Roseovarius pelagicus sp. nov., a facultatively anaerobic bacterium with potential for degrading polypropylene, isolated from Arctic seawater

A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacterial strain, designated HL-MP18T, was isolated from Arctic seawater after a prolonged incubation employing polypropylene as the sole carbon source. Phylogenetic analyses of the 16S rRNA gene sequence revealed that strain HL-MP18T was affiliated to the genus Roseovarius with close relatives Roseovarius carneus LXJ103T (96.8 %) and Roseovarius litorisediminis KCTC 32327T (96.5 %). The complete genome sequence of strain HL-MP18T comprised a circular chromosome of 3.86 Mbp and two circular plasmids of 0.17 and 0.24 Mbp. Genomic comparisons based on average nucleotide identity and digital DNA-DNA hybridization showed that strain HL-MP18T was consistently discriminated from its closely related taxa in the genus Roseovarius. Strain HL-MP18T showed optimal growth at 25 °C, pH 7.0 and 2.5 % (w/v) sea salts. The major cellular fatty acids were C18 : 1  ω6c and/or C18 : 1  ω7c (49.6 %), C19 : 0 cyclo ω8c (13.5 %), and C16 : 0 (12.8 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of the strain was 59.2 mol%. The phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strain HL-MP18T is distinguishable from the recognized species of the genus Roseovarius. Therefore, we propose that strain HL-MP18T represents a novel species belonging to the genus Roseovarius, for which the name Roseovarius pelagicus sp. nov. is proposed. The type strain is HL-MP18T (=KCCM 90405T=JCM 35639T).

Patient-specific analysis of periodontal and peri-implant microbiomes

Periodontally involved teeth have been implicated as 'microbial reservoirs' in the etiology of peri-implant diseases. Therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the degree of congruence between adjacent peri-implant and periodontal microbiomes in states of health and disease. Subgingival and peri-implant biofilm samples were collected from 81 partially edentulous individuals with periodontal and peri-implant health and disease. Bacterial DNA was isolated, and the 16S rRNA gene was amplified and sequenced by pyrotag sequencing. Chimera-depleted sequences were compared against a locally hosted curated database for bacterial identification. Statistical significance was determined by paired Student's t tests between tooth-implant pairs. The 1.9 million sequences identified represented 523 species. Sixty percent of individuals shared less than 50% of all species between their periodontal and peri-implant biofilms, and 85% of individuals shared less than 8% of abundant species between tooth and implant. Additionally, the periodontal microbiome demonstrated significantly higher diversity than the implant, and distinct bacterial lineages were associated with health and disease in each ecosystem. Analysis of our data suggests that simple geographic proximity is not a sufficient determinant of colonization of topographically distinct niches, and that the peri-implant and periodontal microbiomes represent microbiologically distinct ecosystems.

Stereospecific microbial production of isoflavanones from isoflavones and isoflavone glucosides

A Gram-negative anaerobic microorganism, MRG-1, isolated from human intestine showed high activities of deglycosylation and reduction of daidzin, based on rapid TLC analysis. A rod-shaped strain MRG-1 was identified as a new species showing 91.0% homology to Coprobacillus species, based on 16S rRNA sequence analysis. The strain MRG-1 showed β-glucosidase activity toward daidzin and genistin, and daidzein and genistein were produced, respectively. However, the strain MRG-1 did not react with flavone glycosides, flavanone glycosides, and isoflavone C-glucoside. Besides, MRG-1 showed stereoselective reductase activity to isoflavone, daidzein, genistein, 7-hydroxyisoflavone, and formononetin, resulting in the formation of corresponding R-isoflavanone enantiomers. The new isoflavanones of 7-hydroxyisoflavanone and dihydroformononetin were characterized by NMR, and the absolute configurations of the enantiomers were determined with CD spectroscopy. The kinetic study of the anaerobic biotransformation showed both activities were exceptionally fast compared to the reported conversion by other anaerobic bacteria.

[Symbiotic microflora in fishes of different ecological groups]

Published data on the taxonomic composition of the intestinal bacterial flora in fishes living under different conditions (marine and freshwater fishes) and differing in the type of feeding are reviewed. The results confirm the conclusion that the composition of intestinal microflora differs depending on fish ecology. A limited number of bacterial taxa found in the intestines of some fish species may be evidence not only for a low diversity of these bacteria but also for insufficient knowledge about them. Considerable differences in the composition of intestinal microflora in marine and freshwater fishes are described.

The division "Synergistes"

The "Synergistes" group of organisms are a phylogenetic cluster of Gram-negative anaerobes related to Synergistes jonesii, sufficiently distinct from all other phyla to be considered a distinct phylum or Division. They are widely distributed in nature although normally only a minor constituent of the bacterial community in each habitat. They have evolved to adapt to each habitat, and therefore exhibit a wide range of physiological and biochemical characteristics, although all cultivable taxa so far studied have the ability to degrade amino acids. They are found in the human mouth where they appear to be more numerous in tooth and gum disease than health. They have also been found in the human gut and soft tissue infections. Their role in human disease has yet to be established but improved knowledge of the characteristics that enable their identification should increase the likelihood of their recognition when present at diseased sites.

[Characteristic of clinical strains of gram-negative obligate anaerobes]

The aim of the study was to assess prevalence and antibiotic susceptibility profiles ofGram-negative strictly anaerobic bacteria isolated from clinical specimens taken from hospitalized patients in 2005-2006. Biochemical identification and antibiotic susceptibility were done in an automated system ATB Expression (bioMerieux sa). From 12262 specimens examined 867 strains of obligate anaerobes were isolated. Gram-negative strictly anaerobic bacteria were cultured in number of 138 strains (15,9%). All cultures were performed on Columbia agar and Schaedler agar media (bioMerieux sa) supplemented with 5% sheep blood and incubated at 37 degrees C for 48-120 h in 85% N2, 10% H2, 5% CO2. Most frequently isolated was Bacteroides spp. (41,3%). For this group beta-lactamase activity was evaluated by using nitrocefin disc test (Cefinase BBL, Becton Dickinson and Co., Cockeysville, MD, USA). Production of ESBLs was detected with the use of two disc diffusion methods: the double-disc synergy test (DDST) according to Jarlier et al. and the diagnostic disc (DD) test according to Appleton. ESBLs were produced by 5,3% strains of Bacteroides spp. For all Bacteroides spp. strains MIC values were determined by gradient diffusion method Etest (AB BIODISK, Sweden). ESBLs and MIC were performed on Wilkins-Chalgren solid medium supplemented with 5% sheep blood (Difco Lab., USA) and all plates were incubated at 35 degrees C for 48 hours in 85% N2, 10% H2, 5% CO2. Most Gram-negative obligate anaerobes isolated from clinical specimens are still susceptible to imipenem (100%), metronidazole (99,3%) and beta-lactam antibiotics with beta-lactamase inhibitors: piperacillin/tazobactam (99,3%), ticarcillin/clavulanate (99.3%), amoxicillin/clavulanate (97.8%).

