- Volume 39, Issue 2, 1989
Volume 39, Issue 2, 1989
- Original Papers Relating To Systematic Bacteriology
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Utility of a Bifunctional Tryptophan Pathway Enzyme for the Classification of the Herbicola-Agglomerans Complex of Bacteria †
More LessAbstractBifunctional proteins are the result of relatively infrequent genetic events that are faithfully conserved. They are reliable markers that define phylogenetic clusters. The bifunctional protein anthranilate synthase: anthranilate 5-phosphoribosylpyrophosphate phosphoribosyltransferase (AS:PRT) separates two enteric clusters. Previously published data show that this bifunctional protein is present in the lineage shared by Escherichia coli, Salmonella typhimurium, Citrobacter freundii, Klebsiella pneumoniae, Enterobacter aerogenes, and Enterobacter cloacae, but is absent in Erwinia carotovora, Serratia marcescens, Proteus vulgaris, Morganella morganii, and Hafnia alvei. It has been postulated that aerogenic and anaerogenic strains of Enterobacter agglomerons belong to different groups, which correspond to the clusters mentioned above, respectively. In confirmation of this, we found that Enterobacter agglomerons ATCC 29915 (aerogenic) possesses bifunctional AS:PRT, whereas Enterobacter agglomerons ATCC 27155T (T = type strain) (anaerogenic) lacks AS:PRT. We also found that Erwinia herbicola 33243T lacks AS:PRT. Beji et al. (Int. J. Syst. Bacteriol. 38:77-88) recently showed that the type strains of Enterobacter agglomerons (ATCC 27155) and Erwinia herbicola (ATCC 33243) belong to the same genomic species. We suggest that Enterobacter agglomerons (= Erwinia herbicola) should be excluded from the genus Enterobacter. We further suggest that strains currently designated Enterobacter agglomerons can be grouped with Erwinia herbicola or with the enteric cluster containing Enterobacter depending upon whether bifunctional AS:PRT is absent or present, respectively.
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Deoxyribonucleic Acid Homology Studies of Lactobacillus casei, Lactobacillus paracasei sp. nov., subsp. paracasei and subsp. tolerans, and Lactobacillus rhamnosus sp. nov., comb. nov.
More LessAbstractDeoxyribonucleic acid (DNA)-DNA hybridizations were performed on strains of Lactobacillus casei. Our results indicate that this species as presently constituted is genomically very heterogeneous. The majority of strains designated L. casei subsp. casei, together with members of L. casei subsp. alactosus, L. casei subsp. pseudoplantarum, and L. casei subsp. tolerans, exhibited high levels of DNA relatedness with each other but were distinct from the type strain of L. casei subsp. casei. Strains of L. casei subsp. rhamnosus also formed a genomically homogeneous group unrelated to all members of the other L. casei subspecies examined. On the basis of the present and previous findings we suggest that members of L. casei subsp. alactosus, L. casei subsp. pseudoplantarum, and L. casei subsp. tolerans and the majority of L. casei subsp. casei strains be given separate species status, for which we propose the names L. paracasei sp. nov., L. paracasei subsp. paracasei (type strain, NCDO 151), and L. paracasei subsp. tolerans (type strain ATCC 25599). We also propose that L. casei subsp. rhamnosus be elevated to species status, as L. rhamnosus sp. nov. (type strain, ATCC 7469).
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Deoxyribonucleic Acid Hybridization Study of Methanogenium and Methanocorpusculum Species, Emendation of the Genus Methanocorpusculum, and Transfer of Methanogenium aggregans to the Genus Methanocorpusculum as Methanocorpusculum aggregans comb. nov.
More LessAbstractDeoxyribonucleic acid hybridization indicated that species of the genera Methanogenium and Methanocorpusculum are phylogenetically diverse. The 10 strains examined in this study fall into four phylogenetically defined groups. The first group (Methanogenium marisnigri, Methanogenium bourgense, Methanogenium olentangyi, and Methanogenium thermophilicum) is physiologically the most diverse, containing mesophiles and thermophiles and containing marine and nonmarine organisms. The second group (Methanogenium aggregans, Methanocorpusculum parvum, and Methanocorpusculum labreanum) contains very small mesophilic coccoid organisms from anaerobic digestors. The third group contains a single species, Methanogenium tationis, which was isolated from a solfataric mud pool, and the fourth group contains the type species, Methanogenium cariaci, which is a marine organism. Based on the high deoxyribonucleic acid sequence similarity between Methanogenium aggregans and Methanocorpusculum parvum, we propose to transfer Methanogenium aggregans to the genus Methanocorpusculum, naming it Methanocorpusculum aggregans comb. nov. The type strain is strain MSt (= DSM 3027 = OGC 21). The species in the other three major groups are placed in the genus Methanogenium, although the lack of phylogenetic relatedness indicates that some of these organisms should be separated from Methanogenium cariaci into new genera. However, we propose that cataloging or sequencing of ribosomal ribonucleic acid from these species must be completed before new genera are designated.
