Showing papers in "International Journal of Systematic and Evolutionary Microbiology in 1990"
TL;DR: The phylogenetic relatedness within the slow-growing species did not reflect the Runyon classification of photochromogenic, scot chromogenic, and nonchromogenic mycobacteria, and an exception was M. gastri, which was indistinguishable from M. kansasii when this kind of analysis was used, and M. simiae occupies phylogenetically an intermediate position between these two groups.
Abstract: 16S rRNA sequences from Mycobacterium tuberculosis, M. avium, M. gastri, M. kansasii, M. marinum, M. chelonae, M. smegmatis, M. terrae, M. gordonae, M. scrofulaceum, M. szulgai, M. intracellulare, M. nonchromogenicum, M. xenopi, M. malmoense, M. simiae, M. flavescens, M. fortuitum, and M. paratuberculosis were determined and compared. The sequence data were used to infer a phylogenetic tree, which provided the basis for a systematic phylogenetic analysis of the genus Mycobacterium. The groups of slow- and fast-growing mycobacteria could be differentiated as distinct entities. We found that M. simiae occupies phylogenetically an intermediate position between these two groups. The phylogenetic relatedness within the slow-growing species did not reflect the Runyon classification of photochromogenic, scotochromogenic, and nonchromogenic mycobacteria. In general, the phylogenetic units identified by using rRNA sequences confirmed the validity of phenotypically defined species; an exception was M. gastri, which was indistinguishable from M. kansasii when this kind of analysis was used.
445 citations
TL;DR: The moderately saccharolytic, predominantly oral Bacteroides species, which include B. melaninogenicus, B. oralis, and related species, form a phenotypically and phylogenetically coherent group of species which differ so significantly from the emended description of the genus Bactroides that they should not be classified in the same genus.
Abstract: It was recently proposed that the genus Bacteroides should be restricted to Bacteroides fragilis (the type species) and closely related organisms (viz., B. caccae, B. distasonis, B. eggerthii, B. merdae, B. ovatus, B. stercoris, B. thetaiotaomicron, B. uniformis, and B. vulgatus). By contrast, the moderately saccharolytic, predominantly oral Bacteroides species, which include B. melaninogenicus, B. oralis, and related species, form a phenotypically and phylogenetically coherent group of species which differ so significantly from the emended description of the genus Bacteroides that they should not be classified in the same genus. Therefore, we formally propose that these species be reclassified in a new genus, Prevotella. The type species is Prevotella melaninogenica.
439 citations
TL;DR: It is proposed that the species should be divided into subspecies which correspond to pathogenicity and host range characteristics as well as the results of the phenotypic study, which showed characteristics that were useful for discriminating between clusters 1 and 3.
Abstract: We performed a numerical taxonomy analysis of 38 Mycobacterium paratuberculosis and related mycobacterial strains, including wood pigeon mycobacteria; this analysis was based on 22 tests, which were selected for their potential discriminative value from a total of 51 tests studied and produced four well-defined clusters. Cluster 1 contained the M. paratuberculosis strains, including two strains isolated from Crohn's disease patients; cluster 2 contained Mycobacterium avium and Mycobacterium intracellular reference strains; cluster 3 consisted of the wood pigeon mycobacteria; and the only strain in cluster 4 was M. paratuberculosis 316F, which is used for antigen and vaccine production. Strains in cluster 1 were mycobactin dependent even when they were subcultured, whereas strains in cluster 3 were unable to grow on egg medium and their growth was stimulated by pH 5.5. Growth stimulation by pyruvate, resistance to d-cycloserine (50 μg/ml), and alkaline phosphatase activity also were characteristics that were useful for discriminating between clusters 1 and 3. The results of previous DNA-DNA hybridization studies have demonstrated that M. avium Chester 1901, M. paratuberculosis Bergey et al. 1923, and the wood pigeon mycobacteria belong to a single genomic species, and we propose that the name of this species should be M. avium. On the basis of the results of previous genomic analyses based on restriction fragment length, the results of polymorphism studies, and DNA patterns determined by field inversion gel electrophoresis as well as the results of our phenotypic study, we propose that the species should be divided into subspecies which correspond to pathogenicity and host range characteristics. An emended description of M. avium Chester 1901 and descriptions of M. avium subsp. avium subsp. nov., M. avium subsp. paratuberculosis subsp. nov., and M. avium subsp. silvaticum subsp. nov. are presented; strains ATCC 25291, ATCC 19698, and CIP 103317 are the type strains of the three new subspecies, respectively.
