Molecular analysis of the root canal microbiota associated with endodontic treatment failures.

INTRODUCTION: The failure of endodontic treatment is usually caused by persistent/secondary intraradicular infections and Enterococcus faecalis has been considered to be the main pathogen involved. Nevertheless, the breadth of bacterial diversity involved with endodontic treatment failures remains to be consistently explored by culture-independent approaches. METHODS: This study determined the intraradicular microbiota of root-canal-treated teeth with post-treatment apical periodontitis using 16S ribosomal RNA gene clone library analysis. RESULTS: Bacteria were present in all cases, confirming the infectious etiology of post-treatment disease. Seventy-four bacterial taxa belonging to six phyla were found in the nine cases investigated. Of these, 55% were identified as as-yet-uncultivated phylotypes, which also made up a significant proportion of the microbiota in many cases. Twenty-five new phylotypes were identified. Most teeth harbored a mixed consortium, with a mean number of 10 taxa per case. Only 11 taxa were found in more than one case, revealing a high interindividual variability in the composition of the microbiota. CONCLUSION: The current findings revealed new candidate endodontic pathogens, including as-yet-uncultivated bacteria and taxa other than E. faecalis, which may participate in the mixed infections associated with post-treatment apical periodontitis.

A novel keratinase from Clostridium sporogenes bv. pennavorans bv. nov., a thermotolerant organism isolated from solfataric muds.

A bacterium which can grow on chicken feathers and which exhibits keratinolytic activity was isolated from solfataric muds. It was classified as belonging to the genus Clostridium and closely related to C. sporogenes. Based on its unique capability to degrade chicken feathers, it was designated as Clostridium sporogenes bv. pennavorans bv. nov. The keratinase purified from the culture supernatant is a monomer of 28.7kDa molecular mass. The enzyme is relatively thermostable and is active over a broad range of temperature and pH. Specific enzymatic assays demonstrate that keratinase can act on a large variety of soluble and insoluble protein substrates.

Fluctuation of fecal microbiota in individuals with Japanese cedar pollinosis during the pollen season and influence of probiotic intake.

BACKGROUND: We have previously reported the results of a randomized, double-blind, placebo-controlled trial that found the intake of yogurt supplemented with a probiotic strain, Bifidobacterium longum BB536, alleviates symptoms and affects blood parameters in individuals with Japanese cedar pollinosis (JCPsis) during the pollen season. OBJECTIVE: In the present study, fecal microbiota were investigated to examine whether any changes occur during the pollen season and whether any influence is exerted by probiotic intake. METHODS: Yogurt either with BB536 (BB536 yogurt) or without BB536 (placebo yogurt) was administered for 14 weeks at 2 x 100 g per day to 40 subjects (17 men, 23 women) with a clinical history of JCPsis. Fecal samples were obtained from 23 subjects (placebo group, n=13; BB536 group, n=10) before and during the intervention (weeks 4, 9 and 13) and fecal microbiota were analyzed using terminal-restriction fragment length polymorphism and real-time polymerase chain reaction (PCR) methods. RESULTS: From the fluctuation patterns of terminal-restriction fragments, the Bacteroides fragilis group and bifidobacteria were among the species that changed most with pollen dispersion. Real-time PCR analyses indicated that the cell numbers of the B fragilis group increased significantly along with pollen dispersion in both BB536 and placebo groups. Cell numbers of bifidobacteria were significantly higher in the BB536 group compared with the placebo group (P < .05 at weeks 4 and 9). The ratio of cell numbers of the B fragilis group to bifidobacteria increased significantly during the pollen season in the placebo group (P < .01 at weeks 9 and 14), but not in the BB536 group. An in vitro study using peripheral blood mononuclear cells from JCPsis subjects indicated that strains of the B fragilis group induced significantly more helper T cell (T(H)) type2 cytokines (interleukin [IL]-6) but fewer T(H)1 cytokines (IL-12 and interferon) compared with those of bifidobacteria. CONCLUSIONS: These results suggest a relationship between fluctuation in intestinal microbiota and pollinosis allergy. Furthermore, intake of BB536 yogurt appears to exert positive ihfluences on the formation of anti-allergic microbiota.

Effects of heat-killed Lactobacillus kunkeei YB38 on human intestinal environment and bowel movement: a pilot study.

