- Volume 42, Issue 2, 1992

In 1979 and 1980, more than 400 harbor seals (Phoca vitulina) along the New England coast of the United States died of epizootic pneumonia that was attributed to an influenza virus. Six mycoplasma isolates that were recovered from the respiratory tracts of affected seals were investigated and were found to be serologically identical and distinct from previously described species. These isolates required serum for growth, did not possess a cell wall, and did not hydrolyze urea. Arginine was hydrolyzed, glucose was not fermented, film and spots were observed on horse serum agar, phosphatase was produced, tetrazolium was not reduced, and serum and casein were not digested. The guanine-plus-cytosine content of the DNA was 27.8 mol%. We propose the name Mycoplasma phocidae for these isolates. The type strain of M. phocidae is strain 105 (= ATCC 33657).

A total of 66 serovars of potentially pathogenic Leptospira species were examined by slot blot hybridization, and 57 of these serovars were classified in six DNA homology groups. In cases in which common serovars were studied, the results were in general agreement with the results of previous workers, who used different DNA homology methods. However, we propose a new species, Leptospira kirschneri, comprising the following serovars: Bulgarica, butembo, cynopteri, dania, grippotyphosa, kabura, kambale, ramisi, and tsaratsovo. Seven of these serovars have not had their DNAs studied by other workers.

The nucleotide sequence of the 16S rRNA gene of Mycoplasma flocculare was determined and was compared with the sequence of a related porcine mycoplasma, Mycoplasma hyopneumoniae. While the overall level of DNA-DNA homology was approximately 11%, sequence alignment of the two 16S rRNA genes yielded a homology value of more than 95%, emphasizing the highly conserved nature of the 16S rRNA gene. Multiple sequence alignments with other mollicutes indicated that M. flocculare, M. hyopneumoniae, and Mycoplasma hyorhinis form a subcluster within the fermentans phylogroup, and this subcluster is distinct from the Mycoplasma pneumoniae phylogroup. Thus, the three mycoplasmas isolated from porcine respiratory systems exhibit phylogenetic similarities.

Restriction fragments containing the 16S rRNA gene of the western aster yellows mycoplasmalike organism (SAY-MLO) were identified in Southern blots probed with cloned fragments of the western X-disease mycoplasmalike organism 16S rRNA gene. Two fragments which contained the entire SAY-MLO 16S rRNA gene and flanking DNA were cloned in M13 and sequenced. The SAY-MLO 16S rRNA gene is approximately 1,535 bp long, has a G+C content of 47 mol%, and has an overall secondary structure similar to that proposed for Escherichia coli. Putative rRNA promoter sequences and sequences involved in processing of the primary rRNA transcript were similar in the SAY-MLO, two Mycoplasma species, and Bacillus subtilis, suggesting that these prokaryotes and the mycoplasmalike organisms may have similar transcriptional and processing enzymes. We identified two tRNA genes, a tRNATyr (GTA) gene upstream from the 16S rRNA gene and a tRNAIle (GAT) gene in the spacer region between the 16S and 23S rRNA genes. Comparisons of the SAY-MLO 16S rRNA nucleotide sequence with 16S rRNA sequences of other organisms indicated that the SAY-MLO is phylogenetically related most closely to other plant-pathogenic mycoplasmalike organisms, followed by Anaeroplasma species, Acholeplasma species, and some Mycoplasma species.

Arthrobacter oxydans DSM 419 and DSM 420 have chemical and microbiological properties that are consistent with assignment to the genus Arthrobacter. Both organisms have the lysine-alanine-threonine-alanine peptidoglycan type. DNA-DNA pairing studies indicated that A. oxydans DSM 419 should be reclassified as Arthrobacter ureafaciens and that A. oxydans DSM 420T forms the nucleus of a distinct genomic species. We propose that A. oxydans DSM 420 should be reclassified as Arthrobacter nicotinovorans sp. nov. The type strain is strain DSM 420.