393 citations
TL;DR: A new Saccharopolyspora species isolated from soil collected in a sugar mill rum still is described, characterized by pale yellowish pink aerial hyphae that bear long chains of spores encased in distinctive spore sheaths.
Abstract: A new Saccharopolyspora species isolated from soil collected in a sugar mill rum still is described. This organism is characterized by pale yellowish pink aerial hyphae that bear long chains of spores encased in distinctive spiny spore sheaths. Fragmentation occurs when the organism is cultured in liquid media. The new species contains meso-diaminopimelic acid, arabinose, and galactose (cell wall chemotype IV), has whole-cell sugar pattern type A, contains no mycolic acids, and contains phosphatidylcholine (phospholipid pattern type PIII). The single isolate has chemical and morphological properties consistent with the genus Saccharopolyspora. A comparison with previously described species of the genus in which we used standard techniques plus fatty acid analyses showed that this organism differs from previously described species. The name proposed for this new species is Saccharopolyspora spinosa. The type strain is strain A83543.1 (= NRRL 18395). The description is based on a single isolate.
292 citations
TL;DR: It is indicated that the grapevine isolates are distinct from the type strains of the four previously described Agrobacterium species, and a new species, AgRobacterium vitis, is proposed.
Abstract: Agrobacterium isolates from grapevines that were previously characterized as biovar 3 strains were compared with the type strains of the four previously described species of the genus Agrobacterium, Agrobacterium tumefaciens, Agrobacterium radiobacter, Agrobacterium rhizogenes, and Agrobacterium rubi. Ten grapevine isolates were distinguished from other Agrobacterium species phenotypically by a number of biochemical tests and by their reaction with a monoclonal antibody raised to biovar 3. Levels of DNA binding between the type strains of previously described species and three grapevine isolates were estimated by optical measurement of initial DNA renaturation rates. The levels of DNA binding between grapevine isolates were 78 to 92%, and the levels of DNA binding with other type strains ranged from 7 to 47%. Our results indicate that the grapevine isolates are distinct from the type strains of the four previously described Agrobacterium species. A new species, Agrobacterium vitis, is proposed; the type strain is strain NCPPB 3554.
222 citations
TL;DR: Cells of species in the genus Methanosaeta are obligately anaerobic, gram-negative, nonmotile rods with flat ends, enclosed within a proteinaceous, cross-striated sheath, used as the sole source of energy and carbon sources for growth.
Abstract: Methanosaeta concilii gen. nov., sp. nov. (“Methanothrix concilii”) is described. Cells of species in the genus Methanosaeta are obligately anaerobic, gram-negative, nonmotile rods (length, 2.5 to 6.0 μm) with flat ends. The cells are enclosed within a proteinaceous, cross-striated sheath. Growth can occur as long filaments which represent chains of individual cells separated by spacer plugs and continuously enclosed by the tubular sheath. Acetic acid is used as the sole source of energy; its metabolism results in the production of about equimolar amounts of CH4 and CO2. Acetic acid and CO2 are carbon sources for growth. The description of Methanosaeta concilii, the type species, is based on type strain GP6 (= DSM 3671 = OGC 69 = NRC 2989 = ATCC 35969).
217 citations
TL;DR: These organisms form a separate group within the acidovorans rRNA complex, and it is proposed to transfer them to a new genus, Acidovorax.
Abstract: Pseudomonas facilis and Pseudomonas delafieldii are inappropriately assigned to the genus Pseudomonas. They belong to the acidovorans rRNA complex in rRNA superfamily III (i.e., the beta subclass of the Proteobacteria). The taxonomic relationships of both of these species, two groups of clinical isolates (E. Falsen [EF] group 13 and EF group 16), and several unidentified or presently misnamed strains were examined by using DNA:rRNA hybridization, numerical analyses of biochemical and auxanographic features and of fatty acid patterns, polyacrylamide gel electrophoresis of cellular proteins, and DNA:DNA hybridization. These organisms form a separate group within the acidovorans rRNA complex, and we propose to transfer them to a new genus, Acidovorax. We describe the following three species in this genus: The type species, Acidovorax facilis (formerly Pseudomonas facilis), with type strain LMG 2193 (= CCUG 2113 = ATCC 11228); Acidovorax delafieldii (for the former Pseudomonas delafieldii and most of the EF group 13 strains), with type strain LMG 5943 (= CCUG 1779 = ATCC 17505); and Acidovorax temperans (for several former Pseudomonas and Alcaligenes strains and most of the EF group 16 strains), with type strain CCUG 11779 (= LMG 7169).