It is well known that lactic acid bacteria supplementation is beneficial for intestinal conditions such as microbiota; however, the effects of killed-lactic acid bacteria on intestinal conditions are largely unclear. This study aimed to evaluate the effect of heat-killed Lactobacillus kunkeei YB38 (YB38) at a dose of approximately 10 mg/day on human intestinal environment and bowel movement. This single-blind study enrolled 29 female subjects with a low defecation frequency who consumed heat-killed YB38 at four increasing dosage levels: 0 (placebo), 2, 10, and 50 mg. Each dose was consumed daily for two weeks, with a two-week baseline period preceding the dosing-period and a two-week washout period ending the study. Observed levels of Bacteroides fragilis group significantly decreased with intake of heat-killed YB38 at ≥10 mg/day compared with levels during placebo intake (P<0.01). Faecal pH significantly decreased with 10 and 50 mg/day intake (P<0.01 and 0.05, respectively). Acetic acid levels tended to increase in faeces at the 50 mg/day dose (P<0.1). Bowel movement tended to increase in all heat-killed YB38 intake periods (P<0.1). In conclusion, heat-killed YB38 altered human intestinal microbiota at doses of ≥10 mg/day and tended to increase bowel movement at ≥2 mg/day. This is the first study to show the intestinal microbiota-altering effect of L. kunkeei and to report the bowel movement-improving effect of heat-killed lactic acid bacteria.

Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study.

Diet has a significant influence on the intestinal environment. In this study, we assessed changes in the faecal microbiota induced by an animal-based diet and the effect of the ingestion of yoghurt supplemented with a probiotic strain on these changes. In total, 33 subjects were enrolled in an open, randomised, parallel-group study. After a seven-day pre-observation period, the subjects were allocated into three groups (11 subjects in each group). All of the subjects were provided with an animal-based diet for five days, followed by a balanced diet for 14 days. Subjects in the first group ingested dairy in the form of 200 g of yoghurt supplemented with Bifidobacterium longum during both the animal-based and balanced diet periods (YAB group). Subjects in the second group ingested yoghurt only during the balanced diet period (YB group). Subjects who did not ingest yoghurt throughout the intervention were used as the control (CTR) group. Faecal samples were collected before and after the animal-based diet was provided and after the balanced diet was provided, followed by analysis by high-throughput sequencing of amplicons derived from the V3-V4 region of the 16S rRNA gene. In the YB and CTR groups, the animal-based diet caused a significant increase in the relative abundance of Bilophila, Odoribacter, Dorea and Ruminococcus (belonging to Lachnospiraceae) and a significant decrease in the level of Bifidobacterium after five days of intake. With the exception of Ruminococcus, these changes were not observed in the YAB group. No significant effect was induced by yoghurt supplementation following an animal-based diet (YB group vs CTR group). These results suggest that the intake of yoghurt supplemented with bifidobacteria played a role in maintaining a normal microbiota composition during the ingestion of a meat-based diet. This study protocol was registered in the University Hospital Medical Information Network: UMIN000014164.

Mucosa-associated bacteria in ulcerative colitis before and after antibiotic combination therapy.

BACKGROUND: We proposed that Fusobacterium varium is one of the causative agents in ulcerative colitis. AIM: To examine the efficacy of antibiotic combination therapy against F. varium and to investigate the mucosa-associated bacteria before and after the therapy using a new molecular approach. METHODS: Twenty patients with ulcerative colitis were randomly assigned into the antibiotic treatment group (amoxicillin, tetracycline and metronidazole for 2 weeks) and no-antibiotics group. Clinical assessment, colonoscopic and histological evaluations were performed at 0 and 3-5 months after the treatment. DNA from mucosal bacteria was isolated from biopsy specimens. We investigated the mucosa-associated bacterial components by terminal restriction fragment length polymorphism with the restriction enzyme HhaI and MspI, and quantified the change in the number of bacteria by real-time polymerase chain reaction. Immunohistochemical detection of F. varium in biopsy specimens was also performed. RESULTS: After the treatment, the clinical assessment, colonoscopic and histological scores improved in the antibiotic group compared with the control group. Three peaks of terminal restriction fragment length polymorphism decreased after treatment only in the antibiotic group. Eubacterium rectale, Dorea formicigenerans, Clostridium clostridioforme and F. varium were included in these peaks. Based on the real-time polymerase chain reaction study, only F. varium was significantly reduced after treatment. In the immunostaining, post-treatment scores in treatment group were significantly lower than that in control group. CONCLUSIONS: Antibiotics combination therapy was effective for ulcerative colitis. The number of mucosa-associated F. varium significantly decreased after the treatment.

Quantification of Blautia wexlerae and Blautia luti in human faeces by real-time PCR using specific primers.