Desulfurobacterium atlanticum sp. nov., Desulfurobacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria

Three thermophilic, anaerobic, strictly chemolithoautotrophic, sulphur- and/or thiosulphate-reducing bacteria, designated SL17T, SL19T and SL22T, were isolated from deep-sea hydrothermal samples collected at 13 °N (East Pacific Rise), Guaymas Basin (Gulf of California) and 23 °N (Mid-Atlantic Ridge), respectively. These strains differed in their morphology, temperature range and optimum for growth, energy substrates and 16S rRNA gene sequences. The G+C content of the genomic DNA was 41 mol% (SL22T), 42 mol% (SL17T) and 46 mol% (SL19T). Comparative analysis of phenotypic and phylogenetic traits indicated that strains SL17T and SL22T represented two novel species of the genus Desulfurobacterium and that strain SL19T should be considered as a novel species of the genus Thermovibrio. The names Desulfurobacterium pacificum sp. nov. (type strain SL17T=DSM 15522T=JCM 12127T), Desulfurobacterium atlanticum sp. nov. (type strain SL22T=DSM 15668T=JCM 12129T) and Thermovibrio guaymasensis sp. nov. (type strain SL19T=DSM 15521T=JCM 12128T) are proposed for these organisms. Furthermore, phylogenetic data based on 16S rRNA gene sequence analyses correlated with the significant phenotypic differences between members of the lineage encompassing the genera Desulfurobacterium, Thermovibrio and Balnearium and that of the families Aquificaceae and Hydrogenothermaceae. It is therefore proposed that this lineage represents a new family, Desulfurobacteriaceae fam. nov., within the order Aquificales.

Anaerobic respiration on tellurate and other metalloids in bacteria from hydrothermal vent fields in the eastern Pacific Ocean

This paper reports the discovery of anaerobic respiration on tellurate by bacteria isolated from deep ocean (1,543 to 1,791 m) hydrothermal vent worms. The first evidence for selenite- and vanadate-respiring bacteria from deep ocean hydrothermal vents is also presented. Enumeration of the anaerobic metal(loid)-resistant microbial community associated with hydrothermal vent animals indicates that a greater proportion of the bacterial community associated with certain vent fauna resists and reduces metal(loid)s anaerobically than aerobically, suggesting that anaerobic metal(loid) respiration might be an important process in bacteria that are symbiotic with vent fauna. Isolates from Axial Volcano and Explorer Ridge were tested for their ability to reduce tellurate, selenite, metavanadate, or orthovanadate in the absence of alternate electron acceptors. In the presence of metal(loid)s, strains showed an ability to grow and produce ATP, whereas in the absence of metal(loid)s, no growth or ATP production was observed. The protonophore carbonyl cyanide m-chlorophenylhydrazone depressed metal(loid) reduction. Anaerobic tellurate respiration will be a significant component in describing biogeochemical cycling of Te at hydrothermal vents.

Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections

The purpose of the present study was to use terminal restriction fragment length polymorphism analysis and the 16S rRNA gene clone library to investigate the diversity of the microbiota associated with asymptomatic and symptomatic endodontic infections and to compare the bacterial community structure in these two clinical conditions. Samples were taken from asymptomatic endodontic infections associated with chronic periradicular lesions and from symptomatic infections clinically diagnosed as acute abscesses. 16S rRNA genes from DNA isolated from clinical samples were used to construct clone libraries or were subjected to terminal restriction fragment length polymorphism analysis. Sequence analysis of 186 clones revealed 42 taxa; 23 (55%) were uncultivated phylotypes, of which seven were unique to endodontic infections. Clone sequencing and terminal restriction fragment length polymorphism analysis revealed that the most commonly detected taxa were Fusobacterium nucleatum (including terminal restriction fragment types 1 and 2), Peptostreptococcus micros/Peptostreptococcus sp. oral clone AJ062/BS044/FG014, Prevotella species, Dialister species, Mogibacterium species, Lachnospiraceae oral clone 55A-34, Filifactor alocis, Megasphaera sp. oral clone CS025/BS073, and Veillonella sp. oral clone BP1-85/Veillonella dispar/V. parvula. Bacteroides-like sp. oral clone X083/Bacteroidales oral clone MCE7_20 and Dialister sp. oral clone BS016/MCE7_134 were detected only in asymptomatic teeth. On the other hand, F. nucleatum terminal restriction fragment type 2, Prevotella intermedia, Dialister pneumosintes, and some phylotypes were exclusively detected in symptomatic samples. Bacterial profiles of symptomatic endodontic infections generated by terminal restriction fragment length polymorphism analysis were clearly different from those of asymptomatic infections. Overall, the average number of terminal restriction fragments in symptomatic samples was significantly larger than in asymptomatic samples. Molecular analysis of the microbiota associated with symptomatic or asymptomatic endodontic infections indicates that the endodontic bacterial diversity is greater than previously described by culture methods and that the structure of the microbiota differ significantly between asymptomatic and symptomatic infections.

Paludibacter propionicigenes gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil in Japan

A strictly anaerobic, propionate-producing bacterial strain (WB4T) isolated from rice plant residue in anoxic rice-field soil in Japan was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short rods. The strain utilized various sugars and produced propionate and acetate as major fermentation products with a small amount of succinate. The optimum growth temperature was 30 degrees C. Oxidase, catalase and nitrate-reducing activities were negative. The major cellular fatty acids were anteiso-C(15 : 0), C(15 : 0) and anteiso-C(17 : 0) 3-OH. Menaquinone MK-8(H4) was the major respiratory quinone. The genomic DNA G+C content was 39.3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the phylum 'Bacteroidetes'. The closest relative to strain WB4T was an environmental clone from water contaminated with equine manure (sequence similarity of 99.7 %) and the strain formed a distinct cluster with other environmental clones mainly from freshwater sediments. The closest recognized species were members of the genus Dysgonomonas, with 16S rRNA gene sequence similarities of 90.9-89.8 %. Bacteroides merdae was the next closest recognized species (similarity of 88.7 % to the type strain). Given that the ecological, physiological and chemotaxonomic characteristics of strain WB4T were different from those of any related species, a new genus and species Paludibacter propionicigenes gen. nov., sp. nov., is proposed to accommodate it. The type strain is WB4T (= JCM 13257T = DSM 17365T).

Responses of the anaerobic bacterial community to addition of organic C in chromium(VI)- and iron(III)-amended microcosms

Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO2) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the Geobacteraceae family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO2 production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as Pantoea, Pseudomonas, and Enterobacter species. Geobacteraceae were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential.

Asaccharolytic anaerobic gram-negative coccobacilli (AAGNC) isolated from infected root canals and periodontal pockets

BACKGROUND/AIMS

Culture-difficult bacteria, including asaccharolytic anaerobic gram-negative coccobacilli (AAGNC), may constitute a predominant group of organisms in oral sites. This study aimed to characterize phylogenetically 10 AAGNC isolated from endodontic lesions and periodontal pockets.

METHODS

16S rDNA sequence and G + C content were determined. Strains sharing more than 98% sequence similarities and similar G + C content were considered the same bacterial species.