208 citations
208 citations
TL;DR: On the basis of phenotypic, genotyping, and chemotaxonomic data, Xanthomonas oryzae (ex Ishiyama 1922) sp.
Abstract: On the basis of phenotypic, genotypic, and chemotaxonomic data, Xanthomonas oryzae (ex Ishiyama 1922) sp. nov., nom. rev. is proposed; this species comprises Xanthomonas oryzae pv. oryzae (Ishiyama 1922) comb. nov. and Xanthomonas oryzae pv. oryzicola (Fang, Ren, Chen, Chu, Faan, and Wu 1957) comb. nov., the causal agents of bacterial blight and bacterial leaf streak of rice, respectively.
197 citations
TL;DR: Four strains of tetrodotoxin-producing bacteria isolated from a red alga and from pufferfish were characterized and two of these strains are members of the genus Listonella MacDonell and Colwell and placed in new species.
Abstract: Four strains of tetrodotoxin-producing bacteria isolated from a red alga and from pufferfish were characterized. Two of these strains are members of the genus Listonella MacDonell and Colwell. The phenotypic characteristics, guanine-plus-cytosine contents, and base sequences of the 16S rRNAs of these organisms indicated that they are members of Listonella pelagia (Vibrio pelagius) biovar II. The other two strains are members of the genus Alteromonas Baumann et al. and the genus Shewanella MacDonell and Colwell. These two strains are mutually distinct and distinct from the previously described Alteromonas and Shewanella species and therefore are placed in new species. The names Shewanella alga and Alteromonas tetraodonis are proposed for these organisms; the type strains are strains OK-1 and GFC, respectively.
188 citations
TL;DR: DNAs of type strains and representative members of Actinomyces groups from the human periodontal flora and from other habitats were compared by using the S1 nuclease procedure to determine their genetic relatedness.
Abstract: DNAs of type strains and representative members of Actinomyces groups from the human periodontal flora and from other habitats were compared by using the S1 nuclease procedure to determine their genetic relatedness. One rather common group from the human periodontal flora, previously called “Actinomyces D08,” is phenotypically distinct from, and genetically unrelated to, previously described species. We propose the name Actinomyces georgiae for this organism; the type strain is strain ATCC 49285. Another common group from the human periodontal flora is Actinomyces israelii serotype II, which was found to be genetically distinct from the type strain of A. israelii (serotype I) and from other previously described species of Actinomyces. We propose the name Actinomyces gerencseriae for this organism; the type strain is strain ATCC 23860. A. naeslundii serotype I strains were distinct from the other strains studied. A separate genospecies which included strains of A. naeslundii serotypes II and III and A. viscosus serotype II was delineated. Strains of Actinomyces serotype WVA 963 constitute an additional distinct genospecies. Because there are no reliable phenotypic tests, other than serological analyses, to differentiate Actinomyces serotype WVA 963 and the two genospecies of A. naeslundii, no taxonomic changes are proposed for these three genospecies.
TL;DR: The phylogenetic interrelationships of members of the genus Carnobacterium and some atypical lactobacilli isolated from diseased salmonid fish were investigated by using reverse transcriptase sequencing of 16S rRNA and clearly demonstrated that carnobacteria are phylogenetically closer to the genera Enterococcus and Vagococcus than to members ofThe genus Lactobacillus.
Abstract: The phylogenetic interrelationships of members of the genus Carnobacterium and some atypical lactobacilli isolated from diseased salmonid fish were investigated by using reverse transcriptase sequencing of 16S rRNA. The four species Carnobacterium piscicola, Carnobacterium divergens, Carnobacterium gallinarum, and Carnobacterium mobile exhibited a high degree of sequence similarity with each other (ca. 96 to 98%) and formed a phylogenetically coherent group that was quite distinct from all other lactic acid bacteria. The sequence data clearly demonstrated that carnobacteria are phylogenetically closer to the genera Enterococcus and Vagococcus than to members of the genus Lactobacillus. The strains from fish were found to be phylogenetically related to the genus Vagococcus and represent a new species, Vagococcus salmoninarum. The type strain of Vagococcus salmoninarum is strain NCFB 2777.