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Bacillus glucanolyticus, a New Species That Degrades a Variety of β-Glucans
More LessAbstractA new species, Bacillus glucanolyticus, is proposed for a group of facultatively anaerobic endospore-forming bacteria isolated from soil that hydrolyze various β-glucans, including carboxymethyl cellulose and pustulan. Of the 14 strains examined, 11 were phenotypically homogeneous, and five of these strains showed high levels of deoxyribonucleic acid (DNA) relatedness (>68%) to a reference strain. Two pustulan-hydrolyzing strains were atypical, with low levels of DNA relatedness (52 to 57%), and a third strain was not classified as B. glucanolyticus. B. glucanolyticus strains produce motile microcolonies similar to those of Bacillus alvei but can be distinguished from this taxon by several phenotypic characteristics and a higher DNA base composition (48 mol%). B. glucanolyticus is similar to Bacillus circulans and related species; indeed, four strains were received as B. circulans, but distinctive phenotypic characteristics and low levels of DNA homology with B. circulans, Bacillus amylolyticus, Bacillus lautus, Bacillus pabuli, and Bacillus validus strains support its introduction as a new species. The type strain of B. glucanolyticus is strain S93 (= DSM 5162T).
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Paracoccus alcaliphilus sp. nov., an Alkaliphilic and Facultatively Methylotrophic Bacterium
More LessAbstractAlkaliphilic facultatively methanol-utilizing bacteria were investigated with respect to their phenotypic and chemotaxonomic characteristics. These bacteria were gram-negative, nonsporeforming, nonmotile, coccoid or short rod-shaped organisms, grew at pH 7.0 to 9.5, and did not grow below pH 6.5 and above pH 10.0. The deoxyribonucleic acid (DNA) base composition was 64 to 66 mol% guanine plus cytosine. These bacteria resemble Paracoccus denitrificans with respect to morphological and chemotaxonomic characteristics, but are distinguished from P. denitrificans by physiological characteristics and DNA-DNA homology. These methanol- utilizing bacteria are described as a new species, Paracoccus alcaliphilus Urakami, Tamaoka, Suzuki, and Komagata. The type strain of P. alcaliphilus sp. nov. is strain TK 1015 (= JCM 7364).
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Syntrophomonas wolfei subsp. saponavida subsp. nov., a Long-Chain Fatty-Acid-Degrading, Anaerobic, Syntrophic Bacterium; Syntrophomonas wolfei subsp. wolfei subsp. nov.; and Emended Descriptions of the Genus and Species
More LessAbstractMost probable numbers for Syntrophomonas-like bacteria degrading stearate were 1.5 x 106 to 4.6 x 106, 2.4 × 105, and 4.6 × 102 cells per ml of municipal anaerobic digester sludge, swine waste lagoon sediment, and cow ruminai fluid, respectively. Strain SD2, which was isolated from digestor sludge in coculture with the H2-utilizing bacterium Desulfovibrio sp. strain G-11, plus sulfate, was a long-chain saturated fatty-acid-using bacterium identified as a strain of the genus Syntrophomonas. Strain SD2 differed from Syntrophomonas wolfei subsp. wolfei subsp. nov. in its usually smaller size and in its ability to catabolize C9 to C18 saturated fatty acids. It differed from Syntrophomonas sapovorans in not needing relatively high concentrations of Ca2+ and in its inability to catabolize unsaturated fatty acids, such as oleic or linoleic acid. A strain SD2 coculture was further adapted to grow on crotonate and was subsequently purified without sulfate, with cells of strain G-11 only rarely seen. A 16S ribosomal ribonucleic acid sequence analysis (H. Zhao, D. Yang, C. Woese, and M. P. Bryant, manuscript in preparation) indicated that strain SD2 is phylogenetically very closely related to S. wolfei. Thus, we propose the name Syntrophomonas wolfei subsp. saponavida for this organism (strain DSM 4212T) (T = type strain) because of its ecologically important ability to use stearate and other long-chain saturated fatty acids. Emended descriptions of the genus and species are given.
