[Show abstract][Hide abstract] ABSTRACT: The occurrence of Porphyromonas gulae, Porphyromonas macacae, Fusobacterium nucleatum and Fusobacterium canifelinum in subgingival plaque from dogs with and without periodontitis as well as their antimicrobial susceptibility were evaluated. From 50 dogs with periodontitis were identified 38 P. gulae, 8 P. macacae, 26 F. nucleatum and 15 F. canifelinum, and from 50 dogs without periodontitis were identified 15 P. gulae, 12 F. nucleatum and 11 F. canifelinum. All strains were susceptible to most of the antibiotics tested, however, different resistance rates to clarithromycin, erythromycin and metronidazole among strains were observed. The role of P. gulae, P. macacae, F. nucleatum and F. canifelinum in periodontal disease of household pets needs to be defined to a better prevention and treatment of the canine periodontitis.
[Show abstract][Hide abstract] ABSTRACT: A rapid PCR approach was developed to detect Porphyromonas gulae strains from subgingival samples of dogs with and with periodontitis. The presence of P. gulae was observed in 92% and 56%, respectively, in dogs with and without periodontitis. The new primer pair was specific to detect this microorganism, and this technique could be used to evaluate a correlation between periodontitis and P. gulae in companion animals.
[Show abstract][Hide abstract] ABSTRACT: Our goal was to establish a quantitative real-time PCR (QRT-PCR) method to detect Bacteroides fragilis group and related organisms from clinical specimens. Compared to conventional anaerobic culture, QRT-PCR can provide accurate and more rapid detection and identification of B. fragilis group and similar species. B. fragilis group and related organisms are the most frequently isolated anaerobic pathogens from clinical samples. However, culture and phenotypic identification is quite time-consuming. We designed specific primers and probes based on the 16S rRNA gene sequences of Bacteroides caccae, Bacteroides eggerthii, B. fragilis, Bacteroides ovatus, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Odoribacter splanchnicus (Bacteroides splanchnicus), Parabacteroides distasonis (Bacteroides distasonis) and Parabacteroides merdae (Bacteroides merdae), and detected these species by means of QRT-PCR in 400 human surgical wound infection samples or closed abscesses. The target bacteria were detected from 31 samples (8%) by culture, but from 132 samples (33%) by QRT-PCR (p-value < 0.001). B. uniformis was the most common species (44 positive samples) according to QRT-PCR while culture showed it to be B. fragilis (16 positive samples). Additionally, for each species QRT-PCR detected higher counts than culture did; this may reflect detecting DNA of dead organisms by QRT-PCR. QRT-PCR is a rapid and sensitive method which has great potential for detection of B. fragilis group and related organisms in wound samples.
[Show abstract][Hide abstract] ABSTRACT: There is evidence of genetic predisposition to autism, but the percent of autistic subjects with this background is unknown. It is clear that other factors, such as environmental influences, may play a role in this disease. In the present study, we have examined the fecal microbial flora of 33 subjects with various severities of autism with gastrointestinal symptoms, 7 siblings not showing autistic symptoms (sibling controls) and eight non-sibling control subjects, using the bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) procedure. The results provide us with information on the microflora of stools of young children and a compelling picture of unique fecal microflora of children with autism with gastrointestinal symptomatology. Differences based upon maximum observed and maximum predicted operational taxonomic units were statistically significant when comparing autistic and control subjects with p-values ranging from <0.001 to 0.009 using both parametric and non-parametric estimators. At the phylum level, Bacteroidetes and Firmicutes showed the most difference between groups of varying severities of autism. Bacteroidetes was found at high levels in the severely autistic group, while Firmicutes were more predominant in the control group. Smaller, but significant, differences also occurred in the Actinobacterium and Proteobacterium phyla. Desulfovibrio species and Bacteroides vulgatus are present in significantly higher numbers in stools of severely autistic children than in controls. If the unique microbial flora is found to be a causative or consequent factor in this type of autism, it may have implications with regard to a specific diagnostic test, its epidemiology, and for treatment and prevention.
[Show abstract][Hide abstract] ABSTRACT: Eleven clinical strains isolated from infected wound specimens were subjected to polyphasic taxonomic analysis. Sequence analysis
of the 16S rRNA gene showed that all 11 strains were phylogenetically related to Slackia exigua. Additionally, conventional and biochemical tests of 6 of the 11 strains were performed as supplementary methods to obtain
phenotypic identification by comparison with the phenotypes of the relevant type strains. S. exigua has been considered an oral bacterial species in the family Coriobacteriaceae. This organism is fastidious and grows poorly, so it may easily be overlooked. The 16S rRNA gene sequences and the biochemical
characteristics of four of the S. exigua strains isolated for this study from various infections indicative of an intestinal source were almost identical to those
of the validated S. exigua type strain from an oral source and two of the S. exigua strains from oral sources evaluated in this study. Thus, we show for the first time that S. exigua species can be isolated from extraoral infections as well as from oral infections. The profiles of susceptibility to selected
antimicrobials of this species were also investigated for the first time.
