- Volume 47, Issue 1, 1997
Volume 47, Issue 1, 1997
- Original Papers Relating To Systematic Bacteriology
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Thermonema rossianum sp. nov., a New Thermophilic and Slightly Halophilic Species from Saline Hot Springs in Naples, Italy
More LessSix slightly halophilic, thermophilic bacterial strains were isolated from saline hot springs along the Bay of Naples, Italy. These strains produce bright yellow colonies and have a filamentous morphology and an optimum growth temperature of about 60°C. Lipid composition and 16S ribosomal DNA sequence analyses showed that these strains belong to the genus Thermonema, a member of the cytophaga-flavobacter-bacteroides phylum. Growth was observed in medium containing 1 to 3% NaCl. The DNA G+C content was 50.9 mol%. DNA-DNA hybridization studies showed that these strains represent a new species of the genus Thermonema. We propose that strain NR-27T (T = type strain) and the other strains represent a new species, Thermonema rossianum. Strain NR-27 (= DSM 10300) is the type strain of this species.
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A Proposal To Reclassify Nocardia pinensis Blackall et al. as Skermania piriformis gen. nov., comb. nov.
More LessAbstractThe type strain of Nocardia pinensis was the subject of chemotaxonomic and 16S ribosomal DNA sequencing studies. The resultant nucleotide sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordona, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella, and phylogenetic trees were generated by using the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, and neighbor-joining methods. It was evident from the phylogenetic analyses that N. pinensis represents a distinct phyletic line that is most closely associated with the Gordona clade. This genealogical evidence, together with chemotaxonomic and phenotypic data derived from this and previous studies, indicates that N. pinensis merits generic status within the family Nocardiaceae. Therefore, we propose that N. pinensis Blackall et al. 1989 be reclassified as Skermania piniformis gen. nov., comb. nov. The type strain of Skermania piniformis cleaved an array of conjugated substrates based on the fluorophores 7-amino-4-methylcoumarin and 4-methylumbelliferone.
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Genome Organization of Pseudomonas stutzen and Resulting Taxonomic and Evolutionary Considerations
More LessAbstractIn order to determine the genome variability within Pseudomonas stutzeri, 20 strains representing the seven described genomovars and strain JM300 were analyzed by using various resolution levels of rare cutting enzymes. XbaI and SpeI fingerprints revealed a high degree of heterogeneity of restriction patterns that did not correlate with the division into genomovars. However, a fragment pattern comparison led to the establishment of several groups of clonal variants within genomovars. One circular chromosome ranging in size from 3.75 to 4.64 Mb constitutes the genome of P. stutzeri strains. The I-CeuI, PaI, and SwaI low-resolution map of P. stutzeri type strain CCUG 11256 shows the locations of 12 genes, including rrn operons and the origin of replication. I-CeuI digests of the 20 strains studied plus the positions of six genes allowed a comparison of the rrn backbone organization within genomovars; the four rrn operons seemed to be at similar locations with respect to the origin of replication, as did the rest of the genes. However, a comparison of I-CeuI cleavage maps of the genomovar reference strains revealed a diverse genome organization in the genomovars relative to rrn operons and gene locations. In most genomovars, rrn operons are not arranged around the origin of replication but are equally distributed on the chromosome. Strain JM300 does not belong to any described genomovar, as determined from the organization of its genome. Large chromosomal rearrangements seem to be responsible for the differences in superordinate genome structure and must have played an important role in P. stutzeri diversification and niche colonization. An ancestral chromosome is suggested, and some plausible pathways for the generation of the various genome structures are proposed.
