Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case–control study in India

Abstract

BackgroundAlterations in the fecal bacterial flora occur in inflammatory bowel disease (IBD). We examined the abundance and diversity of Clostridium leptum group, an important group of carbohydrate-fermenting bacteria, in the feces of patients with IBD and compared them with healthy controls.MethodsSeventeen healthy controls (HC), 20 patients with Crohn’s disease (CD) and 22 patients with ulcerative colitis (UC) participated in the study. DNA extracted from fecal samples was amplified by PCR targeting 16S rRNA gene sequences specific to C. leptum group. The PCR product was subjected to temporal temperature gradient electrophoresis (TTGE) and the number and position of individual bands were noted and diversity was estimated. The identity of bands at different positions was confirmed by cloning and sequencing. Real time quantitative PCR with Mesa Green, targeted at specific 16S rRNA gene sequences, was used to quantitate C. leptum group and its most prominent constituent, Faecalibacterium prausnitzii.ResultsTwenty five different operational taxonomic units (OTUs, equivalent to species) were identified constituting the C. leptum group in these participants. Their sequences were deposited in GenBank [accession numbers GQ465348 to GQ465370]. OTU number was significantly reduced in CD (7.7±3.7, mean±SD) and UC (9.0±3.0) compared to HC (11.9±2.2) (P=0.0005). The Simpson D index of alpha diversity was not significantly different between the three groups. Total numbers of C. leptum group bacteria and F. prausnitzii were reduced in both CD and UC compared to HC (P=0.0036 and P<0.0001 respectively). Disease activity did not influence numbers of C. leptum or F. prausnitzii in patients with CD or UC.ConclusionC. leptum numbers and diversity were significantly reduced in both CD and UC suggesting that alterations noted were not specific to one disease. This could contribute to reduced short chain fatty acid production in IBD.

Complete genome sequence of Ruminococcaceae bacterium CPB6: A newly isolated culture for efficient n -caproic acid production from lactate

“…It consists of highly diverse bacterial species, many of which can produce short chain fatty acids (Miyake et al, 2015). leptum and Faecalibacterium, the most abundant members of this group, have been reported as major producers of butyrate through carbohydrate fermentation (Kabeerdoss et al, 2013;Louis and Flint, 2009). However, few species of Clostridium cluster IV have been reported to produce medium-chain carboxylic acid with the exception of Clostridium sp.…”

Mori Cortex regulates P-glycoprotein in Caco-2 cells and colons from rats with experimental colitis via direct and gut microbiota-mediated mechanisms

“…The reduction of total microbial diversity, increases of Enterobacteriaceae, Bacteroides-Prevotella, and decrease of Firmicutes were found in IBD patients. 38 These microbial alterations were accompanied with the immune imbalance and are believed to play a crucial role in inammatory events in IBD. In our study, using the 16S rRNA-based PCR analysis, we determined the changes of total gut bacteria and 5 specic bacteria that have been reported to be implicated in UC patients.…”

Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease

“…The firmicute Faecalibacterium prausnitzii (Ruminococcaceae) is one of the three most abundant species, representing approximately 6 to 8% of the gut microbial community in healthy subjects, although it can reach up to 20% in some individuals (1,(4)(5)(6)(7)(8)(9)(10)(11). In contrast, depletion of F. prausnitzii has been reported to occur in several pathological disorders (for a review, see reference 12 and references therein), such as Crohn's disease (CD) (12-19), ulcerative colitis (UC) (11,14,15,17,(20)(21)(22)(23)(24)(25)(26), irritable bowel syndrome (IBS) of alternating type (27), colorectal cancer (CRC) (28, 29), and diabetes (30-32).Many studies have shown the potential role of F. prausnitzii in promoting gut health through the secretion of anti-inflammatory compounds, such as butyrate (16,(33)(34)(35)(36), and in reducing the severity of colitis induced in mice (16,37). Despite being a relatively abundant bacterium capable of regulating gut homeostasis (38, 39) and interacting in several host pathways (40), few studies have paid attention to the distribution of phylotypes within Faecalibacterium populations in the human gut.…”

“…The firmicute Faecalibacterium prausnitzii (Ruminococcaceae) is one of the three most abundant species, representing approximately 6 to 8% of the gut microbial community in healthy subjects, although it can reach up to 20% in some individuals (1,(4)(5)(6)(7)(8)(9)(10)(11). In contrast, depletion of F. prausnitzii has been reported to occur in several pathological disorders (for a review, see reference 12 and references therein), such as Crohn's disease (CD) (12-19), ulcerative colitis (UC) (11,14,15,17,(20)(21)(22)(23)(24)(25)(26), irritable bowel syndrome (IBS) of alternating type (27), colorectal cancer (CRC) (28, 29), and diabetes (30-32).…”