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Clostridium tetanomorphum sp. nov., nom. rev.
More LessAbstractA total of 46 glutamate-degrading strains of the genus Clostridium, including 36 new isolates, were examined for deoxyribonucleic acid (DNA)-DNA homology, protein patterns produced by polyacrylamide gel electrophoresis, and physiological characteristics in order to determine the differences between Clostridium cochlearium and “Clostridium tetanomorphum.” Thirty-four newly isolated strains could be assigned to the “C. tetanomorphum” group; two strains were classified as nontoxigenic Clostridium tetani strains. The levels of DNA-DNA homology between C. cochlearium and “C. tetanomorphum” were only 10 to 19%, and the protein patterns showed that there were great differences between both groups and other glutamate-degrading species. Biochemical tests supported these results. In contrast to C. cochlearium, all “C. tetanomorphum”, strains fermented carbohydrates (at least glucose and maltose); they also produced lipase and degraded ethanolamine. Moreover, C. cochlearium, like other glutamate-degrading species, needed a higher concentration of yeast extract than “C. tetanomorphum” when it was grown on glutamate. On the basis of our results we propose C. tetanomorphum sp. nov., nom. rev. The type strain is strain NCTC 543 (= DSM 4474).
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Numerical Taxonomy of Pseudomonas alcaligenes, P. pseudoalcaligenes, P. mendocina, P. stutzeri, and Related Bacteria
More LessAbstractA numerical phenotypic analysis, in which the unweighted pair group average linkage method and Dice similarity coefficient were used, was performed on 155 strains received as Pseudomonas alcaligenes, Pseudomonas pseudoalcaligenes, Pseudomonas mendocina, or Pseudomonas stutzeri. These organisms are the clinically important nonfluorescent species belonging to ribosomal ribonucleic acid group I of Palleroni and co-workers. Six major clusters, which could be further divided into 20 subclusters, were formed. Most strains received as P. alcaligenes fell into three subclusters (subclusters Al, A2, and Bl), whereas strains received as P. pseudoalcaligenes were mainly classified in two other subclusters (subclusters C2 and C3). All but two strains (subcluster D1) of organisms received as P. mendocina were grouped in subcluster D2. Most of the 45 strains received as P. stutzeri were contained in a large subcluster, subcluster E2 (39 strains). Strains belonging to fluorescent pseudomonad species (Pseudomonas aeruginosa, Pseudomonas fluorescens, and Pseudomonas putida), which were included in the analysis for control purposes, were contained in one cluster, which comprised seven subclusters.
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A Halophilic Denitrifier, Bacillus halodenitrificans sp. nov.
More LessAbstractA new halotolerant denitrifier, which was isolated from a solar saltern by enrichment culture in liquid medium supplemented with 1.06 M (9%) NaNO3, grew optimally in media containing 0.5 to 1.35 M NaCI, survived and multiplied in media ranging in salinity from 0.35 to 4.25 M NaCI, and tolerated high nitrite ion concentrations, as well as high nitrate ion concentrations. The salt requirement could be provided by 1 M KNO3 or KC1 instead of NaCI. For this nonfermentative organism, nitrate and nitrite were the only electron acceptors tested that supported anaerobic growth on a complex medium. Washed cells reduced both nitrate and nitrite at significant rates. The isolate lacked a nitrous oxide reductase activity, utilized a variety of substrates as carbon and energy sources, and required both growth factors and organic (reduced) sulfur. Ammonia served as a nitrogen source for growth, but nitrate did not. Despite the failure of the organism to sporulate, assignment to the genus Bacillus appeared to be consistent with results of cell constituent analyses and partial 16S ribosomal ribonucleic acid sequencing. We propose the name Bacillus halodenitrificans for this organism. A type culture has been deposited with the American Type Culture Collection, Rockville, Md., as strain ATCC 49067.
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Actinomadura malachitica and Microtetraspora viridis Are Synonyms and Should Be Transferred as Actinomadura viridis comb. nov.
More LessAbstractWe compared strain SF2461, Microtetraspora viridis JCM 3112T (T = type strain), Microtetraspora viridis subsp. intermedia JCM 3113T, and Actinomadura malachitica JCM 3297T by using morphological, cultural, physiological, and chemotaxonomic characteristics, as well as deoxyribonucleic acid homology. All of our results indicated that these four strains belong to the same species and that they are far from the other type strains of Microtetraspora species. Therefore, we propose that Actinomadura malachitica is a synonym of Microtetraspora viridis and that Microtetraspora viridis should be transferred to the genus Actinomadura as Actinomadura viridis comb, nov., with strain JCM 3112 (= ATCC 27103) as the type strain.
