Alterations in the intestinal microbiota have been suggested as an etiological factor in the pathogenesis of irritable bowel syndrome (IBS). This study used a molecular fingerprinting technique to compare the composition and biodiversity of the microbiota within fecal and mucosal niches between patients with diarrhea-predominant IBS (D-IBS) and healthy controls. Terminal-restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the bacterial 16S rRNA gene was used to perform microbial community composition analyses on fecal and mucosal samples from patients with D-IBS ( n = 16) and healthy controls ( n = 21). Molecular fingerprinting of the microbiota from fecal and colonic mucosal samples revealed differences in the contribution of T-RFs to the microbiota between D-IBS patients and healthy controls. Further analysis revealed a significantly lower (1.2-fold) biodiversity of microbes within fecal samples from D-IBS patients than healthy controls ( P = 0.008). No difference in biodiversity in mucosal samples was detected between D-IBS patients and healthy controls. Multivariate analysis of T-RFLP profiles demonstrated distinct microbial communities between luminal and mucosal niches in all samples. Our findings of compositional differences in the luminal- and mucosal-associated microbiota between D-IBS patients and healthy controls and diminished microbial biodiversity in D-IBS fecal samples further support the hypothesis that alterations in the intestinal microbiota may have an etiological role in the pathogenesis of D-IBS and suggest that luminal and mucosal niches need to be investigated.

BackgroundRecent studies have suggested a role for an altered intestinal microbiota in the pathophysiology of irritable bowel syndrome (IBS). However, no consensus has been reached regarding the association between specific enteric bacterial groups and IBS. The aim of this study was to investigate the fecal and mucosal-associated microbiota using two independent techniques in intestinal samples from diarrhea-predominant IBS (D-IBS) and healthy controls.MethodsFecal and colonic mucosal biopsy samples were obtained from 10 D-IBS patients and 10 healthy controls. Colonic tissue was collected during a un-sedated un-prepped flexible sigmoidoscopy. Fecal and tissue samples were processed immediately upon collection for culture under aerobic and anaerobic conditions or frozen for further molecular analysis. DNA was extracted from all frozen samples and used to enumerate specific bacterial groups using quantitative real-time PCR (qPCR).ResultsCulture analysis of intestinal samples demonstrated a significant reduction in the concentration of aerobic bacteria in fecal samples from D-IBS patients when compared to healthy controls (1.4 × 107 vs. 8.4 × 108 CFUs/g feces, P = 0.002). qPCR analysis demonstrated a significant 3.6 fold increase (P = 0.02) in concentrations of fecal Lactobacillus species between D-IBS patients and healthy controls.ConclusionsOur culture and molecular data indicate that quantitative differences exist in specific bacterial groups in the microbiota between D-IBS and healthy subjects.

One strain of Lactobacillus salivarius, two strains of Lactobacillus reuteri and Lactobacillus amylovorus, and two strains of Bifidobacterium thermacidophilum with antagonistic effect against Clostridium perfringens were isolated from porcine gastrointestinal tract. Isolates were assayed for their ability to survive in synthetic gastric juice at pH 2.5 and were examined for their ability to grow on agar plate containing porcine bile extract. There was a large variation in the survival of the isolates in gastric juice and growth in the medium containing 0.3% (w/v) bile. L. salivarius G11 and L. amylovorus S6 adhered to the HT-29 epithelial cell line. Cell-free supernatant of L. amylovorus S6 showed higher antagonistic activity as effective as the antibiotics such as neomycin, chlortetracycline, and oxytetracycline against bacterial pathogens including C. perfringens, Salmonella typhimurium, Staphylococcus aureus, Vibrio cholerae, Edwardsiella tarda, and Aeromonas salmonicida subsp. salmonicida.

Two red pigment-producing bacterial strains with a metallic green sheen were isolated from a sediment sample of getbol, the Korean tidal flat. Phylogenetic analysis based on 16S rDNA sequences showed that these isolates represent a phyletic lineage within the c-Proteobacteria that is distantly related to the genus Hahella. No bacterial species with validly published names showed ¢92 % 16S rRNA similarity with the getbol isolates. The strains were Gram-negative, chemo-organotrophic, aerobic and required NaCl (1-7 %) for growth. They produced pigments with maximum absorption at 540 nm, which indicated the presence of prodigiosin, a well-known red pigment previously detected in Serratia marcescens. The major isoprenoid quinone was ubiquinone-9. The predominant cellular fatty acids were saturated and monounsaturated straight-chain fatty acids. The DNA G+C contents ranged from 40 to 42 mol%. The combination of physiological, biochemical and chemotaxonomic data clearly separated the test strains from other phylogenetically related genera in the c-Proteobacteria. On the basis of polyphasic evidence from this study, it is proposed that the two getbol isolates should be classified in a novel genus, Zooshikella gen. nov., as Zooshikella ganghwensis sp. nov.The Korean tidal flat, called getbol, is the neutral zone that connects land and sea; it is largely found along the west coast of the Korean peninsula. It has been well-known for its vital biological functions, such as bioremediation of pollutants, fishery products, flood control, spawning and nursery grounds for marine animals, which may result from microbial activities and diversity (Korea Ocean Research & Development Institute, 1998). However, members of microbial communities in getbol are largely unknown, as they have never been the subject of systematic taxonomic investigation. Recently, we have initiated a study that involves the isolation and identification of members of the aerobic bacterial community from getbol. In this study, we present the taxonomic properties of two isolates, for which the name Zooshikella ganghwensis sp. nov. is proposed. IsolationTwo aerobic, halophilic bacterial strains were isolated from a sediment sample collected from the getbol of Ganghwa Island in Korea (37u 359 31?90 N, 126u 279 24?50 E). The sample was diluted with sterilized artificial sea water (ASW; Lyman & Fleming, 1940), spread onto a plate containing marine agar 2216 (MA; Difco) and incubated at 25 uC for 3 weeks. The isolates were routinely cultured on MA and maintained as glycerol suspensions (20 %, w/v) at 280 uC. Molecular systematics16S rDNA was enzymically amplified from a single colony. Primers, PCR conditions and sequencing were performed as described elsewhere (Chun & Goodfellow, 1995). The 16S rDNA sequences of strains JC2044T and JC2045 were manually aligned with representative sequences of the c-Proteobacteria obtained from GenBank. Phylogenetic trees were inferred by using the Fitch-Margoliash (Fitch & Margoliash, 1967), maximum-likelihood (Felsenstein, 1993, ...

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