TL;DR: An extremely halophilic red archaebacterium isolated from the Dead Sea belongs to the genus Haloarcula and differs sufficiently from the previously described species of the genus to be designated a new species; the name Haloarculateda marismortui (Volcani sp. nov.) is proposed because of the close resemblance of this organism to "Halobacterium marismortsui," which was first described by Volcani in 1940.
Abstract: An extremely halophilic red archaebacterium isolated from the Dead Sea (Ginzburg et al., J. Gen. Physiol. 55: 187-207, 1970) belongs to the genus Haloarcula and differs sufficiently from the previously described species of the genus to be designated a new species; we propose the name Haloarcula marismortui (Volcani) sp. nov., nom. rev. because of the close resemblance of this organism to "Halobacterium marismortui," which was first described by Volcani in 1940. The type strain is strain ATCC 43049.
TL;DR: An extensive phenotypic description and an improved classification and nomenclature of the genus Xanthomonas are presented, and a number of dubious Pseudomonas species were identified as members of or as being close to Xanthomanas species.
Abstract: An extensive phenotypic description and an improved classification and nomenclature of the genus Xanthomonas are presented. A total of 266 strains obtained from different geographical areas, including representative strains of all species of the genus Xanthomonas and most pathovars of Xanthomonas campestris, as well as strains which might be genetically related to the genus Xanthomonas, were examined for 295 morphological, biochemical, and physiological features. Similarities among the strains were expressed numerically by using the coefficient of Sokal and Michener. Clustering was performed by using the unweighted average pair group method. The conclusions described below were reached. (i) The genus Xanthomonas comprises at least the following eight phena: X. campestris, Xanthomonas albilineans, Xanthomonas axonopodis, Xanthomonas fragariae, Xanthomonas populi, Xanthomonas maltophilia, Xanthomonas oryzae Swings et al. 1990, and X. campestris pv. graminis Egli and Schmidt 1982 [not X. campestris pv. graminis (Egli et al. 1975) ISPP List 1980]. (ii) X. populi (Ride 1958) Ride and Ride 1978 is a separate species. (iii) X. maltophilia Swings et al. 1983 forms a separate species. (iv) X. campestris pv. oryzae ISPP List 1980 can no longer be regarded as pathovar of X. campestris, and its recent reclassification as a new species, X. oryzae (Swings et al., Int. J. Syst. Bacteriol. 40:309-311, 1990), is supported. (v) X. campestris pv. graminis Egli and Schmidt 1982 [not X. campestris pv. graminis (Egli et al. 1975) ISPP List 1980] seems to form a separate complex of highly related pathovars obtained from members of the Poaceae; the taxonomic implications of this are discussed. (vi) Strains of nearly all X. campestris pathovars cluster together in the X. campestris phenon. Within this species we were able to differentiate some entities on phenotypic grounds; these groups sometimes corresponded to named pathovars (e.g., X. campestris pv. manihotis, X. campestris pv. cassavae, X. campestris pv. phlei). In several other cases, pathovars were found to be heterogeneous. (vii) A number of dubious Pseudomonas species were identified as members of or as being close to Xanthomonas species. Both Pseudomonas betle and Pseudomonas hibiscicola are synonyms of X. maltophilia. We also confirmed that Pseudomonas mangiferaeindicae, Pseudomonas vitiswoodrowii, and Pseudomonas gardneri belong to X. campestris. (viii) Forty phenotypic features allow the differentiation of the eight Xanthomonas phena. (ix) A number of additional features of the genera Xanthomonas and Xylophilus are described.
TL;DR: A collection of 47 strains of obligately anaerobic, gram-negative, rod-shaped bacteria that were isolated mainly from spoiled beer and pitching yeast was studied to learn more about their taxonomic positions, finding in good agreement with the presence of a peptidoglycan that contains diamine.
Abstract: A collection of 47 strains of obligately anaerobic, gram-negative, rod-shaped bacteria that were isolated mainly from spoiled beer and pitching yeast was studied to learn more about their taxonomic positions. A new species of the genus Pectinatus, Pectinatus frisingensis, a new species of the genus Selenomonas, Selenomonas lacticifex, and a new genus comprising two species, Zymophilus raffinosivorans and Zymophilus paucivorans, are described. All of the strains contained directly cross-linked meso-diaminopimelic acid-containing peptidoglycan and in addition the diamine cadaverine or (rarely) putrescine. The diamine was covalently linked to the α-carboxyl group of d-glutamic acid in the peptide subunit of peptidoglycan. Lipid F was also found as a characteristic cellular compound. The phylogenetic relationships of members of these new species were examined by reverse transcriptase sequencing of 16S rRNA or by DNA-DNA hybridization studies or both. All of the organisms belong to the subdivision containing species with gram-negative cell walls within the phylum of gram-positive bacteria. This finding is in good agreement with the presence of a peptidoglycan that contains diamine.