RESULTS

One isolate resembled Dialister pneumosintes (the type species of the genus Dialister) with 35 mol% G + C content and 97% sequence similarity. Of eight isolates having 45-47 mol% G + C content, seven were identified as D. invisus and one resembled Dialister invisus with 97% sequence similarity. However the 16S rDNA sequence similarities with D. pneumosintes were relatively low, indicating the strains may belong to a new genus. The last isolate revealed 35 mol% G + C content, but had higher 16S rDNA sequence similarity with D. invisus than with D. pneumosintes.

CONCLUSION

The group of oral AAGNC isolates need to be reclassified.

Prevalence of putative periodontopathogens in subgingival dental plaques from gingivitis lesions in Korean orthodontic patients

The objective of this study was to detect and compare the presence of periodontopathogens in the subgingival plaques of gingivitis lesions in adults who wore fixed orthodontic appliances, as opposed to adults who did not wear any orthodontic appliances. Thirty-six individuals participated in this study. Nineteen of these subjects did not wear any orthodontic appliances, and these subjects comprised the control group. The other 17 individuals had been wearing fixed orthodontic appliances for at least 3 months each. After a periodontal examination, we collected subgingival plaque samples from the gingivitis lesions of each patient. Using PCR based on 16S rDNA, we detected the presence of 6 putative periodontopathogenic species, Treponema denticola, Porphyromonas gingivalis, Tannerella forsythia (formerly Bacteroides forsythus), Prevotella nigrescens, Prevotella intermedia, and Actinobacillus actinomycetemcomitans. With regard to the presence of individual periodontopathogens, we found that T. forsythia, T. denticola, and P. nigrescens were significantly more common in the samples obtained from the orthodontic patients than in the samples obtained from the non-orthodontic patient controls. Our results indicate that the local changes associated with the wearing of fixed orthodontic appliances may affect the prevalence of periodontopathogens in subgingival dental plaques.

Desulfonatronum cooperativum sp. nov., a novel hydrogenotrophic, alkaliphilic, sulfate-reducing bacterium, from a syntrophic culture growing on acetate

A novel alkaliphilic, sulfate-reducing bacterium was isolated from a syntrophic acetate-decomposing community enriched from samples of the soda lake Khadin, Tuva, Russia; the isolate was designated strain Z-7999T. Cells of strain Z-7999T were vibrioid, Gram-negative, 0·4–0·5×1·0–2·5 μm and motile by means of a polar flagellum. The temperature range for growth was 15–40 °C, with an optimum of 35–38 °C. The pH range for growth was 6·7–10·3, with an optimum of pH 8·0–9·0. The NaCl concentration range for growth was 1–80 g l−1. The novel isolate was obligately anaerobic, was alkaliphilic with a broad pH range and had an obligate requirement for carbonate ions in the growth medium. In the presence of sulfate as electron acceptor, it grew with hydrogen, formate and lactate. It was not able to ferment sugars, organic acids, amino acids or peptides. During growth on formate, strain Z-7999T reduced sulfite and thiosulfate to sulfide. It was able to grow lithoheterotrophically with sulfate and formate when acetate was added as a carbon source for biosynthesis of biomass. The G+C content of the genomic DNA of strain Z-7999T was 56·5 mol%. Results of comparative 16S rRNA gene sequence analyses revealed that strain Z-7999T was part of the δ-Proteobacteria and clustered with other members of the genus Desulfonatronum (similarity values of 95·2 and 95·3 % to Desulfonatronum lacustre and Desulfonatronum thiodismutans, respectively). DNA–DNA hybridization with D. lacustre was 37 %. On the basis of physiological and phylogenetic data, it is proposed that strain Z-7999T (=DSM 16749T=VKM B-2329T) should be placed in the genus Desulfonatronum as a representative of a novel species, Desulfonatronum cooperativum sp. nov.

Syntrophomonas erecta sp. nov., a novel anaerobe that syntrophically degrades short-chain fatty acids

Two novel anaerobes, strains GB4-38T and SB9-1, were isolated from an upflow anaerobic sludge blanket reactor for treating bean-curd farm wastewater and lotus field mud, respectively. The strains degraded straight-chain fatty acids with 4–8 carbon atoms in syntrophic association with methanogens and converted 1 mol butyrate into about 2 mol acetate and presumably 2 mol H2. None of the branched-chain fatty acids tested could be degraded. Benzoate was not degraded. Fumarate, sulfate, thiosulfate, sulfur and nitrate did not serve as electron acceptors for butyrate degradation. In the absence of a methanogen partner, strain GB4-38T grew on crotonate in pure culture; the generation time was about 5 h at 37 °C. However, strain SB9-1 grew on butyrate plus pentenoate, but not crotonate, in pure culture and the generation time was 18 h at 37 °C. Cells of GB4-38T and SB9-1 were straight rods and stained Gram-negative. The major cellular fatty acids of GB4-38T were C14 : 0 (29·74 %), C16 : 0 (17·00 %), C16 : 1 ω5c (16·63 %) and isoC17 : 1 I (15·34 %). ll-Diaminopimelic acid existed in the cellular peptidoglycan. The genomic DNA G+C content of strain GB4-38T was 43·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences supported clustering of the two strains with syntrophic bacterial species of the genus Syntrophomonas (89·6–92·4 % sequence similarity), but phenotypic, chemotaxonomic and genetic characters differentiated the two strains from members of this genus. Therefore, it is proposed that the two strains are representatives of a novel species, Syntrophomonas erecta sp. nov. The type strain is GB4-38T (=CGMCC 1.5013T=DSM 16215T).

Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium

The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T).

Epidemiological and clinical characteristics of occult bacteremia in an adult emergency department in Spain: influence of blood culture results on changes in initial diagnosis and empiric antibiotic treatment

A prospective study was carried out to analyze the usefulness of blood culture results for adult patients who were discharged from the emergency department with bacteremia. Over a 29-month period, 110 patients with significant bacteremia who were seen in the emergency department and discharged home were studied. The mean age of the patients was 61.8 years. The most frequent initial major diagnosis was urinary tract infection (UTI) (n=63; 57.3%). Gram-negative organisms were isolated in 79 (71.8%) cases. A change in diagnosis (44.5% cases) was more common when the initial diagnosis was something other than UTI or when empiric antimicrobial therapy was ineffective or was not given (P<0.001). The significant predictors of modification of the initial empiric antibiotic therapy were ineffective empiric antimicrobial therapy and transfer of the patient from the emergency department to an infectious diseases outpatient clinic (P=0.01). Blood culture results may be useful for achieving the correct diagnosis in adult patients with bacteremia and for guiding treatment in the subsequent management of outpatients.

Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9 degrees 50' N. Cells of the organism were Gram-negative, motile rods that were about 1.0 microm in length and 0.6 microm in width. Growth occurred between 60 and 80 degrees C (optimum at 75 degrees C), 0.5 and 4.5% (w/v) NaCl (optimum at 2%) and pH 5 and 7 (optimum at 5.5). Generation time under optimal conditions was 1.57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2 and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54.6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domain Bacteria and formed a deep branch within the phylum Aquificae, with Thermovibrio ruber as its closest relative (94.4% sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genus Thermovibrio. The type strain is Thermovibrio ammonificans HB-1T (=DSM 15698T=JCM 12110T).

