Non-sporeforming Rods Research Articles

Description of Pseudogemmobacter faecipullorum sp. nov., isolated from poultry manure.

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST710T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST710T were aerobic, Gram-stain-negative, nonmotile, nonspore-forming rods, displaying positive reactions for catalase, and oxidase activities. Strain CC-YST710T was found to grow optimally at 30°C, pH 7.0, and in the presence of 2% (w/v) NaCl. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminolipids, one unidentified aminophospholipid, and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C16:0, C18:0, and C18:1ω7c/C18:1ω6c. Based on 16S rRNA gene analysis, this isolate showed the closest phylogenetic relationship with 'Pseudogemmobacter humicola' (97.6%), followed by Pseudogemmobacter bohemicus (97.2%) and 'Pseudogemmobacter hezensis' (97.5%). The draft genome (4.3 Mb) had 62.9 mol% G+C content. CC-YST710T can be distinguished from other Pseudogemmobacter species due to the exclusive presence of key genes encoding p-hydroxybenzoate hydroxylase, protocatechuate 3, 4-dioxygenase (α and β chain), and homogentisate 1, 2-dioxygenase involved in the degradation of phenolic compounds such as p-hydroxybenzoic acid, protocatechuate, and homogentisate, respectively. Orthologous average nucleotide identity (OrthoANI) of the isolate with the type strains of the genera Pseudogemmobacter were 77.6%‒78.0% (n=3), followed by Tabrizicola (72.3%‒73.7%, n=5), and Gemmobacter(72.3%‒73.5%, n=7). Based on its distinct phylogenetic, phenotypic, and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST710T is considered to represent a novel Pseudogemmobacter species, for which the name Pseudogemmobacter faecipullorum sp. nov. (type strain CC-YST710T=BCRC 81286T=JCM 34182T).

Rufibacter soli sp. nov., a Bacterium Isolated from Soil.

A gram-negative bacterium, designated FJY1(T), was isolated from a soil sample obtained from a university campus in South Korea. Examination showed that FJY1(T) was red-pigmented, aerobic, motile, and composed of nonspore-forming rods. This strain grew in a temperature range of 15-37°C and a pH range of 7-9. Based on 16S rRNA gene sequence similarity, strain FJY1(T) was most closely related to Rufibacter roseus H359(T) and Rufibacter tibetensis 1351(T), with sequence similarities of 95.98 and 95.46%, respectively. Its major cellular fatty acids were iso-C15:0 (18.16%) and summed feature 4 (C17:1 iso I and C17:1 anteiso B; 15.17%). The DNA G+C content of FJY1(T) was 49.7mol%; its predominant quinone was MK-7; and its major polar lipid was phosphatidylethanolamine. Phylogenetic analysis and analysis of its physiological and biochemical characteristics indicated that this isolate constituted a novel species, for which we propose the name Rufibacter soli sp. nov., with the type strain FJY1(T) (=KCTC 42815(T)=JCM 31024(T)).

Triparesis caused by gas-containing extensive epidural abscess secondary to Aeromonas hydrophila infection of a thoracic vertebroplasty: a case report

Background contextAeromonas hydrophila is a motile gram-negative non-sporeforming rod with facultative anaerobic metabolism. Except for gastrointestinal disease, skin and soft-tissue infections represent the second most common site of human Aeromonas infections. However, to our knowledge, A. hydrophila infection of the spine has not been reported to date. PurposeTo report the first case of A. hydrophila spinal infection of the T7 vertebra after vertebroplasty. Study designCase report. MethodsA 72-year-old man was transferred to our emergency department with chief complaints of severe midthoracic pain and triparesis. He had undergone vertebroplasty for a painful vertebral fracture at T7 5 weeks before transfer. Magnetic resonance imaging showed an infection of the T7 vertebroplasty and an extensive epidural abscess. The epidural abscess originating from the infected T7 vertebroplasty extended from the T8 to the C4 epidural space. Computed tomography demonstrated sparsely scattered gas in the epidural abscess, strongly suggestive of an anaerobic infection. ResultsEmergency multilevel laminectomies from C5 to T8 and a posterior instrumentation from T3 to T10 were performed. A. hydrophila was isolated from the blood cultures. The patient was treated with intravenous ampicillin/sulbactam. Posterior decompression and stabilization in combination with appropriate antibiotic treatment completely resolved the neurologic deficit and infection without the need for further anterior corpectomy of the infected T7 vertebroplasty. ConclusionsThis is the first reported case of spine infection caused by A. hydrophila. The infection developed after vertebroplasty for the management of a painful vertebral fracture. Triparesis occurred rapidly due to an extensive epidural abscess containing gas. Emergency decompression and stabilization in combination with appropriate antibiotic treatment achieved a successful clinical outcome.

