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Small, obligately anaerobic strains 13CB8C T , 13CB11C T , 13CB18C T and 13GAM1G T were isolated from a faecal sample in a patient with Parkinson's disease with a history of duodenal resection. After conducting a comprehensive polyphasic taxonomic analysis including genomic analysis, we propose the establishment of one new genus and four new species. The novel bacteria are Desulfovibrio falkowii sp. nov. (type strain JCM 36128 T = DSM 116810 T ), Porphyromonas miyakawae sp. nov. (type strain JCM 36129 T = DSM 116947 T ), Mediterraneibacter flintii sp. nov. (type strain JCM 36130 T = DSM 116866 T ) and Owariibacterium komagatae gen. nov. sp. nov. (type strain JCM 36131 T = DSM 116982 T ), respectively.

Although anaerobic bacteria exist in abundance in cystic fibrosis (CF) airways, their role in disease progression is poorly understood. We hypothesized that the presence and relative abundance of the most prevalent, live, anaerobic bacteria in sputum of adults with CF were associated with adverse clinical outcomes. This is the first study to prospectively investigate viable anaerobic bacteria present in the sputum microbiota and their relationship with long-term outcomes in adults with CF. We performed 16S rRNA analysis using a viability quantitative PCR technique on sputum samples obtained from a prospective cohort of 70 adults with CF and collected clinical data over an 8 year follow-up period. We examined the associations of the ten most abundant obligate anaerobic bacteria present in the sputum with annual rate of FEV 1 change. The presence of Porphyromonas pasteri and Prevotella nanceiensis were associated with a greater annual rate of FEV 1 change; -52.3 ml yr -1 (95 % CI-87.7;-16.9), -67.9 ml yr -1 (95 % CI-115.6;-20.1), respectively. Similarly, the relative abundance of these live organisms were associated with a greater annual rate of FEV 1 decline of -3.7 ml yr -1 (95 % CI: -6.1 to -1.3, P =0.003) and -5.3 ml yr -1 (95 % CI: -8.7 to -1.9, P =0.002) for each log 2 increment of abundance, respectively. The presence and relative abundance of certain anaerobes in the sputum of adults with CF are associated with a greater rate of long-term lung function decline. The pathogenicity of anaerobic bacteria in the CF airways should be confirmed with further longitudinal prospective studies with a larger cohort of participants.

An obligatory anaerobic, Gram-stain-negative coccobacillus with black-pigmented colonies was isolated from the oral cavity of selected Australian marsupial species. Phenotypic and molecular criteria showed that this bacterium was a distinct species within the genus Porphyromonas, and was closely related to Porphyromonas gingivalis and Porphyromonas gulae. This putative novel species and P. gulae could be differentiated from P. gingivalis by catalase activity. Further characterization by multi-locus enzyme electrophoresis of glutamate dehydrogenase and malate dehydrogenase enzyme mobility and matrix-assisted laser desorption ionization time-of-flight MS showed that this putative novel species could be differentiated phenotypically from P. gingivalis and P. gulae. Definitive identification by 16S rRNA gene sequencing showed that this bacterium belonged to a unique monophyletic lineage, phylogenetically distinct from P. gingivalis (94.9 % similarity) and P. gulae (95.5 %). This also was supported by 16S-23S rRNA intergenic spacer region and glutamate dehydrogenase gene sequencing. A new species epithet, Porphyromonas loveana sp. nov., is proposed for this bacterium, with DSM 28520T (=NCTC 13658T=UQD444T=MRK101T), isolated from a musky rat kangaroo, as the type strain.

A bacterial strain, designated KUFDS01T, isolated from human saliva was characterized using a polyphasic taxonomic approach that included analysis of physiological and biochemical features, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. Cells of the strain were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. Growth of the strain was inhibited on medium containing 20% bile. The 16S rRNA gene sequence analysis showed that the strain was a member of the genus Porphyromonas. Strain KUFDS01T was closely related to Porphyromonas catoniae JCM 13863T (96.6% sequence similarity). An hsp60 gene sequence analysis indicated that strain KUFDS01T was different from P. catoniae JCM 13863T, with a sequence similarity value of 87.8%. The major cellular fatty acids of strain KUFDS01T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0, C18 : 2ω6, 9c and C18 : 1ω9c. The DNA G+C content of strain KUFDS01T was 57.7 ± 0.66 mol%. On the basis of these data, strain KUFDS01T represents a novel species of the genus Porphyromonas, for which the name Porphyromonas pasteri sp. nov. is proposed. The type strain of P. pasteri is KUFDS01T ( = JCM 30531T = CCUG 66735T).