Molecular microbiology of gut bacteria: genetic diversity and community structure analysis

Recently developed molecular biology approaches make possible the detailed genetic, taxonomic and ecological examination of microorganisms from various habitats. Animal gut represents one of the most complex microbial ecosystems with a large degree of microbial biodiversity present. Bacteria inhabiting the gut usually play important roles in metabolic transformations of substrates and sometimes, e.g. in ruminants, they make the basis for an obligate symbiosis with the host. Here we discuss molecular microbiology as a strategy for examination of gut bacteria, concentrating on a typical and in such environment dominant group of strictly anaerobic Gram-negative bacteria from the phylogenetic group Cytophaga/Flexibacter/Bacteroides. The bacteria from the genus Prevotella are the most abundant Gram-negative bacteria in the rumen and form a distinctive phylogenetic cluster, clearly separated from prevotellas isolated from other ecological niches. They may represent a good choice for a model organism in genetic manipulation experiments and for studies of gene transfer mechanisms taking place in the gut. The molecular tools for detection and monitoring of ruminal prevotellas are discussed.

Microbiological analysis of infected root canals from symptomatic and asymptomatic teeth with periapical periodontitis and the antimicrobial susceptibility of some isolated anaerobic bacteria

The purpose of the present study was to investigate the correlation between the composition of the bacterial flora isolated from infected root canals of teeth with apical periodontitis with the presence of clinical signs and symptoms, and to test the antibiotic susceptibility of five anaerobic bacteria mostly commonly found in the root canals of symptomatic teeth against various substances using the E-test. Microbial samples were taken from 48 root canals, 29 symptomatic and 19 asymptomatic, using adequate techniques. A total of 218 cultivable isolates were recovered from 48 different microbial species and 19 different genera. Root canals from symptomatic teeth harbored more obligate anaerobes and a bigger number of bacterial species than the asymptomatic teeth. More than 70% of the bacterial isolates were strict anaerobes. Statistical analysis used a Pearson Chi-squared test or a one-sided Fisher's Exact test as appropriate. Suggested relationships were found between specific microorganisms, especially gram-negative anaerobes, and the presence of spontaneous or previous pain, tenderness to percussion, pain on palpation and swelling amoxicillin, amoxicillin + clavulanate and cephaclor were effective against all the strains tested. The lowest susceptibility rate was presented by Prevotella intermedia/nigrescens against Penicillin G. Our results suggested that specific bacteria are associated with endodontic symptoms of infected teeth with periapical periodontitis and the majority of the anaerobic bacterial species tested were susceptible to all antibiotics studied.

A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring

A novel type of a sulfate-reducing microorganism, represented by strain Na82T, was isolated from a hot spring in Narugo, Japan. The isolate was a moderate thermophilic autotroph that was able to grow on H2/CO2 by sulfate respiration. The isolate could grow with nitrate in place of sulfate, and possessed menaquinone-7 and menaquinone-7(H2) as respiratory quinones. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Na82T was a member of the domain Bacteria and distant from any known bacteria, as well as from other sulfate-reducing bacteria (sequence similarities less than 80%). The phylogenetic analysis of the dsrAB gene (alpha and beta subunits of dissimilatory sulfite reductase) sequence also suggested that strain Na82T was not closely related to other sulfate reducers. On the basis of the phenotypic and phylogenetic data, a new taxon is established for the isolate. We proposed the name Thermodesulfobium narugense gen. nov., sp. nov. with strain Na82T (=DSM 14796T=JCM 11510T) as the type strain. Furthermore, a new family, Thermodesulfobiaceae fam. nov., is proposed for the genus.

PCR methodology as a valuable tool for identification of endodontic pathogens

OBJECTIVES

This paper reviews the principles of polymerase chain reaction (PCR) methodology, its application in identification of endodontic pathogens and the perspectives regarding the knowledge to be reached with the use of this highly sensitive, specific and accurate methodology as a microbial identification test.

DATA SOURCES

Studies published in the medical, dental and biological literature.

STUDY SELECTION

Evaluation of published epidemiological studies examining the endodontic microbiota through PCR methodology.

CONCLUSIONS

PCR technology has enabled the detection of bacterial species that are difficult or even impossible to culture as well as cultivable bacterial strains showing a phenotypically divergent or convergent behaviour. Moreover, PCR is more rapid, much more sensitive, and more accurate when compared with culture. Its use in endodontics to investigate the microbiota associated with infected root canals has expanded the knowledge on the bacteria involved in the pathogenesis of periradicular diseases. For instance, Tannerella forsythensis (formerly Bacteroides forsythus), Treponema denticola, other Treponema species, Dialister pneumosintes, and Prevotella tannerae were detected in infected root canals for the first time and in high prevalence when using PCR analysis. The diversity of endodontic microbiota has been demonstrated by studies using PCR amplification, cloning and sequencing of the PCR products. Moreover, other fastidious bacterial species, such as Porphyromonas endodontalis, Porphyromonas gingivalis and some Eubacterium spp., have been reported in endodontic infections at a higher prevalence than those reported by culture procedures.

Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer

A polyphasic taxonomic study was performed on a novel facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotroph recently isolated from subsurface hot aquifer water in a Japanese gold mine. The cells were straight to slightly curved rods, with a single polar flagellum. Growth was observed at 40-70 degrees C (optimum 60-65 degrees C; 80 min doubling time) and at pH 6.4-8.8 (optimum pH 7.5). The isolate was unable to use complex organic compounds, carbohydrates, amino acids or organic acids as sole energy and carbon sources. The G + C content of the genomic DNA was 31.3 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was closely related to an uncultivated group of micro-organisms within the order Aquificales obtained from Icelandic and Japanese hot spring microbial mats, but distantly related to previously identified genera of the Aquificales such as Persephonella, Aquifex and Hydrogenobacter. The name Sulfurihydrogenibium subterraneum gen. nov., sp. nov. is proposed for this novel species; the type strain is HGMK1(T) (= JCM 11477(T) = ATCC BAA-562(T) = DSM 15120(T)).

Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent

A novel anaerobic, heterotrophic thermophile was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. The cells were bent, flexible rods, with a single polar flagellum. Growth was observed between 40 and 70 degrees C (optimum temperature: 60-65 degrees C; doubling time, 40 min) and between pH 5.0 and 7.5(optimum pH 6.5). The isolate was a strictly anaerobic heterotroph capable of using complex organic compounds (yeast extract, tryptone, peptone, casein and Casamino acids), ethanol and various organic acids as energy and carbon sources. Hydrogen could serve as a supplementary energy source. Elemental sulfur (S(0)), nitrate or arsenate was required for growth as an electron acceptor. The G + C content of the genomic DNA was 38.6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that isolate SSM1(T) is closely related to Deferribacter thermophilus BMA(T) (98.1%). However, the novel isolate could be clearly differentiated from D. thermophilus BMA(T) on the basis of its physiological and genetic properties. The name Deferribacter desulfuricans sp. nov. (type strain SSM1(T) = JCM 11476(T) = DSM 14783(T)) is proposed.