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Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov., an Alkaliphilic, Sulfate-Reducing Bacterium
More LessA new alkaliphilic, sulfate-reducing bacterium, strain Z-7935T (T = type strain), was isolated from a soda-depositing lake, Lake Magadi in Kenya. This organism is a motile vibrio which utilizes only hydrogen and formate as electron donors and sulfate, sulfite, and thiosulfate, but not sulfur, as electron acceptors. Thiosulfate is dismutated. Strain Z-7935T is an obligately sodium-dependent alkaliphile which grows in sodium carbonate medium and does not grow at pH 7; the maximum pH for growth is more than pH 10, and the optimum pH is 9.5 to 9.7. The optimum NaCl concentration for growth is 3% (wt/vol). The optimum temperature for growth is 37°C. The G+C content of the DNA is 48.6 mol%. 16S ribosomal DNA sequence analysis revealed that strain Z-7935T represents a new lineage with genus status in the delta subclass of the Proteobac-teria. The name Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov. is proposed for this organism; the type strain of D. hydrogenovorans is strain Z-7935 (= DSM 9292).
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Anaerobaculum thermoterrenum gen. nov., sp. nov., a Novel, Thermophilic Bacterium Which Ferments Citrate
More LessA thermophilic anaerobic bacterium designated strain RWcit2T (T = type strain) was isolated from the production water of a petroleum reservoir. The cells of this organism are straight to slightly curved rods that are gram negative and nonmotile. Spore formation has not been demonstrated. Growth occurs at temperatures ranging from 28 to 60°C, with optimum growth occurring at 55°C, and at pH values ranging from 5.5 to 8.6, with optimum growth occurring between pH 7 and 7.6. Growth occurs in media containing 0 to 20 g of NaCl per liter, and optimum growth occurs in the presence of 10 g of NaCl per liter. Strain RWcit2T grows on a range of organic acids, including citrate, pyruvate, malate, fumarate, and tartrate; on protein extracts; and on a limited number of carbohydrates. Sulfur, thiosulfate, and cystine are reduced to hydrogen sulfide. Sulfate, sulfite, and nitrate are not reduced. The DNA base composition is 44 mol% G+C. The 16S ribosomal DNA sequence revealed that strain RWcit2T is a member of the domain Bacteria and forms a branch that is approximately equidistant from Dictyoglomus thermophilum and Thermoanaerobacter spp. (level of similarity, 82%). Strain RWcit2T cannot be placed in any previously described taxon based on its phylogenetic and physiological traits and is named Anaerobaculum thermoterrenum gen. nov., sp. nov.
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Schwartzia succinivorans gen. nov., sp. nov., Another Ruminai Bacterium Utilizing Succinate as the Sole Energy Source
More LessAbstractFour strains of gram-negative, anaerobic, non-spore-forming bacteria that were curved rods which were motile by means of flagella originating from the concave side of the cells and which fermented succinate quantitatively to propionate were isolated from high dilutions of rumen ingesta obtained from cows on pasture. The bacteria were asaccharolytic and not proteolytic and did not ferment amino acids or peptides. Succinate was the only substrate fermented. Rumen fluid together with yeast extract was required for good growth on succinate. Growth on succinate was enhanced in the presence of fumarate. The strains did not grow at 22°C, and growth at 45°C was in all cases less than growth at 39°C. The cellular fatty acid compositions of all four strains were determined. The DNA base composition was about 46 mol% G+C. The complete 16S ribosomal DNA sequence of the type strain (strain Sl-1) was determined, and the phylogenetic relationships were analyzed. The most closely related genera were the genera Selenomonas, Zymophilus, and Pectinatus, whereas the recently described succinate-fermenting organism Succiniclasticum ruminis was distantly related. The name proposed for these strains is Schwartzia succinivorans gen. nov., sp. nov.; the type strain is strain S1-1 (=DSM 10502). These organisms are common inhabitants of the rumina of cows on pasture.