TL;DR: A new subspecies, Staphylococcus schleiferi subsp.
Abstract: A new subspecies, Staphylococcus schleiferi subsp. coagulans, was isolated from the external auditory meatus of dogs suffering from external ear otitis and is described on the basis of studies of 21 strains. Phenotypic studies showed that these strains are more closely related to Staphylococcus intermedius than to other staphylococci, but DNA hybridization studies indicated that they are closely related to Staphylococcus schleiferi N850274T. On the basis of biochemical distinctiveness (positive test tube coagulase test and different carbohydrate reactions) and the etiological importance (frequent isolation from otitis specimens from dogs) of these strains, we propose to classify them as a subspecies of S. schleiferi. The strains of this new subspecies are coagulase tube test, β-hemolysin, and heat-stable nuclease positive but clumping factor negative. A simple scheme for the differentiation of S. schleiferi subsp. coagulans from the other coagulase-positive staphylococci is presented. The type strain is GA211 (=JCM 7470).
TL;DR: In this article, the 16S rRNA sequences of Kingella indologenes, Cardiobacterium hominis, and Bacteroides nodosus were determined by direct RNA sequencing, using a modified Sanger method.
Abstract: The 16S rRNA sequences of Kingella indologenes, Cardiobacterium hominis, and Bacteroides nodosus were determined by direct RNA sequencing, using a modified Sanger method. Sequence comparisons indicated that these three species represent a novel family in the gamma division of Proteobacteria. On the basis of these data, K. indologenes and B. nodosus cannot retain their current generic status as they are not closely related to other members of their assigned genera. Therefore, we propose transfer of K. indologenes to the new genus Suttonella as Suttonella indologenes and transfer of B. nodosus to the new genus Dichelobacter as Dichelobacter nodosus and assign the genera Cardiobacterium, Suttonella, and Dichelobacter to a new family, Cardiobacteriaceae, in the gamma division of Proteobacteria.
TL;DR: Evidence from numerical taxonomic analysis and DNA-DNA hybridization supports the proposal of new species in the genera Actinobacillus and Pasteurella.
Abstract: Evidence from numerical taxonomic analysis and DNA-DNA hybridization supports the proposal of new species in the genera Actinobacillus and Pasteurella. The following new species are proposed: Actinobacillus rossii sp. nov., from the vaginas of postparturient sows; Actinobacillus seminis sp. nov., nom. rev., associated with epididymitis of sheep; Pasteurella bettii sp. nov., associated with human Bartholin gland abscess and finger infections; Pasteurella lymphangitidis sp. nov. (the BLG group), which causes bovine lymphangitis; Pasteurella mairi sp. nov., which causes abortion in sows; and Pasteurella trehalosi sp. nov., formerly biovar T of Pasteurella haemolytica, which causes septicemia in older lambs.
TL;DR: Two methylamine- and N,N-dimethylformamide-utilizing Paracoccus spp.
Abstract: Two methylamine- and N,N-dimethylformamide-utilizing Paracoccus spp. are described. These bacteria are gram-negative, nonsporeforming, nonmotile, coccoid or short rod-shaped organisms. Their DNA base composition is 62 to 68 mol% G+C. Their cellular fatty acids include large amounts of C18:1 acid. Their major hydroxy acids are 3-OH C10:0 and 3-OH C14:0 acids. The major ubiquinone is Q-10. These bacteria are distinguished from Paracoccus denitrificans and Paracoccus alcaliphilus by physiological characteristics and by DNA-DNA homology. Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov. are proposed. The type strain of P. aminophilus is DM-15 (= JCM 7686), and the type strain of P. aminovorans is DM-82 (= JCM 7685). Paracoccus halodenitrificans is distinguished from other Paracoccus species on the basis of cellular fatty acid composition, hydroxy fatty acid composition, and DNA-DNA homology. It may not be a valid member of the genus Paracoccus.
TL;DR: Three strains of gram-positive, facultatively anaerobic, sporeforming, rod-shaped bacteria were isolated from composts of manure with grass and rice straw and DNA-DNA homology determinations did not show relatedness to strains of representative species of the genera Bacillus, Clostridium, and Sporolactobacillus.