Identification of equine cecal bacteria producing amines in an in vitro model of carbohydrate overload

Acute laminitis has been associated with the overgrowth of gram-positive bacteria within the equine hindgut, causing the release of factor(s) leading to ischemia-reperfusion of the digits. The products of fermentation which trigger acute laminitis are, as yet, unknown; however, vasoactive amines are possible candidates. The objectives of this study were to use an in vitro model of carbohydrate overload to study the change in populations of cecal streptococci and lactobacilli and to establish whether certain species of these bacteria were capable of producing vasoactive amines from amino acids. Cecal contents from 10 horses were divided into aliquots and incubated anaerobically with either corn starch or inulin (fructan; both at 1 g/100 ml). Samples were taken at 6-h intervals over a 24-h period for enumeration of streptococci, lactobacilli, and gram-negative anaerobes by a dilution method onto standard selective growth media. The effects of the antibiotic virginiamycin (1 mg/100 ml) and calcium hydrogen phosphate (CaHPO(4); 0.3 g/100 ml) were also examined. Fermentation of excess carbohydrate was associated with increases in numbers of streptococci and lactobacilli (2- to 3.5-log unit increases; inhibited by virginiamycin) but numbers of gram-negative anaerobes were not significantly affected. A screening agar technique followed by 16S rRNA gene sequence analysis enabled the identification of 26 different bacterial strains capable of producing one or more vasoactive amines. These included members of the species Streptococcus bovis and five different Lactobacillus spp. These data suggest that certain bacteria, whose overgrowth is associated with carbohydrate fermentation, are capable of producing vasoactive amines which may play a role in the pathogenesis of acute laminitis.

Phylogenetic analysis of some Sporomusa sub-branch members isolated from human clinical specimens: description of Megasphaera micronuciformis sp. nov

Two unknown, Gram-negative, catalase-negative and strictly anaerobic cocci were isolated from two independent human samples (strains AIP 49.01 and AIP 412.00T). Comparative 16S rRNA gene sequencing demonstrated that these two organisms displayed 99.8% sequence identity and that they are members of the Sporomusa sub-branch of the low-G + C Gram-positive bacteria. The most closely related 16S rDNA sequences were from Megasphaera sp. oral clone BU057 (99.8%) and from isolates of Megasphaera cerevisiae and Megasphaera elsdenii (94.5 and 93.8%, respectively). Phylogenetic analysis based on 16S rDNA sequences showed that these two strains were most closely related to M. elsdenii and belonged to the Megasphaera genus. Differences from previously described Megasphaera species in terms of size, biochemical tests (particularly the analysis of metabolic end products), gas production and DNA G+C content indicated that the two strains studied represent a novel species of anaerobic Gram-negative cocci. The name Megasphaera micronuciformis sp. nov. is proposed for these two isolates. It is also proposed that the uncultured organism previously deposited as Megasphaera sp. oral clone BU057 should be named 'Candidatus Megasphaera micronuciformis'. The type strain of Megasphaera micronuciformis is AIP 412.00T (=CIP 107280T =CCUG 45952T).

Leptotrichia amnionii sp. nov., a novel bacterium isolated from the amniotic fluid of a woman after intrauterine fetal demise

A novel bacterium was isolated and characterized from the amniotic fluid of a woman who experienced intrauterine fetal demise in the second trimester of pregnancy. The bacterium was a slow-growing, gram-negative anaerobic coccobacillus belonging to the genus LEPTOTRICHIA: Unlike Leptotrichia sanguinegens, the isolate did not grow in chopped-meat glucose broth or on sheep blood agar upon subculturing. The isolate was characterized by sequencing and analyzing its 16S rRNA gene. The 1,493-bp 16S ribosomal DNA sequence had only 96% homology with L. sanguinegens. Several phylogenetic analyses indicated that L. amnionii is a distinct species and most closely related to L. sanguiegens.

Recent taxonomic changes and terminology update of clinically significant anaerobic gram-negative bacteria (excluding spirochetes)

Because of access to 16S rDNA sequencing, changes in the taxonomy and nomenclature of anaerobic gram-negative bacteria have occurred lately. New genera and species have been described, and existing taxa have been reclassified. The present article compiles a list of clinically relevant anaerobes and provides synonyms as well as the old nomenclature used for these bacteria. Although names and classifications of anaerobic bacteria are changing quickly, it is important to keep track of new bacterial names to work toward better description and recognition of bacterium-disease associations.

Dysgonomonas mossii sp. nov., from human sources

Phenotypic and phylogenetic studies were performed on seven unidentified gram-negative, facultatively anaerobic, coccobacillus-shaped organisms isolated from human clinical specimens. Comparative 16S rRNA gene sequencing demonstrated that four of the strains corresponded to Dysgonomonas capnocytophagoides whereas the remaining three isolates represent a new sub-line within the genus Dysgonomonas, displaying greater than 5% sequence divergence with Dysgonomonas capnocytophagoides and Dysgonomonas gadei. The three novel isolates were readily distinguished from D.capnocytophagoides and D. gadei by biochemical tests. The DNA base composition of the novel species was consistent with its assignment to the genus Dysgonomonas. Based on phylogenetic and phenotypic evidence it is proposed that the unknown species, be classified as Dysgonomonas mossii sp. nov. The type strain of Dysgonomonas mossii is CCUG 43457T (= CIP 107079T).

Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor

A novel, anaerobic, non-spore-forming, mobile, Gram-negative, thermophilic bacterium, strain TMOT, was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 C with methanol as the sole substrate. The G+C content of the DNA of strain TMOT was 39.2 mol%. The optimum pH, NaCl concentration, and temperature for growth were 7.0, 1.0%, and 65 degrees C, respectively. Strain TMOT was able to degrade methanol to CO2 and H2 in syntrophic culture with Methanothermobacter thermautotrophicus AH or Thermodesulfovibrio yellowstonii. Thiosulfate, elemental sulfur, Fe(III) and anthraquinone-2,6-disulfonate were able to serve as electron acceptors during methanol degradation. In the presence of thiosulfate or elemental sulfur, methanol was converted to CO2 and partly to alanine. In pure culture, strain TMOT was also able to ferment methanol to acetate, CO2 and H2. However, this degradation occurred slower than in syntrophic cultures or in the presence of electron acceptors. Yeast extract was required for growth. Besides growing on methanol, strain TMOT grew by fermentation on a variety of carbohydrates including monomeric and oligomeric sugars, starch and xylan. Acetate, alanine, CO2, H2, and traces of ethanol, lactate and alpha-aminobutyrate were produced during glucose fermentation. Comparison of 16S rDNA genes revealed that strain TMOT is related to Thermotoga subterranea (98%) and Thermotoga elfii (98%). The type strain is TMOT (= DSM 14385T = ATCC BAA-301T). On the basis of the fact that these organisms differ physiologically from strain TMOT, it is proposed that strain TMOT be classified as a new species, within the genus Thermotoga, as Thermotoga lettingae.