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Stenotrophomonas africana sp. nov., an Opportunistic Human Pathogen in Africa
More LessAbstractA gram-negative bacterium was isolated from a cerebrospinal fluid sample from an HIV-seropositive Rwandan refugee with primary meningoencephalitis. This Marseille-Goma sample B isolate, strain MGB1 (T = type strain), was found to exhibit evolutionary homology with Stenotrophomonas maltophilia, as determined by a 16S rRNA gene sequence analysis, and this finding was reflected by similar phenotypic traits. MGBT could, however, be distinguished from the 5. maltophilia type strain by using a number of biochemical and physiological tests, and a genotypic analysis of the two strains in which DNA homology was used revealed only 35% homology between them. Furthermore, the antibiotic susceptibility of MGBT was restricted to netilmicin, ciprofloxacin, trimethoprim-sulfamethoxazole, and colimycin. On the basis of these results we propose that MGBT is a representative of a new species in the genus Stenotrophomonas, Stenotrophomonas africana.
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Clostridium pascui sp. nov., a New Glutamate-Fermenting Sporeformer from a Pasture in Pakistan
More LessAbstractFour strains of an obligately anaerobic spore-forming bacterium were isolated from soil samples from a donkey pasture in Pakistan. Comparative 16S rRNA sequence analysis demonstrated that the strains are members of phylogenetic cluster I of the genus Clostridium (Collins et al. 1994). The strains are mesophilic, nonsaccharolytic, and nonproteolytic, utilize glutamate and histidine, and produce indole. Acetate, butyrate, ethanol, hydrogen, and carbon dioxide are the products of fermentation. Although the strains phenotypically resemble the classical glutamate-fermenting Clostridia, such as Clostridium cochlearium, Clostridium tetanomor-phum, Clostridium tetani, and especially Clostridium malenominatum, they differ from these organisms in sugar utilization, cellular fatty acid composition, and cellular protein pattern and by a 16S rRNA sequence divergence value of approximately 4 to 8%. Phylogenetically, the strains are more closely related to Clostridium estertheticum (sequence divergence, approximately 5%) and Clostridium subterminale (sequence divergence, approximately 5%) but are phenotypically readily distinguished from these species. On the basis of phenotypic and genotypic criteria, we conclude that the four strains are members of a new species of the genus Clostridium, for which the name Clostridium pascui is proposed. The type strain is strain Cm19 (= DSM 10365).
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Identification of Two Pathogenic Avian Mycoplasmas as Strains of Mycoplasma pullorum
More LessAbstractTwo mycoplasma strains were isolated from dead turkey embryos. Growth properties, biochemical and serological characteristics, and protein profiles indicated that these strains were closely related to Mycoplasma pullorum CKKT (T = type strain). This was confirmed by 16S rRNA sequence analysis, and the phylogenetic position of M. pullorum was established. Pathogenicity studies showed that the two strains, as well as M. pullorum CKKT, induced a statistically significant level of mortality after inoculation into chicken embryos.
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Spirochetes from Digital Dermatitis Lesions in Cattle Are Closely Related to Treponemes Associated with Human Periodontitis
More LessAbstractDigital dermatitis (DD), first described in 1974 by Cheli and Mortellaro (R. Cheli and C. Mortellaro, p. 208–213, in Proceedings of the 8th International Conference on Diseases of Cattle, 1974), is a major problem in dairy cows and beef cattle causing significant economic losses worldwide. Lesions are typically found at the volar skin proximal to the heel bulbs. Microscopic examination of biopsies or touch preparations of these lesions revealed a variety of different bacterial morphotypes including significant numbers of spirochetes which often represent the predominant morphotype. We used comparative 16S rRNA sequence analysis to determine the diversity and phylogeny of these hitherto unclassified DD spirochetes. Results indicate that those lesions looked at so far contained at least five spirochetal phylotypes, all clustering within the genus Treponema. Phylotype DDKL-4 was nearly identical (99.4% similarity) to that of a nonpathogenic human treponeme, T. phagedenis. Two phylotypes DDKL-3 and DDKL-13 were closely related to those from treponemes commonly found in human periodontitis lesions, i.e., T. denticola and T. vincentii, exhibiting 95 and 98% similarity, respectively. The other two phylotypes, DDKL-12 and DDKL-20, had no close relatives to any cultivable treponemal species but clustered to previously described group IV oral treponemes. Preliminary analysis using in situ hybridization with fluorescently labeled oligonucleotide probes against smears from DD biopsies revealed that from all lesions analyzed so far, T. denticola-like spirochetes were detected in the highest proportion of all spirochetal morphotypes.