During our investigation of the bacteriology of human wound infections and abscesses, a novel anaerobic, non-spore-forming, Gram-negative bacillus was frequently isolated. On the basis of morphological and biochemical criteria, the strains were tentatively identified as belonging to the family Bacteroidaceae, but they did not appear to correspond to any recognized species of this family. Comparative 16S rRNA gene sequencing showed that the 14 novel strains were genotypically homogeneous and confirmed their placement in the genus Porphyromonas. Sequence divergence values >10 % with respect to reference Porphyromonas species demonstrated that the strains isolated represent a novel species. On the basis of biochemical criteria and phylogenetic considerations, it is proposed that these strains isolated from human sources should be assigned to a novel species of the genus Porphyromonas, named Porphyromonas bennonis sp. nov., with WAL 1926C(T) (=ATCC BAA-1629(T) =CCUG 55979(T)) as the type strain.

Aspirates from 48 chronically inflamed maxillary sinuses from patients who had nasal polyposis were processed for aerobic and anaerobic bacteria. Bacterial growth was present in 46 (96%) specimens. Aerobic or facultative bacteria were present in 6 (13%) specimens, anaerobic bacteria alone in 18 (39%), and mixed aerobic and anaerobic bacteria in 22 (48%). There were 110 bacterial isolates (2.4 per specimen). Thirty-nine of the isolates were aerobic or facultative organisms (0.85 per specimen). The predominant aerobic or facultative organisms were: Staphylococcus aureus, microaerophilic streptococci, Haemophilus influenzae and Moraxella catarrhalis. Seventy-one anaerobes were isolated (1.5 per specimen), Peptostreptococcus spp., Prevotella spp., Porphyromonas asaccharolytica and Fusobacterium spp. being predominant. These findings illustrate for the first time the presence of polymicrobial aerobic-anaerobic flora in patients with chronic maxillary sinusitis who had nasal polyposis.

Molecular methods have been used recently to investigate the bacteria encountered in human endodontic infections. The aim of the present study was to compare the ability of a 16S rDNA-based PCR assay and checkerboard DNA-DNA hybridisation in detecting Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Peptostreptococcus micros, Porphyromonas endodontalis, Por. gingivalis and Treponema denticola directly from clinical samples. Specimens were obtained from 50 cases of endodontic infections and the presence of the target species was investigated by whole genomic DNA probes and checkerboard DNA-DNA hybridisation or taxon-specific oligonucleotides with PCR assay. Prevalence of the target species was based on data obtained by each method. The sensitivity and specificity of each molecular method was compared with the data generated by the other method as the reference--a value of 1.0 representing total agreement with the chosen standard. The methods were also compared with regard to the prevalence values for each target species. Regardless of the detection method used, T. denticola, Por. gingivalis, Por. endodontalis and B. forsythus were the most prevalent species. If the checkerboard data for these four species were used as the reference, PCR detection sensitivities ranged from 0.53 to 1.0, and specificities from 0.5 to 0.88, depending on the target bacterial species. When PCR data for the same species were used as the reference, the detection sensitivities for the checkerboard method ranged from 0.17 to 0.73, and specificities from 0.75 to 1.0. Accuracy values ranged from 0.6 to 0.74. On the whole, matching results between the two molecular methods ranged from 60% to 97.5%, depending on the target species. The major discrepancies between the methods comprised a number of PCR-positive but checkerboard-negative results. Significantly higher prevalence figures for Por. endodontalis and T. denticola were observed after PCR assessment. There was no further significant difference between the methods with regard to detection of the other target species.

A new species, Porphyromonas gulae sp. nov., is proposed to include strains isolated from the gingival sulcus of various animal hosts which are distinct from related strains of Porphyromonas gingivalis of human origin. This bacterium exhibits the following characteristics: black-pigmented colonies; asaccharolytic, obligate anaerobic growth; and Gram-negative, non-motile and non-spore-forming, rod-shaped cells. Colonies do not fluoresce under UV light. Vitamin K1 and haemin are required for growth. Cells haemagglutinate sheep erythrocytes. Major fatty acid end products are butyric acid, isovaleric acid, succinic acid and phenylacetic acid. Strains are catalase-positive and indole is produced. Alkaline phosphatase, trypsin-like and N-acetyl-beta-glucosaminidase activities are strong. A beta-galactosidase and a glutamylglutamic acid arylamidase are also present. The G+C content of the chromosomal DNA is 51 mol%. DNA-DNA homology data and 16S rRNA gene sequence analysis provide strong evidence that strains from the animal biotype of P. gingivalis represent a Porphyromonas species that is distinct from P. gingivalis. The type strain of P. gulae is Loup 1T (= ATCC 51700T = NCTC 13180T).