[Show abstract][Hide abstract] ABSTRACT: Two strains of previously unknown Gram-stain-positive, anaerobic, coccus-shaped bacteria from human wound specimens were characterized using phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies and distinguishable biochemical characteristics demonstrated that these two unknown strains, WAL 1855C(T) and WAL 2038E, are genotypically homogeneous and constitute a novel lineage within Clostridium cluster XIII. There was 13-14 % 16S rRNA gene sequence divergence between the novel strains and the most closely related species, Parvimonas micra, Finegoldia magna and species of Helcococcus. Based on the phenotypic and phylogenetic findings, a novel genus and species, Murdochiella asaccharolytica gen. nov., sp. nov., are proposed. Strain WAL 1855C(T) (=ATCC BAA-1631(T) =CCUG 55976(T)) is the type strain of Murdochiella asaccharolytica.
Full-text · Article · Sep 2009 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: Three strains of an unidentified Gram-stain-variable, fastidious, catalase-negative, capnophilic, non-spore-forming, coccus-shaped bacterium from human wound specimens were characterized by phenotypic and molecular taxonomic methods. Initially, these strains were anaerobic; with repeated culture, they became aerotolerant. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically homogeneous and constituted a novel subline within the genus Gemella. The unknown bacterium was readily distinguished from other Gemella species by biochemical tests. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from clinical specimens be classified as Gemella asaccharolytica sp. nov. The type strain is WAL 1945J(T) (=ATCC BAA-1630(T) =CCUG 57045(T)).
Full-text · Article · Sep 2009 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: A coryneform strain, 06-1773O(T) (=WAL 19168(T)), derived from a groin abscess sample was characterized using phenotypic and molecular taxonomic methods. Comparative analyses revealed more than 3 % divergence of the 16S rRNA gene sequence and about 10 % divergence of the partial rpoB gene sequence from the type strain of Corynebacterium glucuronolyticum. The strain could also be differentiated from C. glucuronolyticum by a set of phenotypic properties. A DNA-DNA relatedness study between strain WAL 19168(T) and C. glucuronolyticum CCUG 35055(T) showed a relatedness value of 13.3 % (13.7 % on repeat analysis). The genotypic and phenotypic data show that the strain merits classification within a novel species of Corynebacterium. We propose the name Corynebacterium pyruviciproducens sp. nov. for the novel species. The type strain is 06-1773O(T) (=WAL 19168(T) =CCUG 57046(T) =ATCC BAA-1742(T)).
Preview · Article · Sep 2009 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: Phenotypic and phylogenetic studies were performed on 15 isolates of an unidentified Gram-positive, anaerobic, non-sporulating coccobacillus-shaped bacterium isolated from human faeces. The novel organisms were catalase-negative, indole-negative and produced acetate and succinate as end products of metabolism. Comparative 16S rRNA gene sequencing demonstrated that the 15 isolates were highly related to each other and formed a hitherto unknown subline within the clostridial rRNA cluster XIVa. The novel isolates formed a robust phylogenetic group with a number of organisms which included Clostridium coccoides, Ruminococcus luti, Ruminococcus obeum and a number of other misclassified ruminococci. On the basis of these studies, a novel genus, Blautia gen. nov., is proposed. It is suggested that Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus, and Ruminococcus schinkii are transferred to this genus as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov. and Blautia schinkii comb. nov. One of the new isolates, the hitherto unknown coccus-shaped bacterial strain WAL 14507T (=ATCC BAA-1564T=DSM 19850T) is proposed as representing the type strain of a novel species, Blautia wexlerae sp. nov.
Preview · Article · Sep 2008 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: Two proposed hypotheses for irritable bowel syndrome (IBS) are acute gastroenteritis and bacterial overgrowth. We studied whether acute infection with Campylobacter could precipitate bacterial overgrowth in a rat model in order to link the two hypotheses.
Sprague-Dawley outbred rats were randomly administered a vehicle or Campylobacter jejuni strain 81-176 by oral gavage. Three months after clearance of the infectious agent, rats had a stool consistency evaluation. After euthanasia, lumenal bacteria counts were measured via quantitative real-time PCR from self-contained segments of the duodenum, jejunum, ileum, cecum and left colon. Adjacent sections of bowel were fixed in formalin for evaluation of intraepithelial lymphocyte counts.