Desulfotignum phosphitoxidans sp. nov., a new marine sulfate reducer that oxidizes phosphite to phosphate

A new sulfate-reducing bacterium was isolated from marine sediment with phosphite as sole electron donor and CO(2) as the only carbon source. Strain FiPS-3 grew slowly, with doubling times of 3-4 days, and oxidized phosphite, hydrogen, formate, acetate, fumarate, pyruvate, glycine, glutamate, and other substrates nearly completely, with concomitant reduction of sulfate to sulfide. Acetate was formed as a side product to a small extent. Glucose, arabinose, and proline were partly oxidized and partly fermented to acetate plus propionate. Growth with phosphite, hydrogen, or formate was autotrophic. Also, in the presence of sulfate, CO dehydrogenase was present, and added acetate did not increase growth rates or growth yields. In the absence of sulfate, phosphite oxidation was coupled to homoacetogenic acetate formation, with growth yields similar to those in the presence of sulfate. Cells were small rods, 0.6 - 0.8 x 2-4 microm in size, and gram-negative, with a G+C content of 53.9 mol%. They contained desulforubidin, but no desulfoviridin. Based on sequence analysis of the 16S rRNA gene and the sulfite reductase genes dsrAB, strain FiPS-3 was found to be closely related to Desulfotignum balticum. However, physiological properties differed in many points from those of D. balticum. These findings justify the establishment of a new species, Desulfotignum phosphitoxidans.

Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov

It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cells are rod shaped, about 0.5 microm by 1.0 to 1.2 microm, and motile and have a single flagellum. Strain FW-1a grows at circumneutral pH, at freshwater salinities, and at temperatures of between 65 and 100 degrees C with an optimum of 85 to 90 degrees C. To our knowledge this is the highest temperature optimum of any organism in the Bacteria. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain FW-1a places it within the Bacteria, most closely related to abundant but uncultured microorganisms whose 16S rDNA sequences have been previously recovered from Obsidian Pool and a terrestrial hot spring in Iceland. While previous studies inferred that the uncultured microorganisms with these 16S rDNA sequences were sulfate-reducing organisms, the physiology of the strain FW-1a, which does not reduce sulfate, indicates that these organisms are just as likely to be Fe(III) reducers. These results further demonstrate that Fe(III) may be helpful for recovering as-yet-uncultured microorganisms from hydrothermal environments and illustrate that caution must be used in inferring the physiological characteristics of at least some thermophilic microorganisms solely from 16S rDNA sequences. Based on both its 16S rDNA sequence and physiological characteristics, strain FW-1a represents a new genus among the Bacteria. The name Geothermobacterium ferrireducens gen. nov., sp. nov., is proposed (ATCC BAA-426).

Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum

A novel anaerobic, moderately thermophilic, peptide-fermenting bacterium, strain NGA(T), was isolated from an anaerobic wool-scouring wastewater treatment lagoon. The cells were gram-negative, straight rods of 0.5-1.0 x 2.0-4.0 microm, motile by means of a single flagellum. The DNA G+C content was 51.5 mol%. The optimum pH and temperature range for growth were 6.6-7.3 and 55-60 degrees C, respectively. The optimum NaCl concentration was 0.08 g l(-1). The bacterium fermented organic acids (malate, tartrate, pyruvate, glycerol and fumarate), a few carbohydrates (starch, glucose, fructose and gluconate), Casamino acids, tryptone and yeast extract. Carbohydrates and organic acids were converted to acetate, hydrogen and CO2. The bacterium oxidized leucine to isovalerate with crotonate as an electron acceptor, but not in co-culture with Methanothermobacter thermoautotrophicus DSM 3720T. Thiosulfate, sulfur and cystine were reduced to sulfide and crotonate was reduced to butyrate with glucose and tryptone-yeast extract as electron donors. Phylogenetic analysis of the 16S rRNA gene indicated that strain NGA(T) was related to Anaerobaculum thermoterrenum (98% similarity), the only described species of the genus. The DNA-DNA hybridization value for strain NGA(T) and A. thermoterrenum ACM 5076T was 40.8%. On the basis of these results, strain NGA(T) is proposed as a novel species of the genus Anaerobaculum, namely Anaerobaculum mobile sp. nov. The type strain is NGA(T) (= DSM 13181T =ATCC BAA-54T).

Anaerophaga thermohalophila gen. nov., sp. nov., a moderately thermohalophilic, strictly anaerobic fermentative bacterium

The strictly anaerobic gram-negative bacterium strain Fru22T grows at 50 degrees C in media containing up to 75 g NaCl l(-1). Hexoses and pentoses are fermented to equal molar amounts of acetate, propionate and succinate, and no CO2 is formed. An orange-red pigment similar to flexirrubin is produced during stationary phase upon exposure to light for several days. Cells also produce a surface-active extracellular compound which lowers the surface tension of the medium. This tenside is heat-tolerant up to 70 degrees C and is destroyed by treatment with proteinase K or trypsin, but not by lipase. Comparative 16S rDNA sequence analysis confirmed a phylogenetic affiliation of strain Fru22T to the phylum Bacteroides (Cytophaga/Flavobacterium/Bacteroides), moderately related to the genus Marinilabilia. Therefore, on the basis of phylogenetic, phenotypic and physiological evidence, a new genus, Anaerophaga, is proposed to harbour strain Fru22T (DSM 12881T, OCM 798T) which is described as the type strain of a new species, Anaerophaga thermohalophila gen. nov., sp. nov.

Prevalence of gram negative anaerobic bacilli in routine clinical specimens

A total of 206 gram negative anaerobic bacilli were isolated from 2591 routine clinical specimens. Majority of them (78.2%) were part of a mixed flora. A high incidence of gram negative anaerobic bacilli was found in post-operative wound infections and diabetic foot infections (30.1%), followed by necrotizing fasciitis and crush injuries (18%), pus of empyema and lung abscesses (14.5%) and aspirates from other deep abscesses (10.7%). Bacteroides fragilis was the most frequently recognized species (42.2%), followed by Fusobacterium sp. (17.4%), Prevotella sp. (15.1%) and Porphyromonas sp. (11.2%). Neomycin blood agar plate yielded the maximum number (72.8%) of strains in pure culture. Gram negative anaerobic bacilli in infective processes are significantly on the rise and so suspected cultures should be processed for both aerobic and anaerobic organisms.

The localization of periodontal-disease-associated bacteria in human periodontal pockets

Some Gram-negative anaerobes are associated with the incidence and progression of periodontal disease. In periodontal pockets, however, the localization of those bacteria is unknown. We investigated the localization of 5 bacterial species in human periodontal pockets. Fifteen teeth with a part of periodontal pockets from 10 adult periodontitis patients were obtained, and the localization of bacteria was examined immunohistochemically. Positive reactions with anti-Prevotella nigrescens antibody were located at the epithelium-associated plaque area in the middle pocket zones. In the middle and deep pocket zones, Fusobacterium nucleatum and Treponema denticola were especially localized in the unattached plaque area, but Eikenella corrodens was observed in the tooth-attached plaque area. Actinobacillus actinomycetemcomitans, detected in 2 of 15 samples examined, was found in the unattached plaque area, in the middle pocket zone. The present findings indicated that the 5 bacterial species examined localized at distinct regions in human periodontal pockets.