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Intra- and Intergeneric Relationships of Various Actinomycete Strains Based on the Acyl Types of the Muramyl Residue in Cell Wall Peptidoglycans Examined in a Glycolate Test
More LessAbstractA total of 106 actinomycete strains representing 40 genera were studied to gain a better understanding of their intra- and intergeneric relationships by examining the types of acyl groups on the muramyl residues of the peptidoglycans in a glycolate test. The glycolyl type was found in about 43% of the actinomycete strains examined. These strains were distributed in the following two characteristic taxa: the actinoplanetes and their relatives, including species of the genera Actinoplanes, Catellatospora, Couchioplanes, Dactylosporangium, Glycomyces, Micromonospora, and Pilimelia; and the nocardioforms and species of the related genera Gordona, Nocardia, Rhodococcus, Tsukamurella, and Mycobacterium. Only glycolyl type bacteria were found to be present among the strains of these genera tested, except for a few doubtful strains. In contrast, the acetyl type was found extensively in bacteria belonging to the families Pseudonocardiaceae, Streptomycetaceae, Streptosporangiaceae, and Thermomonosporaceae and other taxa. The pattern of acyl type distribution among the actinomycetes correlates very well with the cell wall chemotype sensu Lechevalier and Lechevalier; that is, the chemotype I and III genera were all acetyl type taxa, the chemotype II genera were glycolyl type taxa, and the chemotype IV genera were split into a glycolyl, mycolate-containing group and an acetyl, non-mycolate group. We discuss the idea that combination of both the acyl type system and the cell wall chemotype system should provide a more useful tool for taxonomy of members of the order Actinomycetales.
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Taxonomic Study of Aromatic-Degrading Bacteria from Deep-Terrestrial-Subsurface Sediments and Description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.
AbstractPhylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that six strains of bacteria isolated from deep saturated Atlantic coastal plain sediments were closely related to the genus Sphingomonas. Five of the strains clustered with, but were distinct from, Sphingomonas capsulata, whereas the sixth strain was most closely related to Blastobacter natatorius. The five strains that clustered with S. capsulata, all of which could degrade aromatic compounds, were gram-negative, non-spore-forming, non-motile, rod-shaped organisms that produced small, yellow colonies on complex media. Their G+C contents ranged from 60.0 to 65.4 mol%, and the predominant isoprenoid quinone was ubiquinone Q-10. All of the strains were aerobic and catalase positive. Indole, urease, and arginine dihydrolase were not produced. Gelatin was not liquified, and glucose was not fermented. Sphingolipids were present in all strains; 2OH14:0 was the major hydroxy fatty acid, and 18:1 was a major constituent of cellular lipids. Acid was produced oxidatively from pentoses, hexoses, and disaccharides, but not from polyalcohols and indole. All of these characteristics indicate that the five aromatic-degrading strains should be placed in the genus Sphingomonas as currently denned. Phylogenetic analysis of 16S rRNA gene sequences, DNA-DNA reassociation values, BOX-PCR genomic fingerprinting, differences in cellular lipid composition, and differences in physiological traits all indicated that the five strains represent three previously undescribed Sphingomonas species. Therefore, we propose the following new species: Sphingomonas aromaticivorans (type strain, SMCC F199), Sphingomonas subterranea (type strain, SMCC B0478), and Sphingomonas stygia (type strain, SMCC B0712).