We studied the taxonomic positions of the rapidly growing organism Mycobacterium fortuitum and phenotypically related organisms. We confirmed that “Mycobacterium peregrinum” ATCC 14467T (T = type strain) is genetically independent of M. fortuitum ATCC 6841T by using various DNA hybridization conditions. Strains that were genetically identified as “M. peregrinum” were phenotypically differentiated from M. fortuitum ATCC 6841T. Thus, we propose that “M. peregrinum” should be revived as an independent species, Mycobacterium peregrinum sp. nov., nom. rev. The type strain is strain ATCC 14467. M. fortuitum subsp. acetamidolyticum ATCC 35931T exhibited a high level of DNA relatedness to M. fortuitum ATCC 6841T. The hybridized DNAs maintained stable heteroduplexity at high stringency; thus, we confirmed that M. fortuitum subsp. acetamidolyticum is identical to M. fortuitum ATCC 6841T. We found that A/, chelonae subsp. abscessus ATCC 19977T is genetically different from M. chelonae subsp. chelonae NCTC 946Ton the basis of the results of quantitative hybridization even under optimal conditions. There was no reason to maintain this organism as a subspecies of M. chelonae. Thus, we propose that M. chelonae subsp. abscessus should be elevated to species status as Mycobacterium abscessus (Kubica et al.) comb. nov. The type strain is strain ATCC 19977.

The cellular fatty acids of free-living, nitrogen-fixing cyanobacteria belonging to the genera Anabaena and Nostoc were analyzed to differentiate the genera. The fatty acid compositions of 10 Anabaena strains and 10 Nostoc strains that were grown for 12 days on BG-110 medium were determined by gas-liquid chromatography-mass spectroscopy. Of the 53 fatty acids detected, 17 were major components; the average level for each of these 17 fatty acids was at least 0.9% of the total fatty acids (in at least one of the genera). These fatty acids included (with mean percentages in the Anabaena and Nostoc strains, respectively) the saturated fatty acids 16:0 (30.55 and 23.23%) and 18:0 (0.77 and 1.27%); several unsaturated fatty acids, including 14:1 cis-7 (2.50 and 0.11%), 14:1 cis-9 (3.10 and 3.41%), a polyunsaturated 16-carbon (sites undetermined) fatty acid with an equivalent chain length of 15.30 (1.20 and 1.03%), 16:4 cis-4 (0.95 and 0.87%), 16:3 cis-6 (2.16 and 1.51%), 16:1 cis-7 (1.44 and 0.36%), 16:1 cis-9 (6.53 and 18.76%), 16:1 trans-9 (4.02 and 1.35%), 16:1 cis-11 (1.62 and 0.42%), 18:2 cis-9 (10.16 and 12.44%), 18:3 cis-9 (18.19 and 17.25%), 18:1 cis-9 (4.01 and 5.10%), and 18:1 trans-9 (0.92 and 1.94%); and the branched-chain fatty acids iso-16:0 (2.50 and 1.14%) and iso-15:1 (0.34 and 2.05%). Among the fatty acids or classes of fatty acids that were significantly different in the genera Anabaena and Nostoc, and thus of taxonomic value (with ranges in the Anabaena and Nostoc strains, respectively), were 16:0 (27.39 to 34.72 and 18.50 to 26.10%) and the total saturated, straight-chain, even-carbon fatty acids (class A) (29.06 to 36.61 and 21.06 to 28.62%); in addition, the ratios of class C fatty acids (unsaturated straight-chain fatty acids) to class A fatty acids were significantly different (1.52 to 2.13 and 2.25 to 3.47). On the basis of these parameters, Anabaena variabilis isolate ATCC 29413 has the fatty acid characteristics of a Nostoc strain and should be considered for reclassification as Nostoc variabilis; and strain ATCC 27895, which was originally placed in the species Anabaenopsis circularis, should be retained in the genus Nostoc.