Abstract: Three strains of gram-positive, facultatively anaerobic, sporeforming, rod-shaped bacteria were isolated from composts of manure with grass and rice straw. These organisms grew well in an alkaline medium and digested xylan both in strictly anaerobic cultures when titanium(III) citrate was used as a reducing agent and in aerobic cultures with shaking. The cells contained meso-diaminopimelic acid, and their cellular fatty acids consisted of iso- and anteiso-branched acids and considerable amounts of straight-chain acids. The DNA base composition of these strains ranged from 36 to 38 mol% guanine plus cytosine. Cytochromes, isoprenoid quinones, and catalase activity were not detected. DNA-DNA homology determinations did not show relatedness to strains of representative species of the genera Bacillus, Clostridium, and Sporolactobacillus. Considering the uniqueness of the characteristics, the sequence of the 5S rRNA, and the unique metabolic pathways, we propose Amphibacillus xylanus gen. nov., sp. nov., for these strains. The type strain is strain Ep01 (= JCM 7361).
TL;DR: The heterogeneity of several X. campestris pathovars has been demonstrated by sodium dodecyl sulfate electrophoresis of whole-cell proteins and fatty acid fingerprinting, and on the basis of these data and unpublished data, the usefulness of different phenotypic, chemotaxonomic, and genotypic techniques is discussed.
Abstract: Improvement of the taxonomy of the genus Xanthomonas and especially of Xanthomonas campestris, which is subdivided into more than 125 pathovars, is discussed. Recent contributions to the taxonomy of Xanthomonas are reviewed, and on the basis of these data and unpublished data from several laboratories, the usefulness of different phenotypic, chemotaxonomic, and genotypic techniques is discussed. The heterogeneity of several X. campestris pathovars has been demonstrated by sodium dodecyl sulfate electrophoresis of whole-cell proteins and fatty acid fingerprinting. The host selectivity of the pathovars is not correlated with their relationships as revealed by DNA-DNA hybridization experiments. In order to reveal the phylogenetic relationships among X. campestris pathovars and their relationships to other Xanthomonas species, it will be necessary to perform extensive DNA-DNA homology studies as an essential part of a polyphasic approach. At present, six DNA homology groups within X. campestris have been delineated. A systematic approach to improve the taxonomy of the genus Xanthomonas is proposed.
TL;DR: An examination of the subsurface sediments revealed no methanogens that were capable of growth on methanogenic substrates, such as H2-CO2, formate, or acetate, which is consistent with the results of other studies of hypersaline, sulfate-containing anoxic environments.
Abstract: Methanohalophilus oregonense WAL1T (= OGI 99T = DSM 5435T) (T = type strain) was isolated from an anoxic aquifer (pH 10, with 100 g of dissolved solids per liter of pore water) 3 m deep near Alkali Lake, an alkaline, desert lake in south central Oregon. An examination of the subsurface sediments revealed no methanogens that were capable of growth on methanogenic substrates, such as H2-CO2, formate, or acetate, which is consistent with the results of other studies of hypersaline, sulfate-containing anoxic environments. Strain WAL1T grew on trimethylamine and grew slowly on methanol or dimethylsulfide, but did not catabolize H2-CO2, formate, or acetate. The cells were irregular coccoids (diameter, 1 to 1.5 μm), and cells growing in liquid media also formed clumps of 2 to 15 or more cells. The cells were mesophilic and required one or more vitamins present in yeast extract. Like the only previously described strain of alkaliphilic, methylotrophic methanogen (Methanohalophilus zhilinae WeN5T), strain WAL1T grew most rapidly in medium of moderate salinity; strain WAL1T grew well in the presence of 0.1 to 1.4 M Na+ and grew most rapidly at an Na+ concentration of 0.35 M (specific growth rate, 0.1 h-1). Best growth occurred with about 50 mM Mg2+ and at a pH of 8.4 to 9.0. K+ appeared to be required, with 13 to 130 mM K+ supporting most rapid growth. The guanine-plus-cytosine content of the DNA was 40.9 ± 0.1 mol%.
TL;DR: The levels of genotypic relatedness among Leuconostoc oenos, Leu Conostoc mesenteroides subsp.