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Discrimination of Streptomyces albidoflavus Strains Based on the Size and Number of 16S-23S Ribosomal DNA Intergenic Spacers
More LessAbstractIn an attempt to develop a rapid and accurate method for discrimination of streptomycetes at the strain level, 21 strains identified by fatty acid analysis as Streptomyces albidoflavus and the type strains of nine subjective synonyms of S. albidoflavus were selected for a full or partial 16S ribosomal DNA (rDNA) sequence analysis and an investigation of the 16S-23S rDNA intergenic spacer region. 16S rDNA sequence analysis showed that 27 of the strains exhibited 100% sequence similarity; these strains included the type strain of S. albidoflavus and the type strains of the subjective synonyms Streptomyces canescens, Streptomyces coelicolor, Streptomyces felleus, Streptomyces limosus, Streptomyces odorifer, and Streptomyces sampsonii. The type strains of the other subjective synonyms of S. albidoflavus (i.e., Streptomyces gougerotii, Streptomyces intermedius, and Streptomyces rutgersensis) were found to have levels of 16S rDNA sequence difference of 1.0 to 1.1% when they were compared to the type strain of 5. albidoflavus. In order to discriminate between the strains which had identical 16S rDNA sequences, the 16S-23S rDNA intergenic spacer regions were amplified and cloned, and the sequences of the spacer regions were determined for four S. albidoflavus strains, including the type strain. The 16S-23S rDNA intergenic spacer region was found to vary in length and sequence composition among the strains and within each strain. The sizes and numbers of 16S-23S rDNA intergenic spacer regions for the 27 strains with identical 16S rDNA sequences were determined by high-resolution electrophoresis of FAM-labeled PCR products and a subsequent size analysis with GeneScan 672 software. This was shown to be a useful method for discrimination of S. albidoflavus strains. Strains with the same 16S-23S rDNA intergenic spacer band pattern, as determined by high-resolution electrophoresis of FAM-labeled PCR products, could be further discriminated on the basis of the sequence composition of the spacer region.
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Notes; A Phylogenetic Analysis of Aerobic Polychlorinated Biphenyl-Degrading Bacteria
More LessSeveral bacterial isolates were characterized based on their abilities to degrade specific polychlorinated biphenyls (PCBs) and their 16S rRNA gene sequences. The members of one group of bacteria consisting of Alcaligenes species, including the PCB-degrading bacterium Alcaligenes eutrophus H850, had strong abilities to degrade a broad range of PCBs but not the di-para-chlorine-substituted congeners. The members of another group, which included the PCB-degrading bacterium originally classified as Corynebacterium sp. strain MB1, had strong abilities to degrade di-para-chlorine-substituted PCBs. These bacteria were most likely different members of Rhodococcus species.
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Reassessment of the Phylogenetic Position of Caulobacter subvibrioides
More LessDetermination of the 16S rRNA gene sequence of Caulobacter subvibrioides ATCC 15264T (T = type strain) confirmed that this species is a member of the alpha subclass of the Proteobacteria and showed that it is phylogenetically most closely related to the Caulobacter group comprising the species Caulobacter bacteroides, Caulobacter crescentus, and Brevundimonas (Pseudomonas) diminuta, for which 16S rRNA sequences of the type strains are currently available. The closest known relative of strain ATCC 15264T among these species is B. diminuta (level of direct pairwise sequence similarity, 95%). On the basis of its previously determined 16S rRNA sequence (accession number M83797), C. subvibrioides is most closely related to Sphingomonas adhaesiva in the alpha-4 subgroup (level of similarity, 97.7%). Analysis of the hydroxy fatty acids of C. subvibrioides ATCC 15264T showed that the 2-hydroxymyristic acid which is characteristic of the genus Sphingomonas was absent.