Repeated aspirations of sinus secretions by endoscopy was performed in five patients over a period of 34-50 days and, ultimately, surgical drainage was done in three who presented with acute maxillary sinusitis that did not respond to antimicrobial therapy and became chronic. The aspirates were cultured for aerobic and anaerobic bacteria. Most of the bacteria isolated from the first culture were aerobic or facultative bacteria: Streptococcus pneumoniae (three isolates), Haemophilus influenzae non-type-b (two) and Moraxella catarrhalis (one). Three of these cultures yielded bacteria that were resistant to the antimicrobial agents prescribed for treatment. Failure to respond to therapy was associated with the emergence of resistant aerobic and anaerobic bacteria in subsequent aspirates. These organisms included Fusobacterium nucleatum, pigmented Prevotella and Porphyromonas spp. and Peptostreptococcus spp. Eradication of the infection was achieved in all instances following the administration of antimicrobial agents effective against these bacteria, and in three instances by surgical drainage. This study illustrates the microbial dynamics of maxillary sinusitis that did not respond to antimicrobial therapy.

From 1974 to 1994, 504 isolates of Prevotella and Porphyromonas spp. were obtained from 435 (21%) of 2033 specimens from 418 children. They included 160 (32%) Pr. melaninogenica, 105 (21%) Pr. intermedia, 84 (17%) P. asaccharolytica, 58 (12%) Pr. orisbuccae, and 58 (12%) Pr. oralis. Most Prevotella and Porphyromonas spp. were isolated from abscesses (176), pulmonary infections (85), ear infections (82), wound infections (44), peritonitis (38), paronychia (15) and chronic sinusitis (14). Predisposing conditions were noted in 111 (27%) of the cases; these included previous surgery in 41 (10%), foreign body in 36 (9%), neurological deficiencies in 29 (7%), immunodeficiency in 21 (5%), steroid therapy in 12 (4%), diabetes in 8 (2%) and malignancy in 7 (2%). Prevotella and Porphyromonas spp. were the only isolates in 14 (3%) patients, and mixed infection was encountered in 404 (97%). The micro-organisms most commonly isolated with Prevotella and Porphyromonas spp. were anaerobic cocci (393 isolates), Fusobacterium spp. (108), Bacteroides spp. (B. fragilis group) (95), Escherichia coli (56) and other gram-negative anaerobic bacilli (52). Most Bacteroides spp. and E. coli were isolated from intra-abdominal infections and skin and soft tissue infections around the rectal area, whereas most Fusobacterium spp. were isolated from oropharyngeal, pulmonary and head and neck sites. beta-Lactamase production was detected in 191 (38%) Prevotella and Porphyromonas isolates from all body sites. All patients received antimicrobial therapy, and surgical drainage was performed in 173 (41%) cases. Four patients died from their infection. These data illustrate the spectrum and importance of Prevotella and Porphyromonas spp. in infections in children.

Recent taxonomic studies on black-pigmented anaerobic rods, a group of bacteria found on mucosal surfaces of humans and animals, led to the subdivision of existing species and to the creation of new species. The aim of this study was to characterize all 11 currently recognized species of black-pigmented bacteria (55 strains) for their ability to hydrolyse a variety of natural and synthetic substrates and for their lectin reactivity. Although most of the strains demonstrated some activity against proteinaceous substrates, Porphyromonas gingivalis was the only species able to hydrolyse type I collagen. Most strains possessed glycylprolyl protease activity, elastase-like activity and phospholipase C activity, whereas trypsin-like activity was restricted to P. gingivalis, Porphyromonas salivosa and Bacteroides macacae. beta-Lactamase activity was demonstrated in five strains belonging to the saccharolytic group. The lectin reactivity of the bacteria was determined by a dot-blot procedure using horseradish-peroxidase-conjugated lectins. Three lectins, LOTUS A, RCA-I and ConA, failed to react with any of the bacteria tested. WGA reacted strongly with the cell surface of human biotypes of asaccharolytic black-pigmented bacteria (P. gingivalis, Porphyromonas asaccharolytica and Porphyromonas endodontalis) and Prevotella intermedia. The animal biotype strains of P. gingivalis showed a higher affinity for SBA and PNA than for WGA.