2-Bromoethanesulfonate affects bacteria in a trichloroethene-dechlorinating culture

Long-term exposure to 2-bromoethanesulfonate (BES), an agent known to inhibit methanogenesis, altered the bacterial community structure of an anaerobic enrichment culture that reductively dechlorinated trichloroethene (TCE). BES did not hinder the dechlorination of TCE or other chlorinated ethenes as previously reported, although different intermediates and end products were observed.

[Skin microbiocenosis in patient with chronic dermatoses]

The skin microflora of patients with chronic dermatoses (atopic dermatitis and psoriasis) have been studied by the original "Bactotests" method. The data thus obtained indicate that the clinical picture of the disease is related to the severity of skin dysbacteriosis. The electron-microscopic study of 2 staphylococcal strains isolated from patients has revealed the presence of the immunoglobulin cover (capsule-like outer sheath consisting of immunoglobulins and other humoral protective factors) on the cell wall of these bacteria.

Dysgonomonas gen. nov. to accommodate Dysgonomonas gadei sp. nov., an organism isolated from a human gall bladder, and Dysgonomonas capnocytophagoides (formerly CDC group DF-3)

Results of a polyphasic taxonomic study on an unknown Gram-negative, facultatively anaerobic, coccobacillus-shaped organism isolated from an infected human gall bladder are presented. Phenotypic and molecular taxonomic studies revealed the organism to be close to, but distinct from, organisms designated CDC (Centers for Disease Control and Prevention) group DF-3. The unknown bacterium was readily distinguished from reference strains of Bacteroides, Prevotella, Porphyromonas and related taxa by 16S rRNA gene sequencing, biochemical tests, analysis of cellular long-chain fatty acids and electrophoretic analysis of whole-cell proteins. Based on the results of the present study, it is proposed that the unknown bacterium be classified in a new genus, Dysgonomonas, as Dysgonomonas gadei sp. nov. (type strain CCUG 42882T = CIP 106420T). In addition, a new species, Dysgonomonas capnocytophagoides sp. nov., is proposed to accommodate strains previously belonging to CDC group DF-3. The type species of the genus Dysgonomonas is Dysgonomonas gadei.

Propionispora vibrioides, nov. gen., nov. sp., a new gram-negative, spore-forming anaerobe that ferments sugar alcohols

Anaerobic enrichment cultures, with erythritol as substrate, resulted in the isolation of a strain with properties not yet found in an existing genus in this combination. The strain, FKBS1, was strictly anaerobic, stained gram-negative and formed spores. Cells were small motile vibrios with flagella inserted at the concave side of the cell. Spores were located terminally and caused only slight swelling of the cells if compared to related spore-forming genera. FKBS1 fermented fructose, mannitol, sorbitol, xylitol and erythritol to propionic acid, acetic acid, CO2 and small amounts of H2 to balance the difference in the oxidation-reduction value between substrate and cell mass. The 16S rDNA sequence revealed relationship to the Sporomusa-Pectinatus-Selenomonas group. However, the phylogenetic distance to any of its members was too great to allow it to be placed in one of the existing genera. Morphologically the strain resembled Sporomusa, which, however, performs an acetogenic type of fermentation. The propionic-acid-forming genera of the group are either not spore-formers or, in the case of Dendrosporobacter quercicolus (syn. Clostridium quercicolum), morphologically different. It is therefore proposed to classify strain FKBS1 as a new genus and species, Propionispora vibrioides.

Molecular identification of Dialister pneumosintes in subgingival plaque of humans

Dialister pneumosintes is a nonfermentative, anaerobic, gram-negative rod that grows with small, circular, transparent, shiny, smooth colonies on blood agar. Even though D. pneumosintes has been recovered from deep periodontal pockets, little is known about the relationship between the organism and destructive periodontal disease. This study describes a rapid PCR method to identify D. pneumosintes in periodontal samples. The PCR identification method detected as little as 10 pg of D. pneumosintes DNA or about 1 to 10 cells without nonspecific amplification of various periodontopathic bacteria. Twelve of 22 subgingival samples from adult periodontitis lesions yielded D. pneumosintes either by culture or by PCR identification. In culture-positive samples, D. pneumosintes averaged 3.9% (0.001 to 10.8%) of total isolates. Studies are needed to delineate virulence factors of D. pneumosintes pertinent to periodontal disease.

Development of a competitive polymerase chain reaction assay for the ruminal bacterium Butyrivibrio fibrisolvens OB156 and its use for tracking an OB156-derived recombinant

A competitive polymerase chain reaction assay targeting the 16S rDNA was developed for quantitating the rumen bacterium Butyrivibrio fibrisolvens OB156. A competitor DNA, serving as an internal control in the competitive polymerase chain reaction reaction, was constructed by polymerase chain reaction using a looped oligo longer than the normal primer. Coamplification of the target DNA with known amounts of the competitor DNA allowed quantitation of the target DNA in both pure culture and mixed culture systems, where minimum quantifiable level of OB156 was 1.7x10(2) and 5.6x10(4) cells, respectively. When an erythromycin-resistant recombinant derived from OB156 was inoculated into a rumen fluid culture, its numbers decreased with time. The rate of decrease measured by the competitive polymerase chain reaction assay was much slower than the rate determined by culture enumeration using erythromycin selection. The competitive polymerase chain reaction assay also showed 48 h persistence of the recombinant at 10(4) ml(-1) even after disappearance of culturable recombinant, suggesting maintenance of the target DNA from uncultivable cells. In an in vivo tracking trial, the recombinant became undetectable within 72 h with either assay, indicating rapid hydrolysis and/or outflow of the cells from the rumen.

Denitrovibrio acetiphilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column

A novel dissimilatory, nitrate-reducing bacterium, designated strain N2460T, was isolated from an oil reservoir model column. Strain N2460T is a mesophilic, obligately anaerobic, marine, gram-negative bacterium. The cells are vibrio-shaped and motile by a bipolar flagellum. Strain N2460T reduces nitrate to ammonia in a mineral medium supplied by acetate. The presence of a 2-oxoglutarate dehydrogenase activity indicates that acetate is oxidized via the citric acid cycle. No growth is obtained on formate, higher fatty acids, malate, fumarate, benzoate, alcohols, sugar, yeast extract, crude oil, alkanes, proline, hydrogen, sulfur or thiosulfate with nitrate as electron acceptor. Oxygen, sulfate, thiosulfate and sulfur are not utilized as alternative electron acceptors. Strain N2460T grows fermentatively on fumarate, but not on pyruvate. The G+C content of the DNA is 42.6 mol%. 16S rRNA gene analysis shows that strain N2460T belongs to the Bacteria and that the closest relative is 'Geovibrio ferrireducens' (sequence similarity 86.9%). On the basis of phylogenetic as well as phenotypic data, it is proposed that strain N2460T represents the type strain of a new genus and species, Denitrovibrio acetiphilus gen. nov., sp. nov.