On the basis of the idea that DNA sequences encoding cell surface-exposed regions of outer membrane proteins are genus or species specific, two oligonucleotide probes which were based on the PhoE protein of Klebsiella pneumoniae were evaluated. In slot blot hybridizations and in polymerase chain reactions, no cross-hybridizations were observed with non-Klebsiella strains. When the probes were tested on 75 different K-antigen reference Klebsiella strains, 16 strains were not recognized although they did produce PhoE protein under phosphate starvation. To determine whether these 16 strains belong to (a) different species, the reference strains were also tested for the ability to produce indole and to grow at 10°C and their whole-cell fatty acid patterns were analyzed by gas chromatography. A strong correlation was observed among (i) reaction with the probes, (ii) the inability to produce indole, (iii) the inability to grow at 10°C, and (iv) the presence of the hydroxylated fatty acid C,14:0.2OH. From these results we conclude that the two oligonucleotides are specific for the species K. pneumoniae. Furthermore, analysis of fatty acid patterns appears to be a useful tool to distinguish K. pneumoniae from other Klebsiella species.

A new rapidly growing mycobacterium was isolated from human sputum. This organism grew at 22,31,37, and 41°C and possessed catalase, acid phosphatase, acetamidase, urease, nicotinamidase, pyrazinamidase, and nitrate reductase activities. It did not produce nicotinic acid, hydrolyze Tween, or have benzamidase, isonicotinamidase, succinidamidase, and arylsulfatase activities. A mycolic acid analysis revealed a simple, unique pattern. The organism is susceptible to antituberculotic drugs. A comparative 16S rRNA sequence analysis placed this organism within the confines of the genus Mycobacterium, most closely related to the thermotolerant rapidly growing species. On the basis of the pattern of enzymatic activities and metabolic properties, as well as the unique 16S rRNA sequence, we propose that our single strain represents a new species, for which we propose the name Mycobacterium confluentis. The type strain is strain 1389/90; a culture of this strain has been deposited in the German Collection of Microorganisms and Cell Cultures as strain DSM 44017.

Comparative 16S rRNA (rDNA) sequence analyses performed on the thermophilic Bacillus species Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus revealed that these organisms are sufficiently different from the traditional Bacillus species to warrant reclassification in a new genus, Alicyclobacillus gen. nov. An analysis of 16S rRNA sequences established that these three thermoacidophiles cluster in a group that differs markedly from both the obligately thermophilic organism Bacillus stearother-mophilus and the facultatively thermophilic organism Bacillus coagulans, as well as many other common mesophilic and thermophilic Bacillus species. The thermoacidophilic Bacillus species B. acidocaldarius, B. acidoterrestris, and B. cycloheptanicus also are unique in that they possess ω-alicylic fatty acid as the major natural membranous lipid component, which is a rare phenotype that has not been found in any other Bacillus species characterized to date. This phenotype, along with the 16S rRNA sequence data, suggests that these thermoacidophiles are biochemically and genetically unique and supports the proposal that they should be reclassified in the new genus Alicyclobacillus.

The phylogenetic relationship between Cowdria ruminantium and representative members of the orders Rickettsiales and Chlamydiales has been examined on the basis of the sequence of the 16S rRNA. Phylogeny reconstruction by using both parsimony and distance methods supports the conclusion that C. ruminantium is closely related to the Rickettsiales and in particular to the family Anaplasmataceae. A signature of nine base substitutions delineated the linkage of Anaplasma marginale with C. ruminantium and differentiated these two species from the 45 other members of the alpha group of Proteobacteria examined, and five of these base substitutions were unique among all members of the class Proteobacteria examined to date.

Restriction enzyme digestion and field inversion gel electrophoresis were used to analyze the chromosomes of strains of Mycoplasma hyopneumoniae and the related organism Mycoplasma flocculare. The chromosome size for the M. hyopneumoniae type strain was calculated from individual fragments to be 1,011.3 ± 32.9 kbp. The chromosomes of M. hyopneumoniae field strains were approximately the same size. The restriction patterns obtained for the chromosomes of phenotypically similar M. hyopneumoniae strains were quite different. Therefore, the species M. hyopneumoniae seems to be very heterogeneous. A field inversion gel electrophoresis analysis of the entire chromosomes allowed us to distinguish M. hyopneumoniae strains easily and hence to characterize further the species M. hyopneumoniae. The chromosome size for M. flocculare was calculated to be 988.3 ± 39.5 kbp. Restriction enzyme Xhol, which statistically should cut the M. hyopneumoniae chromosome frequently, did not cut the DNA of any of the M. hyopneumoniae strains but did digest M. flocculare DNA, indicating that there is a site-specific modification at CTCGAG which probably belongs to a restriction modification system in M. hyopneumoniae and is absent in M. flocculare.