Three months after clearance of Campylobacter infection, 57% of Campylobacter infected rats had some alteration in stool consistency compared to 7.4% in mock-infected controls (P < 0.001). Among the rats that received Campylobacter, 27% had evidence of bacterial overgrowth by PCR. These rats also had the highest prevalence of altered stool form and had lower body weight. Consistent with post-infectious IBS in humans, bacterial overgrowth rats demonstrated a significant increase in rectal and left colon intraepithelial lymphocytes.
Acute infection with C. jejuni 81-176 precipitates alterations in stool consistency, bacterial overgrowth and rectal lymphocytosis consistent with findings in IBS patients.
No preview · Article · Apr 2008 · Digestive Diseases and Sciences
[Show abstract][Hide abstract] ABSTRACT: Three groups of previously unknown gram-positive, anaerobic, coccus-shaped bacteria were characterized using phenotypic and
molecular taxonomic methods. Phenotypic and genotypic data demonstrate that these organisms are distinct, and each group represents
a previously unknown subline within Clostridium cluster XIII. Two groups are most closely related to Peptoniphilus harei in the genus Peptoniphilus, and the other group is most closely related to Anaerococcus lactolyticus in the genus Anaerococcus. Based on the findings, three novel species, Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov., are proposed. The type strains of Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov. are WAL 10418T (= CCUG 53341T = ATCC BAA-1383T), WAL 12922T (= CCUG 53342T = ATCC BAA-1384T), and WAL 17230T (= CCUG 53340T = ATCC BAA-1385T), respectively.
[Show abstract][Hide abstract] ABSTRACT: A rapid multiplex PCR approach was developed to detect the bft gene subtypes in Bacteroides fragilis clinical isolates. This technique could be used to look at the epidemiology of enterotoxigenic strains of B. fragilis in clinical infections and whether there is a correlation between disease and the presence of B. fragilis enterotoxin.
Full-text · Article · May 2007 · Journal of Clinical Microbiology
[Show abstract][Hide abstract] ABSTRACT: Gram-positive anaerobic cocci (GPAC) are a heterogeneous group of organisms that are isolated from clinical specimens more often than any group of anaerobic bacteria except Bacteroides species, yet many strains are still difficult or impossible to identify in the diagnostic laboratory. In this study, a total of 124 strains, including 13 reference strains of GPAC species and 111 isolates that had been recovered from clinical specimens previously and identified by 16S rRNA gene sequencing, were subjected to biochemical characterization. Based on the results, a short biochemical scheme that involves the minimum essential biochemical tests for accurate identification of clinically important GPAC was developed.
Preview · Article · Mar 2007 · Journal of Clinical Microbiology
[Show abstract][Hide abstract] ABSTRACT: Two groups of previously unknown Gram-negative, strictly anaerobic, pigment-producing, rod-shaped bacteria, which phenotypically and phylogenetically displayed a close association with the recently described species Alistipes finegoldii, were characterized using phenotypic and molecular taxonomic methods. A 16S rRNA gene sequence divergence of approximately 3 % between the two unknown bacteria and A. finegoldii, as well as distinguishable biochemical characteristics, demonstrates that these organisms are genotypically and phenotypically distinct and that each group represents a previously unknown subline within the genus Alistipes. Chromosomal DNA-DNA reassociation studies further confirmed the separateness of the unidentified bacteria and A. finegoldii. On the basis of the phenotypic and phylogenetic findings, two novel species, Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., are proposed. The type strains of A. onderdonkii and A. shahii are WAL 8169(T) (=CCUG 48946(T)=ATCC BAA-1178(T)) and WAL 8301(T) (=CCUG 48947(T)=ATCC BAA-1179(T)), respectively; their DNA G+C contents are 58 and 56 mol%, respectively.
Full-text · Article · Sep 2006 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: Phenotypic and phylogenetic studies were performed on an unknown gram-negative, strictly anaerobic, rod-shaped bacterium isolated
from human clinical specimens. This organism was indole negative, resistant to 20% bile, produced acetic and a lesser amount
of succinic acids as the major end products of glucose metabolism, and possessed a G+C content of approximately 43 mol%. Comparative
16S rRNA gene sequencing demonstrated that the unidentified bacterium was a member of the Cytophaga-Flavobacter-Bacteroides phylum of gram-negative bacteria and formed a close association (with an average sequence similarity of 93.6%) with the second
subcluster of the Porphyromonas cluster in the Bacteroides subgroup. Phylogenetically and phenotypically it resembled Bacteroides merdae; however, a 16S rRNA gene sequence divergence of approximately 5.5% between the unknown bacterium and B. merdae, as well as distinguishable biochemical characteristics, demonstrate that the unknown bacterium is genotypically and phenotypically
distinct and represents a previously unknown subline within the Porphyromonas phylogenetic cluster. Furthermore, a DNA-DNA reassociation value of 17.8% between isolates WAL 12034T (the type strain of this novel taxon) and ATCC 43184T (B. merdae type strain) also documented the separateness of the unknown species and B. merdae. Based on the phenotypic and phylogenetic findings, a new species, “Bacteroides goldsteinii sp. nov,” is proposed. The G+C content of the DNA is 43 mol% for Bacteroides. The type strain of “B. goldsteinii” is WAL 12034T (= CCUG 48944T = ATCC BAA-1180T).