The Clostridium coccoides group, including the genus Blautia and other genera, is one of the predominant bacterial groups in the human intestine. We re-examined 266 human faecal clones and 58 isolates in the C. coccoides group isolated by Hayashi et al. (2002) in order to elucidate the detailed distribution of Blautia wexlerae and Blautia luti in human faeces. Subsequently, we designed a primer pair specific for B. wexlerae and B. luti based on the 16S ribosomal RNA (16S rRNA) gene sequence. The number of B. wexlerae and B. luti in faecal samples of 12 healthy Japanese subjects was examined by real-time PCR assay. The number of the C. coccoides group in the 12 faecal samples was also determined using C. coccoides group-specific primers. Re-examination of the human faecal clones and isolates revealed that B. wexlerae and B. luti accounted for 19.5% of the clones and 25.9% of the isolates. B. wexlerae and B. luti were detected in all faecal samples with 5.3±3.2×10(9) cells/g faeces (wet weight, average ± standard deviation) as assessed by real-time PCR. Furthermore, B. wexlerae and B. luti constituted 32.3±12.7% (average ± standard deviation) of the C. coccoides group (1.7±0.8×10(10) cells/g faeces). This demonstrates that B. wexlerae and B. luti were presented in human faeces with a high frequency as the dominant bacteria.

Fecal flora of infants with biliary atresia: effects of the absence of bile on fecal flora.

The fecal flora of nine bottle-fed infants with biliary atresia were examined to determine the effects of the absence of bile on the intestinal flora. The numbers of the following fecal flora were significantly reduced compared with healthy infants: bifidobacteria, lecithinase-negative clostridia, streptococci, and staphylococci. Bifidobacteria were reduced to the greatest extent, constituting 75% of total flora in healthy comparison infants but only 2.4% in infants with biliary atresia. The most prevalent bacteria in infants with biliary atresia were enterobacteria.

Influence of lactobacillus spp. from An inoculant and of weissella and leuconostoc spp. from forage crops on silage fermentation

Lactobacillus spp. from an inoculant and Weissella and Leuconostoc spp. from forage crops were characterized, and their influence on silage fermentation was studied. Forty-two lactic acid-producing cocci were obtained from forage crops and grasses. All isolates were gram-positive, catalase-negative cocci that produced gas from glucose, and produced more than 90% of their lactate in the D-isomer form. These isolates were divided into groups A and B by sugar fermentation patterns. Two representative strains from the two groups, FG 5 and FG 13, were assigned to the species Weissella paramesenteroides and Leuconostoc pseudomesenteroides, respectively, on the basis of DNA-DNA relatedness. Strains FG 5, FG 13, and SL 1 (Lactobacillus casei), isolated from a commercial inoculant, were used as additives to alfalfa and Italian ryegrass silage preparations. Lactic acid bacterium counts were higher in all additive-treated silages than in the control silage at an early stage of ensiling. During silage fermentation, inoculation with SL 1 more effectively inhibited the growth of aerobic bacteria and clostridia than inoculation with strain FG 5 or FG 13. SL 1-treated silages stored well. However, the control and FG 5- and FG 13-treated silages had a significantly (P < 0.05) higher pH and butyric acid and ammonia nitrogen contents and significantly (P < 0. 05) lower lactate content than SL 1-treated silage. Compared with the control silage, SL 1 treatments reduced the proportion of D-(-)-lactic acid, gas production, and dry matter loss in two kinds of silage, but the FG 5 and FG 13 treatments gave similar values in alfalfa silages and higher values (P < 0.05) in Italian ryegrass silage. The results confirmed that heterofermentative strains of W. paramesenteroides FG 5 and L. pseudomesenteroides FG 13 did not improve silage quality and may cause some fermentation loss.

Rapid identification and quantification of Collinsella aerofaciens using PCR.

The number and incidence of Collinsella aerofaciens in the human intestine are the highest among Gram-positive non-spore-forming bacilli. Identification of this species is very difficult and requires considerable time. A PCR-based identification system using C. aerofaciens-specific primers is described. Using this PCR method, we identified 181 C. aerofaciens-like species isolated from human feces. These 181 strains were identified using the traditional method in past studies. Results of both methods matched. The direct detection method was performed using human feces samples from seven adults. Nested PCR was applied directly to the samples and all seven samples were positive. Quantification studies were performed using LightCycler¿trade mark omitted¿. The assay uses a double-stranded DNA dye to continuously monitor product formation and in a short time is able to quantify samples to 5 log units in concentration.

Cloning, sequencing and complementation analysis of the recA gene from Prevotella ruminicola.