Approaches to the study of the systematics of anaerobic, Gram-negative, non-sporeforming rods: Current status and perspectives

The present article gives an overview of recent taxonomic changes among the Gram-negative, anaerobic rods, briefly highlighting areas where the biology and ecology have a bearing on recent nomenclatorial changes. The focus is among the genera Bacteroides, Prevotella, Porphyromonas, Leptotrichia, Dysgonomonas, Fusobacterium and the Synergistes group and additionally demonstrates the value of conserved indels and group-specific proteins for identifying and circumscribing many of these taxa and the Bacteroidetes– Chlorobi species in general.

Characterization of the psychrotolerant acetogen strain SyrA5 and the emended description of the species Acetobacterium carbinolicum

A psychrotolerant, obligate anaerobic, acetogenic bacterium designated strain SyrA5 was isolated from black anoxic sediment of a brackish fjord. Cells were Gram-positive, non-sporeforming rods. The isolate utilized H(2)/CO(2), CO, fructose, glucose, ethanol, ethylene glycol, glycerol, pyruvate, lactate, betaine and the methyl-groups of several methoxylated benzoic derivatives such as syringate, trimethoxybenzoate and vallinate. The optimum temperature for growth was 29 degrees C, whilst slow growth occurred at 2 degrees C. The strain grew optimally with NaCl concentrations below 2.7% (w/v), but growth occurred up to 4.3% (w/v) NaCl. Growth was observed in the range from pH 5.9 to 8.5, optimum at pH 8. The G+C content was 44.1 mol%. Based upon 16S rRNA gene sequence analysis and DNA-DNA reassociation studies, the organism was classified in the genus Acetobacterium. Strain SyrA5 shared a 16S rRNA sequence similarity with A. carbinolicum of 100%, a fthfs gene (which codes for the N5,N10 tetrahydrofolate synthetase) sequence identity of 98.5-98.7% (amino acid sequence similarities were 99.4-100%) and a RNA-DNA hybridization homology of 64-68%. Despite a number of phenotypic differences between strain SyrA5 and A. carbinolicum we propose including strain SyrA5 as a subspecies of A. carbinolicum for which we propose the name Acetobacterium carbinolicum subspecies kysingense. The type strain is SyrA5 (=DSM 16427(T), ATCC BAA-990).

Recently described clinically important anaerobic bacteria: medical aspects.

There is still inadequate information on the role of certain newly described or reclassified anaerobes in disease processes, on their normal sites of carriage, and on their antimicrobial susceptibilities. Herein, we summarize this information (most of the literature reviewed is from the past 5 years, but a few of the articles are approximately 10 years old). Porphyromonas species had seemed to be relatively nonpathogenic, but recent work indicates that this belief is incorrect. P. gingivalis, P levii-like organisms, and P. endodontalis-like organisms have been recovered from a variety of oral and extraoral infections. P. macacae has been recovered from infected cat bite wounds. Sutterella wadsworthensis, recently differentiated from Campylobacter gracilis, has been found in a variety of infections. Bilophila wadsworthia has also been recovered from a wide variety of infections. Newly described anaerobic cocci, gram-positive nonsporeforming rods, and clostridia have also been isolated from various infections.

Assignment of Actinomyces pyogenes-like (CDC coryneform group E) bacteria to the genus Actinomyces as Actinomyces radingae sp. nov. and Actinomyces turicensis sp. nov.

