SE ，Morrison M ，Yu Z ，Dore J ，Leclerc M ，McSweeney CS ... -  《-》

Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea.

The bovine gastrointestinal microbiota is a complex polymicrobial ecosystem that plays an important role in maintaining mucosal health. The role of mucosal microbial populations in the pathogenesis of gastrointestinal diseases has been well established in other species. However, limited information is available about changes in the fecal microbiota that occur under disease conditions, such as hemorrhagic diarrhea in feedlot cattle. The objectives of this study were to characterize the differences in fecal microbiota composition, diversity and functional gene profile between feedlot calves with, and without, hemorrhagic diarrhea. Deep fecal swabs were collected from calves with hemorrhagic diarrhea (n = 5) and from pen matched healthy calves (n = 5). Genomic DNA was extracted, and V1-V3 hypervariable region of 16S rRNA gene was amplified and sequenced using the Illumina MiSeq sequencing. When compared to healthy calves, feedlot cattle with hemorrhagic diarrhea showed significant increases in the relative abundance of Clostridium, Blautia and Escherichia, and significant decreases in the relative abundance of Flavobacterium, Oscillospira, Desulfonauticus, Ruminococcus, Thermodesulfovibrio and Butyricimonas. Linear discriminant analysis effect size (LEfSe) also revealed significant differences in bacterial taxa between healthy calves and hemorrhagic diarrhea calves. This apparent dysbiosis in fecal microbiota was associated with significant differences in the predictive functional metagenome profiles of these microbial communities. In summary, our results revealed a bacterial dysbiosis in fecal samples of calves with hemorrhagic diarrhea, with the diseased calves exhibiting less diversity and fewer observed species compared to healthy controls. Additional studies are warranted in a larger cohort of animals to help elucidate the trajectory of change in fecal microbial communities, and their predictive functional capacity, in calves with other gastrointestinal diseases.

Zeineldin M ，Aldridge B ，Lowe J 《-》