Degenerate PCR primers based on conserved RecA protein regions were used to amplify a portion of recA [corrected] from Prevotella ruminicola strain 23, which was used as a probe to isolate the full-length recA gene from the P. ruminicola genomic library. The P. ruminicola recA gene encoded a protein of 340 amino acids with a molecular mass of 36.81 kDa, P. ruminicola RecA was highly similar to other RecA proteins and most closely resembled that of Bacteroides fragilis (75% identity). It alleviated the methyl methanesulfonate and mitomycin C sensitivities of Escherichia coli recA mutants, but did not restore the resistance to UV-light irradiation. Mitomycin C treatment of otherwise isogenic E. coli strains showed a higher level of prophage induction in a recA harboring lysogen.

A small cryptic plasmid from Ruminobacter amylophilus NIAH-3 possesses functional mobilization properties.

The complete nucleotide sequence of a small cryptic plasmid designated pRAO1, from the Gram-negative ruminal bacterium Ruminobacter amylophilus NIAH-3, was determined. The plasmid is a circular DNA molecule, 2140 bp in size, with a GC content of 40%. Computer-assisted analysis identified three open reading frames (ORFs), one of which, ORF3 (347 amino acids), displayed a high degree of amino acid identity with the Mob proteins involved in conjugative mobilization and interplasmid recombination of plasmids from Gram-positive bacteria. We proved the mobilization properties of pRAO1 in the Escherichia coli system using the coresident IncW broad-host-range conjugative plasmid R388. These data demonstrated, for the first time, the mobilization properties of small cryptic plasmids from Gram-negative inhabitants of the rumen.

Impact of LKM512 yogurt on improvement of intestinal environment of the elderly.

Improvement of the intestinal environment by administration of LKM512 yogurt was examined using polyamine, haptoglobin and mutagenicity as indexes which directly reflect the health condition of the host. The concentration of spermine in feces increased significantly by 3-fold (P<0.05) at week 2 of administration of LKM512 yogurt compared with before administration, and that of putrescine, spermidine, and cadaverine also tended to increase with administration of LKM512 yogurt. The haptoglobin content in feces decreased significantly (P<0.05) at week 2 of administration of LKM512 yogurt, and it showed a negative correlation with the polyamine content, indicating that acute intestinal inflammation was suppressed. Fecal mutagenicity was measured using fecal extract and fecal precipitate. Both preparations showed similar significant decreases (P<0.05) by the administration of LKM512 yogurt, as well as a negative correlation with polyamine content. This result indicated that antimutagenicity due to administration of LKM512 yogurt was not based on binding of the mutagen to the bacterial cell wall. Many reports have suggested that polyamines increased by the administration of LKM512 yogurt led to inhibition of inflammation and antimutagenicity in the intestinal tract.

Comparison of mucosal adhesion and species identification of bifidobacteria isolated from healthy and allergic infants.

Fifty bifidobacteria strains were isolated from fecal samples of allergic and age matched healthy infants. Allergic infants were found to have an adult type Bifidobacterium flora with high levels of Bifidobacterium adolescentis. Healthy infants had a typical infant Bifidobacterium flora with high levels of Bifidobacterium bifidum. These isolates were tested for their adhesive properties to human intestinal mucus. The adhesion of the fecal bifidobacteria from healthy infants was significantly higher (P<0.0001) than for allergic infants. This suggests a correlation between allergic disease and the composition of the intestinal bifidobacteria flora which has reduced adhesive abilities to the intestinal mucus. Therefore, dietary supplementation of bifidobacteria typical for healthy infants, may be beneficial in the treatment of allergic disorders.

Modification of the minitek system for identification of lactobacilli.

Seventy-eight strains of 23 Lactobacillus species, including 41 reference strains and 37 fresh isolates from faeces of men and pigs or caecal contents of mice, were used in comparing the conventional tube test with the Minitek system (BBL) to evaluate the feasibility of the latter to identify lactobacilli. In addition, the following parameters were tested: (i) the effect of variation in inoculum broth and cultural methods, (ii) the reproducibility of reactions on each substrate. The Minitek system includes a new lactobacilli inoculum broth (LIB) and three substrates: ribose, melezitose, and amygdalin. The overall correlation was 84% by the anaerobic steel-wool jar method and 72.5% by overlaying sterile oil with the Minitek inoculum broth (MIB) for the identification of anaerobes; whereas with LIB, the overall agreement was 95.4% by the anaerobic jar method and 84.4% by the oil procedure. The agreement of the identification between the Minitek systems and conventional tests was best (85.9%) with LIB by the anaerobic jar method and poorest with the MIB overlaid with oil. In the reproducibility of reactions, 247 (17.2%) of a total of 1,440 sets of disks gave variable reactions with MIB when incubated under the anaerobic jar method as compared to only 29 (2.0%) with LIB. The Minitek system for the identification of lactobacilli is more accurate and reliable when inoculated with LIB and incubated under the anaerobic jar method.

Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., New Species from Abscesses and Feces of Pigs.

Bacteroides pyogenes, Bacteroides suis and Bacteriodes helcogenes, three new species isolated from abscesses and feces of pigs, are described. They are obligately anaerobic, Gram-negative, non-motile, non-pigment-forming, non-spore-forming rods that produce succinic and acetic acids (often with traces of propionic and isovaleric acids) in peptone-yeast-glucose medium and do not grow well in 20% bile. The newly described species are phenotypically similar to strains of B. ruminicola and B. oralis. However, the new species have a low level of DNA /DNA homology with B. ruminicola, B. oralis and related organisms and also with each other.

Treponema socranskii, Treponema denticola, and Porphyromonas gingivalis are associated with severity of periodontal tissue destruction.

BACKGROUND: The aim of the present study was to identify Treponema socranskii in addition to Treponema denticola and Porphyromonas gingivalis by polymerase chain reaction (PCR), and to clarify the relationship between the presence of these microorganisms and the severity of clinical periodontal parameters. METHODS: Saliva and subgingival plaque collected from 123 subjects (38 aggressive periodontitis patients, 65 chronic periodontitis patients, 20 healthy patients) were subjected to PCR to detect the aforementioned 3 microorganisms. RESULTS: Detection frequencies of T. socranskii, T. denticola, and P. gingivalis in plaque samples from aggressive periodontitis patients (71.1%, 73.7%, 84.2%, respectively) and chronic periodontitis patients (89.2%, 93.8%, 95.3%) were much higher than those from healthy subjects (30%, 5.0%, 10.0%). In aggressive and chronic periodontitis patients, these 3 species of bacteria were detected frequently at sites that showed deep periodontal pockets and severe attachment loss. The percentage of these bacteria-positive sites increased as the gingival index score of chronic periodontitis patients increased. T. socranskii was frequently detected together with T. denticola or P. gingivalis at the same sites, and coexistence of these microorganisms was frequently observed in deep periodontal pockets of aggressive periodontitis patients. CONCLUSIONS: T. socranskii, T. denticola, and P. gingivalis were frequently detected in periodontitis patients by PCR. The prevalence of these 3 microorganisms was correlated with various clinical parameters. Taken together, our findings suggest that T. socranskii, T. denticola, and P. gingivalis are associated with the severity of periodontal tissue destruction.

Effects of beta-lactam antibiotics on intestinal microflora and bile acid metabolism in rats.

Wistar male rats were treated for six days with broad spectrum beta-lactam antibiotics, latamoxef, and cefotaxime. On the seventh day, the number of fecal anaerobic microbes decreased, total fecal bile acids decreased, and bile acid pools increased. Secondary bile acids such as beta-hyocholic, hyodeoxycholic, lithocholic, and deoxycholic acids decreased in the feces while the primary bile acids, cholic, beta-muricholic, and chenodeoxycholic acids, became predominant. Coprostanol, a microbial metabolite of cholesterol, also disappeared from the feces during the treatment. The cecum enlarged to almost twice the size of that in control rats, whereas the liver weight was not significantly changed. After treatment was stopped, the number of fecal microbes returned to the initial counts within a week, but restoration of bile acid and cholesterol metabolism required at least three weeks.

Construction of Prevotella ruminicola-Escherichia coli shuttle vector pRAM45 and transformation of P. ruminicola strains by electroporation.

A new plasmid shuttle vector, pRAM45, was constructed from the Escherichia coli plasmid pACYC184 and the cryptic plasmid pRAM4, which was originally isolated by us from Prevotella ruminicola T31 (Ogata et al., Plasmid, 35, 91-97, 1996). The vector was electrotransformed into different P. ruminicola strains. Polymerase chain reaction and Southern hybridization experiments confirmed its integrity in P. ruminicola transformants.

Enzymatic profiles of Erysipelothrix rhusiopathiae and Erysipelothrix tonsillae.

The enzymatic activities of 39 strains of Erysipelothrix rhusiopathiae and 34 of E tonsillae were determined with the API ZYM system. The profiles of these two species were very similar, differing solely in N-acetyl-beta-glucosaminidase activity. Whereas 90 per cent of strains of E rhusiopathiae exhibited strong activity with N-acetyl-beta-glucosaminidase, positive reactions were observed for this enzyme in only 24 per cent of strains of E tonsillae. These results support previous DNA-DNA hybridisation studies and suggest that E tonsillae is a new species of the genus Erysipelothrix.