Preview · Article · Oct 2005 · Journal of Clinical Microbiology
[Show abstract][Hide abstract] ABSTRACT: Porphyromonas levii is an anaerobic, pigmented gram-negative bacillus originally isolated from bovine rumen. We describe 58 human clinical strains
of P. levii-like organisms, isolated from various human clinical specimens that are phenotypically similar to the type strain of P. levii, a rumen isolate (ATCC 29147). Our biochemical, comparative 16S rRNA sequence analyses, and DNΑ-DNA relatedness studies indicate
that the human P. levii-like organisms are similar to each other but genetically different from the P. levii type strain isolated from bovine rumen. We therefore propose the name Porphyromonas somerae to encompass the human P. levii-like organisms. P. somerae was predominantly isolated from patients with chronic skin and soft tissue or bone infections, especially in the lower extremities.
Preview · Article · Oct 2005 · Journal of Clinical Microbiology
[Show abstract][Hide abstract] ABSTRACT: Sequence analysis of the 16S rRNA gene represents a highly accurate and versatile method for bacterial classification and
identification, even when the species in question is notoriously difficult to identify by phenotypic means. In this study,
we evaluated the utility of 16S rRNA gene sequencing as a means of identifying clinically important Bacteroides species. We sequenced 231 clinical isolates that had been identified by a short biochemical scheme. Based on the sequence
analysis, 192 clinical isolates were assigned to an established species, with the other 39 clinical strains revealing five
unique sequences that may represent five novel species. This is in contrast to identification obtained from a short biochemical
scheme, by which only 73.5% (172 of 231) of isolates were correctly identified to species level. Based on the solid identification
obtained from 16S rRNA gene sequencing, the short biochemical scheme was modified and improved to provide clinical laboratories
with an inexpensive and simple alternative for the identification of isolates of clinically significant Bacteroides species.
Preview · Article · May 2005 · Journal of Clinical Microbiology
[Show abstract][Hide abstract] ABSTRACT: Clostridium hathewayi and Campylobacter hominis have not been previously reported in infection. We report a fatal case of septicemia, massive intravascular hemolysis, shock, and disseminated intravascular coagulation; both of these organisms were recovered on blood culture, although it seems likely that the C. hathewayi was responsible for the clinical picture and that the C. hominis was an incidental finding.
[Show abstract][Hide abstract] ABSTRACT: The activities of OPT-80 against 453 intestinal bacteria were compared with those of seven other drugs. OPT-80 showed good
activity against most clostridia, staphylococci, and enterococci, but streptococci, aerobic and facultative gram-negative
rods, anaerobic gram-negative rods, and Clostridium ramosum were resistant. Poor activity against anaerobic gram-negative rods may maintain colonization resistance.
Preview · Article · Jan 2005 · Antimicrobial Agents and Chemotherapy
[Show abstract][Hide abstract] ABSTRACT: Based on the hypothesis that intestinal clostridia play a role in late-onset autism, we have been characterizing clostridia
from stools of autistic and control children. We applied the TaqMan real-time PCR procedure to detect and quantitate three
Clostridium clusters and one Clostridium species, C. bolteae, in stool specimens. Group- and species-specific primers targeting the 16S rRNA genes were designed, and specificity of the
primers was confirmed with DNA from related bacterial strains. In this procedure, a linear relationship exists between the
threshold cycle (CT) fluorescence value and the number of bacterial cells (CFU). The assay showed high sensitivity: as few as 2 cells of members
of cluster I, 6 cells of cluster XI, 4 cells of cluster XIVab, and 0.6 cell of C. bolteae could be detected per PCR. Analysis of the real-time PCR data indicated that the cell count differences between autistic
and control children for C. bolteae and the following Clostridium groups were statistically significant: mean counts of C. bolteae and clusters I and XI in autistic children were 46-fold (P = 0.01), 9.0-fold (P = 0.014), and 3.5-fold (P = 0.004) greater than those in control children, respectively, but not for cluster XIVab (2.6 × 108 CFU/g in autistic children and 4.8 × 108 CFU/g in controls; respectively). More subjects need to be studied. The assay is a rapid and reliable method, and it should
have great potential for quantitation of other bacteria in the intestinal tract.
Preview · Article · Dec 2004 · Applied and Environmental Microbiology