In a previous study the authors reported the characterization of some facultatively anaerobic, Gram-positive, non-sporeforming rods which were found in mixed cultures from various infectious processes, including patients with otitis, empyema, perianal abscesses and decubitus ulcers. Phenotypically these organisms closely resembled Actinomyces pyogenes although their precise taxonomic position remained unknown. In the present investigation the authors have determined the 16S rRNA gene sequences of some representative strains of the Actinomyces pyogenes-like bacteria and report the results of a comparative sequence analysis. On the basis of the results of the present and earlier findings two new Actinomyces species, Actinomyces radingae sp. nov. and Actinomyces turicensis sp. nov. are proposed. The type strains are DSM 9169T and DSM 9168T, respectively.

Anaerobic extremely thermophilic carboxydotrophic bacteria in hydrotherms of Kuril Islands

A new group of extremely thermophilic, obligately anaerobic, carboxydotrophic eubacteria is described. The organisms are characterized by a novel type of chemotrophic metabolism in thermophilic environments. They grow at temperatures up to 80-85°C chemolithotrophically with 100% CO in the gas phase as the sole energy source. The CO oxidation is coupled to H2 and CO2 formation according to the equation CO+H2O → H2+CO2. No other products of metabolism are produced. The group of CO-utilizing, H2-producing anaerobes includes diverse bacteria. They are non-sporeforming rods differing in morphology, CO uptake rates, habitats, and maximum growth temperatures. The new carboxydotrophic thermophilic anaerobes are widely distributed in freshwater and coastal marine hydrotherms of the Kuril Islands.

Aeromonas species: Pathogens of aquatic inhabitants with a human host range

Aeromonads are gram-negative, facultatively anaerobic, fermentative, oxidase-positive, nonsporeforming rods which, in contrast to vibrios, do not require added NaC1 to complex media for growth and are resistant to the inhibitory action of the pteridine vibriostatic compound 0/129. In the fourth edition of Bergey's Manual of Determinative Bacteriology, they are assigned to the family Vibrionaceae within the genus Aeromonas (1), which comprises a single psychrophilic, nonmotile species, Aeromonas salmonicida, and three mesophilic polarly flagellated motile species Aeromonas hydrophila, Aeromonas sobria, and Aeromonas caviae (1, 2). Recently three new mesophilic species, Aeromonas media, Aeromonas veronii, and Aeromonas schubertii have been recognized (3-5). Classification of Aeromonas at the species level is based on DNA homology, guanine + cytosine content, composition of core polysaccharide of the cell wall lipopolysaccharide (1, 2, ~6), and key biochemical characteristics (Table 1). When grown in nutrient broth containing glucose, certain strains of Aeromonas rapidly reduce the pH of the medium even though minimal growth has occurred as inferred from the sparse turbidity in the tubes. Because viable cells cannot be recovered from these broth cultures after 24 h incubation, the phenomenon has been termed (7). This suicide phenomenon has been attributed to the lethal effect of accumulated acetic acid subsequent to glucose fermentation (7). Glucose catabolite repression of the tricarboxylic acid cycle enzymes and stimulation of pyruvate dehydrogenase activates an acetic acidproducing (acetyl phosphate) pathway (8), which leads to the suicide phenomenon.

Fermentation of methoxyacetate to glycolate and acetate by newly isolated strains of Acetobacterium sp.

Three strains of new mesophilic homoacetogenic bacteria were enriched and isolated from sewage sludge and from marine sediment samples with methoxyacetate as sole organic substrate in a carbonate-buffered medium under anoxic conditions. Two freshwater isolates were motile, Gram-positive, non-sporeforming rods. The marine strain was an immotile, Gram-positive rod with a slime capsula. All strains utilized only the methyl residue of methoxyacetate and released glycolic acid. They also fermented methyl groups of methoxylated aromatic compounds and of betaine to acetate with growth yields of 6–10 g dry matter per mol methyl group. H2/CO2, formate, methanol, hexamethylene tetramine, as well as fructose, numerous organic acids, glycerol, ethylene glycol, and glycol ethers were fermented to acetate as well. High activities of carbon monoxide dehydrogenase (0.4–2.2 U x mg protein−1) were detected in all three isolates. The guanine-plus-cytosine-content of the DNA of the freshwater isolates was 42.7 and 44.4 mol %, with the marine isolate it was 47.7 mol %. The freshwater strains were assigned to the genus Acetobacterium as new strains of the species A. carbinolicum. One freshwater isolate, strain KoMac1, was deposited with the Deutsche Sammlung von Mikroorganismen GmbH, Braunschweig, under the number DSM 5193.