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DNA Similarities among Mosquito-Pathogenic and Nonpathogenic Strains of Bacillus sphaericus
More LessBacillus sphaericus strains isolated on the basis of pathogenicity for mosquito larvae and strains isolated on the basis of a reaction with a B. sphaericus DNA homology group IIA 16S rRNA probe were analyzed for DNA similarity. All of the pathogens belonged to homology group IIA, but this group also contained nonpathogens. It appears inappropriate to designate this homology group a species based solely upon pathogenicity.
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Transfer of the Bacteriochlorophyll b-Containing Phototrophic Bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the Genus Blastochloris gen. nov.
More LessAbstractThe phylogenetic positions of the bacteriochlorophyll (BChl) b-producing budding phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis were studied on the basis of 16S rRNA gene sequence information. These bacteria formed a tight cluster with the genus Rhodoplanes as a sister group within the alpha-2 subgroup of the Proteobacteria. Genomic DNA-DNA hybridization assays showed that R. viridis and R. sulfoviridis were closely related but were different species. Creation of the genus Blastochloris gen. nov. is proposed to accommodate these BChl b-producing species of phototrophic bacteria.
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Reclassification of Cytophaga aprica (Lewin 1969) Reichenbach 1989 in Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and of Cytophaga diffluens (ex Stanier 1940; emend. Lewin 1969) Reichenbach 1989 in Persicobacter gen. nov. as Persicobacter diffluens comb. nov.
More LessAbstractPhylogenetically, Cytophaga aprica and Cytophaga diffluens occupy independent positions in the flavobacter-bacteroides phylum. Both of these organisms are gram-negative rods that are motile by gliding, chemoor-ganotrophic, and aerobic, degrade several kinds of biomacromolecules, and inhabit marine environments. Their major isoprenoid quinone is menaquinone 7. The G+C content of the DNA of C. aprica is 35 to 37 mol%, and the G+C content of the DNA of C. diffluens is 40 to 42 mol%. In addition to constituting an independent phylogenetic lineage, each species has a distinctive cellular polyamine constitution. C. aprica is characterized by possessing cadaverine as its major polyamine, and C. diffluens is characterized by possessing spermidine, in contrast to most species of the genera Cytophaga, Flavobacterium, and Flexibacter and related organisms, which possess homospermidine. Transfer of C. aprica to the genus Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and transfer of C. diffluens to the genus Persicobacter gen. nov. as Persicobacter diffluens comb. nov. are proposed.
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Comparison of the 16S/23S Ribosomal Intergenic Regions of “ Candidatus Liberobacter asiaticum” and “Candidatus Liberobacter africanum,” the Two Species Associated with Citrus Huanglongbing (Greening) Disease
More LessAbstract16S/23S intergenic spacer regions from the rRNA operons of two strains of ““ Candidatus Liberobacter asiaticum” and one strain of “Candidatus Liberobacter africanum” were cloned and sequenced. The intergenic spacers of the two “Candidatus L. asiaticum” strains studied are identical and contain the genes for isoleucine tRNA (tRNAIle) and alanine tRNA (tRNAAla) separated by 11 nucleotides. The intergenic spacer of the “Candidatus L. africanum” strain contains only one tRNA gene (tRNAAla). The level of homology between the intergenic spacers of the two liberobacter species is 79.46%. Ribosomal operons with 16S/23S spacer regions other than those studied might be present in the two ““ Candidatus Liberobacter” species.
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Transfer of Pseudomonas cissicola (Takimoto 1939) Burkholder 1948 to the Genus Xanthomonas
More LessAbstractThe type strain of Pseudomonas cissicola (Takimoto 1939) Burkholder 1948, strain ICMP 8561 (= NCPPB 2982), was examined. The strain has the determinative characteristics and the fatty acid profile of the genus Xanthomonas. The nutritional characteristics of the strain as determined by Biolog microplate screening were also consistent with identification as a Xanthomonas species. Some characteristics of the fatty acid profile and reactions to tests on the Biolog microplate were not consistent with characteristics of known Xanthomonas species, suggesting that the strain represents a previously unreported species.
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