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Precise Measurement of the G+C Content of Deoxyribonucleic Acid by High-Performance Liquid Chromatography
More LessAbstractHigh-performance liquid chromatography is a promising alternative for determining the G+C content of bacterial deoxyribonucleic acid (DNA). The method which we evaluated involves enzymatic degradation of the DNA to nucleosides by PI nuclease and bovine intestinal mucosa alkaline phosphatase, separation of the nucleosides by high-performance liquid chromatography, and calculation of the G+C content from the apparent ratios of deoxyguanosine and thymidine. Because the nucleosides are released from the DNA at different rates, incomplete degradation produces large errors in the apparent G+C content. For partially purified DNA, salts are a major source of interference in degradation. However, when the salts are carefully removed, the preparation and degradation of DNA contribute little error to the determination of G+C content. This method also requires careful selection of the chromatographic conditions to ensure separation of the major nucleosides from the nucleosides of modified bases and precise control of the flow rates. Both of these conditions are achievable with standard equipment and C18 reversed-phase columns. Then the method is precise, and the relative standard deviations of replicate measurements are close to 0.1%. It is also rapid, and a single measurement requires about 15 min. It requires small amounts of sample, and the G+C content can be determined from DNA isolated from a single bacterial colony. It is not affected by contamination with ribonucleic acid. Because this method yields a direct measurement, it may also be more accurate than indirect methods, such as the buoyant density and thermal denaturation methods. In addition, for highly purified DNA, the extent of modification can be determined.
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Amended Description of the Genus Kineosporia, Based on Chemotaxonomic and Morphological Studies
More LessAbstractThe description of the genus Kineosporia is amended after chemotaxonomic and morphological studies of the type strain of the type species, Kineosporia aurantiaca JCM 3230. This organism yielded both ll- and meso-diaminopimelic acids, which suggested that the former is present in the mycelium and the latter is present in the spores. There was no characteristic sugar pattern. A diagnostic phospholipid was phosphatidylcholine, and a major menaquinone component was MK-9(H4). No iso/anteiso branched fatty acids and no mycolic acids were observed. Colonies on agar lacked aerial mycelia, formed central projections including spores, and were occasionally accompanied by bunches of spore clusters in the agar. Spores were catenated or were located singly or aggregately at the tips of the vegetative hyphae. Our data indicate that the strain representative of the genus Kineosporia shows some similarity to the spore dome actinomycetes described by Willoughby and by Makkar and Cross.
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Phenotypic Characteristics Correlated with Deoxyribonucleic Acid Sequence Similarities for Three Species of Gluconobacter: G. oxydans (Henneberg 1897) De Ley 1961, G.frateurii sp. nov., and G. asaii sp. nov.
More LessAbstractIn Bergey’s Manual of Systematic Bacteriology, vol. 1, only one species is listed in the genus Gluconobacter. One other species, Gluconobacter ceririus, was proposed by Yamada and Akita in 1984. However, recent deoxyribonucleic acid-deoxyribonucleic acid homology studies have produced evidence of at least three distinct homology groups that are believed to represent three species within this genus. In this paper we report results obtained by using 35 strains and 58 phenotypic characteristics. Three tests were useful in differentiating the three Gluconobacter species. Homology group I strains grew to an optical density (OD) of only 0.5 U or less on medium containing ribitol or arabitol as the primary carbon source, and they grew to an OD of only 0.5 U or less after three passages (24 h of incubation each) in nicotinate-deficient media. We propose that the name Gluconobacter oxydans (Henneberg 1897) De Ley 1961 be retained for these strains. Homology group II strains grew to an OD of more than 1.0 U on medium containing ribitol or arabitol as the primary carbon source, and they grew to an OD of more than 1.0 U after three passages (24 h of incubation each) in nicotinate-deficient media. We propose that the group II gluconobacters be named Gluconobacter frateurii sp. nov. All of the typical strains of homology group ΙΠ grew to an OD of 0.5 U or less on medium containing ribitol or arabitol as the primary carbon source, but they grew to an OD of 1.0 U or more after three passages (24 h of incubation each) in nicotinate-deficient media. We propose that the group III gluconobacters be named Gluconobacter asaii sp. nov.