Fermentative degradation of dipicolinic acid (pyridine-2,6-dicarboxylic acid) by a defined coculture of strictly anaerobic bacteria.

Degradation of dipicolinic acid (pyridine-2,6-dicarboxylic acid) under strictly anaerobic conditions was studied in enrichment cultures from marine and freshwater sediments. In all cases, dipicolinic acid was completely degraded. From an enrichment culture from a marine sediment, a defined coculture of two bacteria was isolated. The dipicolinic acid-fermenting bacterium was a Gram-negative, non-sporeforming strictly anaerobic short rod which utilized dipicolinic acid as sole source of carbon, energy, and nitrogen, and fermented it to acetate, propionate, ammonia, and 2CO2. No other substrate was fermented. This bacterium could be cultivated only in coculture with another Gram-negative, non-sporeforming rod from the same enrichment culture which oxidized acetate to CO2 with fumarate, malate, or elemental sulfur as electron acceptor, similar to Desulfuromonas acetoxidans. Since this metabolic activity is not important in substrate degradation by the coculture, the basis of the dependence of the dipicolinic acid-degrading bacterium on the sulfur reducer may be sought in the assimilatory metabolism.

Accuracy and reproducibility of the 4-hour ATB 32A method for anaerobe identification.

The ATB 32A system (API System SA, La Balme les Grottes, Montalieu-Vercieu, France) was evaluated for use in the identification of 214 anaerobes. Organisms included 73 isolates of the Bacteroides fragilis group, 24 Bacteroides spp., 10 fusobacteria, 43 clostridia, 28 cocci, and 36 gram-positive, nonsporeforming rods. With the concomitant use of Gram stain, pigmentation, catalase testing, and aerobic growth, the ATB 32A system correctly identified 97% of the B. fragilis group isolates, 88% of Bacteroides spp., 50% of fusobacteria, 74% of clostridia, 100% of cocci, and 86% of the gram-positive, nonsporeforming rods. Overall, 188 strains (88%) were correctly identified, with 18 (8%) requiring extra tests, other than the four mentioned above, for correct identification. Eight strains were misidentified, including one Bacteroides sp., three fusobacteria, one Clostridium sp., and three gram-positive, nonsporeforming rods. Reproducibility was very good, with 12 of 14 strains (86%) tested in triplicate yielding identical correct results on each of three occasions and 2 strains (14%) yielding identical correct results on two occasions. There was a low-probability identification (including the correct species) on the third testing. The ATB 32A system represents a worthwhile advance in systems used for the identification of clinically significant anaerobic bacteria.

Enzymes of Diagnostic Importance Within theBacteroidaceae; Use as Possible Ecological Markers

Cell free extracts from a wide variety of Gram-negative, anaerobic, non-sporeforming rods were screened for dehydrogenase enzymes of carbohydrate and nitrogen metabolism. Four enzymes, malate dehydrogenase, glutamate dehydrogenase, glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, were found to be of diagnostic importance. The ‘ Bacteroides fragilis ’ group possessed all four enzymes whereas the ‘ B. melaninogenicus-B. oralis ’ group and the asaccharolytic, pigmented species were characterised by the presence of only malate and glutamate dehydrogenases. The saccharolytic and asaccharolytic pigmented species could be differentiated by the wide difference in pH optimum for malate dehydrogenase. Fusobacterium species and Leptotrichia buccalis both possessed only glutamate dehydrogenase, but there were differences in enzyme activity between both taxa. Other genera such as Anaerorhabdus , Megamonas , Mitsuokella . Rikenella , Sebaldella and Tissierella had characteristic enzyme profiles. These enzymatic data are of diagnostic value within the Bacteroidaceae and may serve as useful markers for studying the ecological interrelationships of these bacteria. Keywords: Bacteroidaceae; Dehydrogenases; Enzyme patterns.