Abstract: The levels of genotypic relatedness among Leuconostoc oenos (53 strains), Leuconostoc mesenteroides subsp. mesenteroides (7 strains), Leuconostoc mesenteroides subsp. dextranicum (5 strains), Leuconostoc paramesenteroides (3 strains), Leuconostoc lactis (3 strains), Leuconostoc sp. (3 strains), and Pediococcus acidilactici (1 strain) were determined. L. oenos is genotypically homogeneous and forms a distinct species. Leuconostoc sp. strains ATCC 21435, ATCC 21436, and ATCC 21437 are genotypically not closely related to any Leuconostoc sp. L. paramesenteroides and L. lactis are regarded as genotypically heterogeneous collections of strains. P. acidilactici ATCC 12697 and L. mesenteroides NCDO 530 should be reclassified as L. paramesenteroides and L. oenos, respectively.
TL;DR: Volcaniella eurihalina gen. nov., sp.
Abstract: A comparison of 16 gram-negative moderately halophilic aerobic rod-shaped bacteria with other halophilic and nonhalophilic gram-negative bacteria supported the establishment of Volcaniella eurihalina gen. nov., sp. nov. This comparison included phenotypic properties, salt requirements, and guanine-plus-cytosine contents of the DNAs, as well as DNA-DNA homology studies. The distinguishing features of this new bacterial genus are as follows: The organisms are nonmotile short rods that are oxidase negative; they are aerobic with a strictly respiratory type of metabolism; they are moderate halophiles, optimal growth occurs at a total salt concentration of 7.5% (wt/vol), and they exhibit a strongly euryhaline character; and they have a specific requirement for Na+ ions (sodium can be supplied as NaCl, Na2SO4, or NaBr). The minimum NaCl concentration required is 1.5% (wt/vol). The guanine-plus-cytosine content of the DNA is 59.1 to 65.7 mol%. This organism was isolated from hypersaline habitats, including saline soils and salt ponds, and from seawater. The type strain is strain F9-6 (= ATCC 49336).
TL;DR: The Clostridium bryantii-Methanospirillum hungatei syntrophic coculture, grown on caproate, was adapted to grow on crotonate, and a 16S rRNA sequence analysis of the pure subculture revealed that, as a member of the gram-positive phylum, it was not closely related to any of the Clostridgeium species with which it was compared.
Abstract: The Clostridium bryantii-Methanospirillum hungatei syntrophic coculture, grown on caproate, was adapted to grow on crotonate. Then, C. bryantii was isolated in pure culture from crotonate bottle plates. A 16S rRNA sequence analysis of the pure subculture revealed that, as a member of the gram-positive phylum, it was not closely related to any of the Clostridium species with which it was compared or to any of the other clusters in the gram-positive phylum with which it was compared. However, it was closely related to another syntrophic fatty acid-degrading bacterium, Syntrophomonas wolfei. On the basis of its phylogeny, physiology, and cell wall ultrastructure, we propose assignment of C. bryantii to Syntrophospora bryantii gen. nov., nov. comb.
TL;DR: Fusobacterium nucleatum should be divided into three subspecies on the basis of electrophoretic patterns of whole-cell proteins and DNA homology, and strains in groups I and II showed greater than 80%DNA homology within groups and less than 75% similarity between groups.
Abstract: Heterogeneity among isolates of Fusobacterium nucleatum has been recognized for many years. The phenotypic properties of 340 strains considered to be F. nucleatum were examined. While these strains were phenotypically similar and fit the description of F. nucleatum, they could be differentiated into three groups on the basis of electrophoretic patterns of whole-cell proteins and DNA homology. Strains in groups I and II showed >80% DNA homology within groups and 85% DNA homology to each other and <65% similarity to strains in groups I and II. We propose that Fusobacterium nucleatum be divided into the following three subspecies: Fusobacterium nucleatum subsp. nucleatum, with type strain ATCC 25586; Fusobacterium nucleatum subsp. polymorphum, with type strain ATCC 10953; and Fusobacterium nucleatum subsp. vincentii, with type strain ATCC 49256.
TL;DR: DNA-rRNA hybridization with suitable, labeled rRNAs and DNAs from 53 strains known or presumed to belong to the Pasteurellaceae is an excellent method to establish whether an organism belongs in the Pasteuredllaceae.