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Ribosomal Ribonucleic Acid Cistron Similarities and Deoxyribonucleic Acid Homologies of Neisseria, Kingella, Eikenella, Simonsiella, Alysiella, and Centers for Disease Control Groups EF-4 and M-5 in the Emended Family Neisseriaceae
AbstractWe detected distinct taxonomic relationships among the true Neisseria species, Kingella kingae, Kingella denitrificans, Eikenella corrodens, all Simonsiella species, the type strain of Alysiella filiformis, and members of Centers for Disease Control groups EF-4 and M-5. All these taxa constitute one large separate cluster having high levels of ribosomal ribonucleic acid cistron similarity (thermal dénaturation temperature range, 74 to 81°C) in ribosomal ribonucleic acid superfamily III. There are at least four subbranches. We found high deoxyribonucleic acid (DNA)-DNA homology values between Neisseria gonorrhoeae and some other true Neisseria species and within the following species: Simonsiella muelleri, Simonsiella crassa, Simonsiella steedae, Kingella denitrificans, and Eikenella corrodens. All of the members of this large cluster have genome base compositions in the range from 42.8 to 57.7 mol% guanine plus cytosine. The molecular complexities of the genomic DNAs are 2.2 x I09 to 2.7 × 109 for Simonsiella and Alysiella species and 1.4 × 109 to 1.8 × 109 for the other members of this large cluster. We formally propose that this large cluster represents the emended family Neisseriaceae containing the following genera and groups: Neisseria, Kingella (not the generically misnamed Kingella indologenes), Eikenella, Simonsiella, Alysiella (not some misnamed strains), and Centers for Disease Control groups EF-4 and M-5. The genera and subgenera Acinetobacter, Moraxella, Branhamella, Psychrobacter, the false neisseriae, and Kingella indologenes should be removed from the Neisseriaceae, as they belong to superfamilies I and II.
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Clostridium thermobutyricum sp. nov., a Moderate Thermophile Isolated from a Cellulolytic Culture, That Produces Butyrate as the Major Product
More LessAbstractA new moderately thermophilic clostridium, Clostridium thermobutyricum, was isolated from cellulolytic enrichment cultures inoculated with horse manure. This organism forms subterminal spores, and the sporangium is not swollen. From glucose, the organism produces butyrate, CO2, and H2 and minor amounts of acetate and lactate. Yeast extract is required for good growth. The temperature range for growth is between 26 and 61.5°C. The pH range is between 5.8 and 9.0. The guanine-plus-cytosine content is 37 mol%. The type strain is C. thermobutyricum JW171K (= DSM 4928).
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- Original Papers Relating To The Systematics Of Yeasts
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Candida populi, a New Species of Yeast Occurring in Exudates of Populus and Betula Species
More LessAbstractDuring a survey of yeasts occurring in exudates of various tree species in the Pacific Northwest of North America, 24 strains of an imperfect yeast were isolated in a wide geographic area, mainly from species of the genus Populus. The isolates were studied by traditional as well as molecular methods, and the results revealed a new species of the genus Candida. The new species is named Candida populi, because its principal habitat is in exudates of Populus species. C. populi resembles Candida molischiana but differs from this species in habitat, guanine-plus-cytosine content of the nuclear deoxyribonucleic acid, maximum growth temperature, and ability to assimilate several carbon compounds. The type strain of C. populi is strain UCD-FST 68-675B (= CBS 7351 = ATCC 64933).
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- Matters Relating To The International Committee On Systematic Bacteriology
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Rejection of the Type Strain of Streptococcus mitis (Andrewes and Horder 1906)
More LessAbstractThe type strain of Streptococcus mitis, strain NCTC 3165 (= ATCC 33399), does not fit the description of the species, and it is genetically unrelated to reference strains that do conform to the description. Strain NCTC 3165, which was deposited as S. mitis in 1930, does fit the description of Streptococcus sanguis White and Niven (1946) and was recognized as a S. sanguis strain by authors of reports that were published prior to 1980, when this reference strain was elevated to the type strain of S. mitis. Streptococcus oralis Bridge and Sneath (1982) fits the description of S. mitis, and its type strain, strain NCTC 11427, is genetically homologous with reference strains that fit the description of S. mitis. S. oralis has the same cell wall characteristics that have been described for S. mitis (“S. mitior”). I propose that S. oralis be considered a later synonym of S. mitis and that the type strain of S. oralis be adopted as the type strain of 5. mitis.
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- Errata
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Volumes and issues
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Volume 74 (2024)
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