Bacteroides salivosus sp. nov., an Asaccharolytic, Black-Pigmented Species from Cats

A new species, Bacteroides salivosus sp. nov., is proposed for black-pigmented, asaccharolytic Bacteroides strains from cats, isolated from subcutaneous abscesses and empyemas, as well as from gingival margins of normal mouths. The bacterium is an obligately anaerobic, gram-negative, brown- or black-pigmented, asaccharolytic, nonmotile, nonsporeforming rod that does not grow in 20% bile and has a guanine-plus-cytosine content of 42 to 44 mol%. It has 12% deoxyribonucleic acid homology with the human type strain of Bacteroides gingivalis (ATCC 33277T) and 1% deoxyribonucleic acid homology with the human type strain of Bacteroides asaccharolyticus (ATCC 25260T). Strain VPB 157 (NCTC 11632T) is the type strain. Unlike B. gingivalis, B. salivosus produces catalase, and the colonies of the type strain fluoresce at 24 and 48 h, although some other strains do not fluoresce. It does not agglutinate sheep erythrocytes. Unlike either B. asaccharolyticus or Bacteroides endodontalis, it has trypsinlike activity and produces large quantities of phenylacetic acid.

Isolation of Cellulolytic Anaerobic Extreme Thermophiles from New Zealand Thermal Sites

Avicel enrichment cultures from 47 thermal-pool sites in the New Zealand Rotorua-Taupo region were screened for growth and carboxymethyl cellulase activity at 75 degrees C. Eight anaerobic cellulolytic cultures were obtained. The effect of temperature on carboxymethyl cellulase activity was measured, and bacteria were isolated from the five best cultures. Bacteria from two sources designated TP8 and TP10 grew at 75 degrees C, accumulated reducing sugar in the growth medium and gave free cellulases with avicelase activity. Bacteria from sources designated Tok4, Tok8, and Wai21 grew at 75 degrees C, accumulated no free sugars in the medium, and gave free carboxymethyl cellulases with virtually no avicelase activity. All were obligate anaerobic nonsporeforming rods which stained gram negative, grew on pentoses as well as hexoses, and gave ethanol and acetate as major fermentation end products. The isolated strain which produced the most active and stable cellulases (trivially designated TP8.T) had lower rates of free endocellulase accumulation at 75 degrees C than did Clostridium thermocellum at 60 degrees C, but its cellulase activity against avicel and filter paper in culture supernatants was comparable. Tested at 85 degrees C, TP8.T carboxymethyl cellulases included components which were very stable, whereas C. thermocellum carboxymethyl cellulases were all rapidly inactivated. The TP8.T avicelase activity was relatively unaffected by Triton X-100, EDTA, and dithiothreitol. Evidence was obtained for the existence of unisolated, cellulolytic extreme thermophiles producing cellulases which were more stable and active than those from TP8.T.

Bacteroides tectum sp. nov. and Characteristics of Other Nonpigmented Bacteroides Isolates from Soft-Tissue Infections from Cats and Dogs

Sixty strains of obligately anaerobic gram-negative nonsporeforming nonpigmented Bacteroides species were isolated from subcutaneous abscesses and pyothoraxes of cats and dogs. All of these strains grew well in bile and produced acetic, propionic, and succinic acids as major products of fatty acid metabolism. Phenotypic and deoxyribonucleic acid (DNA) homology data divided the strains into five groups. Only three strains were members of Bacteroides fragilis, as determined by biochemical and DNA homology analyses. All of the other strains showed negligible levels of DNA homology with human strains of B. fragilis, Bacteroides distasonis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, and Bacteroides ovatus, although they did have substantial ribosomal ribonucleic acid homology with these species. One group comprising 52 strains is proposed as a new species, Bacteroides tectum, having three distinct homology clusters. Strains of B. tectum are obligately anaerobic, gram-negative, nonmotile, nonpigmented, nonsporeforming rods that grow well in bile, do not produce indole, and only weakly ferment carbohydrates. They have a DNA guanine-plus-cytosine ratio of 46 mol% but do not exhibit DNA homology with phenotypically similar human strains of Bacteroides.