Abstract: We performed hybridizations between labeled rRNAs from seven representative members of the family Pasteurellaceae and from three other taxa on the one hand and DNAs from 53 strains known or presumed to belong to the Pasteurellaceae on the other hand. The members of the Pasteurellaceae are most closely related to members of the Enterobacteriaceae, the Vibrionaceae, the Aeromonadaceae, and the genus Alteromonas. The family Pasteurellaceae is very heterogeneous. There are at least seven rRNA branches. Several organisms with the same genus name are dispersed over the entire dendrogram. The “Histophilus ovis,” [Haemophilus] ducreyi, [Actinobacillus] actinomycetemcomitans, and [Haemophilus] aphrophilus rRNA branches are separate and quite remote from the three authentic genera in this family; this might justify eventual later separate generic status. DNA-rRNA hybridization with suitable, labeled rRNA probes is an excellent method to establish whether an organism belongs in the Pasteurellaceae; e.g., some strains of Bisgaard's taxa 7, 13, and 16 and of the gas-producing “SP” group certainly belong in this family, whereas three bovine lymphangitis organisms (strains NCTC 10547, NCTC 10549, and NCTC 10553), [Haemophilus] piscium ATCC 10801T (T = type strain), and [Pasteurella] piscicida ATCC 17911 belong in the Enterobacteriaceae, the Aeromonadaceae, and the Vibrionaceae, respectively.
TL;DR: Methanobacterium espanolae sp.
Abstract: Bacterial strain GP9T (T = type strain), a nonmotile, nonsporeforming, mesophilic, methanogenic bacterium, was isolated from the primary sludge obtained from the waste treatment facility of a major kraft pulp mill in Canada. Single cells were 6.0 by 0.8 μm and stained gram positive. Growth and methane production occurred only with H2-CO2 as the substrate. Acetate, formate, propionate, butyrate, pyruvate, methanol, or trimethylamine could not serve as a sole source of carbon and energy for growth. The optimum pH for growth was between 5.6 and 6.2; consistent growth and methane production were not observed below pH 4.68. The optimum temperature for growth was 35°C, and little or no growth was observed during incubation at 15 and 50°C. Kanamycin and bacitracin were severe inhibitors of growth and methanogenesis, whereas 100 μM bromoethanesulfonic acid caused 30% inhibition. Supernatant from primary sludge enhanced growth by about 10%. The DNA base composition was 34 mol% guanine plus cytosine. On the basis of physiological characteristics, indirect immunofluorescence typing, and DNA-DNA hybridization studies, the isolate is named Methanobacterium espanolae sp. nov.
TL;DR: Two strains of Methanogenium bourgense, strains MS2T (T = type strain) and LX1, were characterized, and, based in part on previously published DNA hybridization data, this species was transferred to a new genus, Methanoculleus, as Methano-Bourgense comb.
Abstract: Two strains of Methanogenium bourgense, strains MS2T (T = type strain) and LX1, were characterized, and, based in part on previously published DNA hybridization data, this species was transferred to a new genus, Methanoculleus, as Methanoculleus bourgense comb. nov. Methanogenium marisnigri JR1T and a new strain of Methanogenium marisnigri, strain AN8, were also characterized. This species was also transferred to the genus Methanoculleus as Methanoculleus marisnigri comb. nov. et emend., and its description was emended to indicate that the species has a temperature optimum near 40°C, is halotolerant, and is slightly alkaliphilic; in contrast, the previous description of this organism indicates that it has a temperature optimum of 20 to 25°C, is halophilic, and is slightly acidophilic. We also propose the transfer of two other phylogenetically related species, Methanogenium thermophilicum and Methanogenium olentangyi, to the genus Methanoculleus as Methanoculleus thermophilicum and Methanoculleus olentangyi, respectively. Methanogenium cariaci JR1T was also further characterized, and its description is emended.
TL;DR: Six strains formed a distinct group containing three highly homologous strains and three strains exhibiting greater than 50% DNA homology, including the type strain of Bacillus alcalophilus Vedder 1934.
Abstract: The DNA base compositions of 78 alkaliphilic Bacillus strains were determined. These strains were grouped as follows: DNA group A, guanine-plus-cytosine (G+C) content of 34.0 to 37.5 mol% (17 strains); DNA group B, G+C content of 38.2 to 40.8 mol% (33 strains); and DNA group C, G+C content of 42.1 to 43.9 mol% (28 strains). DNA group A includes the type strain of Bacillus alcalophilus Vedder 1934. DNA-DNA hybridization studies with DNA group A strains revealed that only one strain, strain DSM 2526, exhibited a high level of DNA homology with B. alcalophilus DSM 485T (T = type strain). Neither strain DSM 485T nor any other DNA group A strain is homologous to any of the Bacillus type strains with comparable base compositions. Six strains formed a distinct group containing three highly homologous strains and three strains exhibiting >50% DNA homology.