Haloanaerobium fermentans sp. nov., a strictly anaerobic, fermentative halophile isolated from fermented puffer fish ovaries

A strain of strictly anaerobic and moderately halophilic bacteria isolated from salted puffer fish ovaries was studied phenotypically, genotypically and phylogenetically. On the basis of its physiological and morphological characteristics, the new isolate is considered to be a member of the genus Haloanaerobium. It is a motile, rod-shaped, non-spore-forming, gram-negative, obligate anaerobe that grows in the presence of 25% (w/v) NaCl. The optimum salt concentration for growth is 10% (w/v). It grows well at 15 and 45 degrees C, but not at 10 or 50 degrees C. The optimum temperature for growth is 35 degrees C. It grows at pH 6.0-9.0 and the optimum pH for growth is 7.5. It ferments N-acetylglucosamine, cellobiose, fructose, galactose, D-glucose, lactose, maltose, D-mannose, raffinose, D-ribose, sucrose and D-xylose. It ferments D-glucose with the production of hydrogen, carbon dioxide, ethanol and organic acids such as acetate, formate and lactate. 16S rRNA gene sequence information confirmed the phylogenetic position of the new isolate, strain R-9T, as a member of the genus Haloanaerobium. DNA-DNA hybridization data revealed that isolate R-9T exhibited low levels of reassociation (less than 30%) with previously described Haloanaerobium species. Based on these results, the new isolate appears to represent a new Haloanaerobium species, for which the name Haloanaerobium fermentans sp. nov. is proposed. The type strain is R-9T (= JCM 10494T).

Thermanaerovibrio velox sp. nov., a new anaerobic, thermophilic, organotrophic bacterium that reduces elemental sulfur, and emended description of the genus Thermanaerovibrio

A moderately thermophilic, organotrophic bacterium with vibrioid cells was isolated from a sample of a cyanobacterial mat from caldera Uzon, Kamchatka, Russia, and designated strain Z-9701T. Cells of strain Z-9701T were curved, Gram-negative rods, 0.5-0.7 x 2.5-5.0 microm in size, with tapering ends and with fast, wavy movement by means of lateral flagella located on the concave side of the cell. Colonies were small, white, irregular or round, 0.2 mm in diameter, and with even edges. Strain Z-9701T was an obligate anaerobe with a temperature optimum at 60-65 degrees C and a pH optimum at 7.3. It fermented glucose, fructose, mannose, N-acetyl-D-glucosamine, adonite, arginine, serine, peptone, yeast extract and Casamino acids. The fermentation products formed during growth on glucose were acetate, lactate, H2, CO2 and ethanol. Strain Z-9701T reduced elemental sulfur to H2S during organotrophic growth with glucose or peptides as energy and carbon sources. In the presence of S0, strain Z-9701T was capable of lithotrophic growth with molecular hydrogen as energy substrate and 0.1 g yeast extract l(-1) as carbon source. Sulfate, thiosulfate, nitrate, Fe(III) and sulfite were not reduced and did not stimulate growth. The G+C content of strain Z-9701T DNA was 54.6 mol%. The results of 16S rDNA sequence analyses revealed that strain Z-9701T belongs to the cluster within the Clostridium group formed by Thermanaerovibrio acidaminovorans, Dethiosulfovibrio peptidovorans, Anaerobaculum thermoterrenum and Aminobacterium colombiense, but the level of sequence similarity with the members of this cluster was not very high (87.6-92.2%). Among these organisms, Thermanaerovibrio acidaminovorans is phenotypically close to strain Z-9701T. However, the two organisms showed a relatively low level of similarity of their 16S rRNA sequences (92.2%) and of DNA-DNA hybridization (15 +/- 1%). Nevertheless, on the basis of the similar morphology and physiology of the new isolate and Thermanaerovibrio acidaminovorans, strain Z-9701T was placed in the genus Thermanaerovibrio and a new species, Thermanaerovibrio velox, proposed for it. The type strain is Z-9701T (= DSM 12556T).

Reductively debrominating strains of Propionigenium maris from burrows of bromophenol-producing marine infauna

Two novel strains of Propionigenium maris able to reductively debrominate 2,4,6-tribromophenol (TBP) to monobromophenols were isolated from marine hemichordate and polychaete burrows. These two strains, DSL-1 and ML-1, were anaerobic, non-motile rods that stained Gram-negative and required 0.05% yeast extract for growth. Strain DSL-1 fermented pyruvate and succinate to predominantly butyrate and strain ML-1 fermented glucose and succinate primarily to propionate. No inorganic terminal electron acceptors were identified. The pH and temperature optima for growth were 7.6 and 30 degrees C for strain DSL-1 and 7.0 and 32 degrees C for strain ML-1, respectively; doubling times for strains DSL-1 and ML-1 were 0.32 h and 0.30 h, respectively. Both strains required 2-3% (w/v) NaCl for optimal growth. Morphological and physiological features, as well as the results of 16S rDNA sequence analysis, showed these to be new strains of Propionigenium maris. Because they differ from the P. maris type strain (DSM 9537T) in a number of respects, including their ability to rapidly debrominate di- and tribromophenols, and in their specific habitats, the species description is amended to include these ecologically important properties.

Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate

A new anaerobic, thermophilic, syntrophic, fatty-acid-oxidizing bacterium designated strain TGB-C1T was isolated from granular sludge in a thermophilic upflow anaerobic sludge blanket (UASB) reactor. The cells were slightly curved rods and were weakly motile. Spore formation was not observed. The optimal temperature for growth was around 55 degrees C and growth occurred in the range 45 to 60 degrees C. The pH range for growth was 5.8-7.5, and the optimum pH was 6.5-7.0. Crotonate was the only substrate that allowed the strain to grow in pure culture. However, in co-culture with the thermophilic, hydrogenotrophic Methanobacterium thermoautotrophicum strain delta H, the isolate could syntrophically oxidize saturated fatty acids with 4-10 carbon atoms, including isobutyrate. During the degradation of isobutyrate by the co-culture, isobutyrate was isomerized to butyrate, which was then oxidized. The strain was not able to utilize sulfate, sulfite, thiosulfate, nitrate, fumarate or Fe(III) as electron acceptor. The DNA base composition was 51.0 mol%. 16S rDNA sequence analysis revealed that the strain belongs to the family Syntrophomonadaceae, but it was only distantly related to other known species of beta-oxidizing syntrophs. Hence, the name Syntrophothermus lipocalidus is proposed for TGB-C1T as a new species of a new genus.

Pelospora glutarica gen. nov., sp. nov., a glutarate-fermenting, strictly anaerobic, spore-forming bacterium

The strictly anaerobic, Gram-negative, spore-forming bacterium strain WoGl3T had been enriched and isolated in mineral medium with glutarate as the sole source of energy and organic carbon. Glutarate was fermented to a mixture of butyrate, isobutyrate, CO2 and small amounts of acetate. Strain WoGl3T grew only with the dicarboxylates glutarate, methylsuccinate and succinate. 16S rDNA sequence analysis revealed an affiliation of strain WoGl3T to the family Syntrophomonadaceae. This monophyletic group is comprised of strain WoGl3T and the genera Syntrophomonas, Syntrophospora and Thermosyntropha, within the phylum of Gram-positive bacteria with a low DNA G + C content. Overall intra-group 16S rRNA sequence similarities of 89.2-93.9% document a separate phylogenetic status for strain WoGl3T. Strain WoGl3T (= DSM 6652T) is described as the type strain of a new species within a new genus, Pelospora glutarica gen. nov., sp. nov.