Reduction of oral flora with rifampin in healthy volunteers.

The effect of a short course of rifampin on the oral microflora was evaluated in 17 healthy volunteers. Salivary specimens were collected before and after two 600-mg doses of rifampin administered 6 h apart. Salivary bacteria were identified to species, and total quantitative colony counts were determined for each isolate. For all 17 subjects, treatment with rifampin led to a reduction in total bacterial colony counts; the mean inhibitory activity was 85.8% (range, 48.3 to 99.8%). Both aerobic and anaerobic bacteria were inhibited in every case: 45.5 to 99.8% for aerobic bacteria, mean inhibitory activity of 85.8%; 40.9 to 100% inhibition for anaerobic bacteria, mean inhibitory activity of 87.6%. However, total counts were reduced by greater than or equal to 2 logarithms in only 18% of individuals; for aerobes, in 29%; and for anaerobes, in 41%. All classes of bacteria were inhibited, with mean inhibitory activities ranging from 8.4 to 99.9%. However, only streptococci, Haemophilus spp., Bacteroides spp., and aerobic and anaerobic gram-positive nonsporeforming rods were reduced in counts close to 2 logarithms after treatment with rifampin. Clinical studies are needed to clarify the significance of these in vitro data and to delineate a possible role for rifampin in preoperative prophylaxis of patients undergoing head and neck cancer surgery.

Oxidation of primary aliphatic alcohols by Acetobacterium carbinolicum sp. nov., a homoacetogenic anaerobe

Four strains of new homoacetogenic bacteria were enriched and isolated from freshwater sediments and sludge with ethanol, propanol, 1,2-propanediol, or 1,2-butanediol as substrates. All strains were Gram-positive nonsporeforming rods and grew well in carbonate-buffered defined media under obligately anaerobic conditions. Optimal growth occurred at 27° C around pH 7.0. H2/CO2, primary aliphatic alcohols C3−C5, glucose, fructose, lactate, pyruvate, ethylene glycol, 1,2-propanediol, 2,3-butanediol, acetoin, glycerol, and methyl groups of methoxylated benzoate derivates and betaine were fermented to acetate or, in case of primary alcohols C3−C5 and 1,2-propanediol, to acetate and the respective fatty acid. In coculture with methanogens methane was formed, probably due to interspecies hydrogen transfer. Strain WoProp 1 is described as a new species, Acetobacterium carbinolicum. It had a DNA base composition of 38.5±1.0% guanine plus cytosine, and contained murein of crosslinkage type B similar to A. woodii.

Acetomicrobium flavidum, gen. nov., sp. nov., a thermophilic, anaerobic bacterium from sewage sludge, forming acetate, CO 2 and H 2 from Glucose

Summary Acetomicrobium flavidum gen. nov., sp. nov. was isolated from a thermophilic, anaerobic sewage sludge digester operated at 60 °c. The Gram-negative, highly motile, non-sporeforming rods form 2 mol acetic acid, 2 mol CO 2 and 4 mol H 2 from 1 mol hexose. They represent at least 25% of the total population (microscopic count) of the fermenting sludge.

Rhodopseudomonas rutila, a New Species of Nonsulfur Purple Photosynthetic Bacteria

Strains R1T (type strain) and R2, two new isolates of nonsulfur purple photosynthetic bacteria, were studied. The cells of these organisms were gram-negative nonsporeforming rods that were motile by means of a single flagellum, and they multiplied by budding. The photosynthetic membrane systems of these strains were of the lamellar type parallel to the cytoplasmic membrane. Cells which formed under anaerobic conditions in the light were red. The cells of these strains contained bacteriochlorophyll a, ubiquinone 10, and carotenoids. No vitamins were required as growth factors, and reduced sulfur compounds could not be utilized by strains R1T and R2. These two strains produced molecular hydrogen anaerobically in the light. On the basis of this study, we propose a new species, Rhodopseudomonas rutila, for strains R1T and R2. The guanine-plus-cytosine contents of the deoxyribonucleic acids of strains R1T and R2 are 67.6 and 69.4 mol%, respectively. The type strain of this new species is strain R1 (= ATCC 33872).