Approximately 500 fatty acid profiles were prepared for 340 strains of plant-pathogenic and other bacteria currently or recently classified in the genus Pseudomonas Migula 1984. Strains representing some infraspecific taxa were included. The fatty acid profiles were stable and reproducible provided that cultural and chemical techniques were standardized. The 2- and 3-hydroxy fatty acids were found to be useful in grouping strains into six major groups, several of which were further differentiated into subgroups. Group 1 contained strains of the following species and subspecies: Pseudomonas aeruginosa, P. agarici, P. asplenii, P. aureofaciens, P. caricapapayae, P. chlororaphis, P. cichorii, P. ficuserectae, P. fluorescens, P. fuscovaginae, “P. gingeri,” P. marginalis, P. meliae, P. putida, “P. reactans,” P. syringae, P. tolaasii, and P. viridiflava (subgroup 1a); P. corrugata (subgroup 1b); P. rubrisubalbicans (subgroup 1c); P. alcaligenes, P. pseudoalcaligenes subsp. Pseudoalcaligenes, and P. stutzeri (subgroup 1d); P. amygdali (subgroup le); and P. cattleyae NCPPB 1874 (subgroup 1f). All group 1 strains contained 10:0 3-OH and 12:0 3-OH, and most group 1 strains also contained 12:0 2-OH. Group 2 contained strains belonging to the following taxa: P. andropogonis, P. caryophylli, P. cepacia, P. gladioli, P. plantarii, and P. glumae (in part) (subgroup 2a); P. glumae (in part) (subgroup 2b); and P. solanacearum, P. syzygii, and the banana blood disease bacterium (subgroup 2c). All of the group 2 strains contained 14:0 3-OH, 16:0 3-OH, and 18:1 2-OH; most also contained 16:1 2-OH and 16:0 2-OH. Group 3 contained strains belonging to the following taxa: Comamonas acidovorans, P. avenae, P. cattleyae NCPPB 961, P. pseudoalcaligenes subsp. citrulli, P. pseudoalcaligenes subsp. konjaci, P. rubrilineans (subgroup 3a); and Comamonas testosteroni (subgroup 3b). All of the group 3 strains contained 10:0 3-OH. The group 4 strains were members of Sphingomonas paucimobilis, and all contained only 14:0 2-OH. The group 5 strains were members of P. ftectens and contained 12:0 2-OH, 14:0 2-OH, and 14:0 3-OH. The group 6 strains were P. betle, P. cissicola, P. hibiscicola, Xanthomonas maltophilia, and Xanthomonas campestris pv. campestris strains, and all contained 12:0 3-OH, 11:0 iso 3-OH, and 13:0 iso 3-OH. Within each group or subgroup, qualitative and quantitative differences in profiles occurred for most species. Differences were also found at the infraspecific level for some taxa. My results support genomic and other data which show that the plant-pathogenic and other pseudomonads tested should be placed in at least six genera.

Using a variety of physiological, biochemical, and molecular systematic analyses, we have shown previously that there are four groups within the species Fusobacterium nucleatum. Two of these groups of strains correspond to the recently proposed taxa F. nucleatum subsp. nucleatum and F. nucleatum subsp. polymorphum. In this paper we show that the two remaining groups are distinct and formally propose that they should be recognized as F. nucleatum subsp. fusiforme (type strain, NCTC 11326) and F. nucleatum subsp. animalis (type strain, NCTC 12276). The tests which we used did not allow a full assessment of the status of F. nucleatum subsp. vincentii compared with F. nucleatum subsp. nucleatum.

The 16S rRNA gene was amplified, cloned, and sequenced from the blood of two dogs that were experimentally infected with the etiologic agent of canine granulocytic ehrlichiosis. The 16S rRNA sequence was found to be unique when it was compared with the sequences of other members of the genus Ehrlichia. The most closely related species were Ehrlichia canis (98.0% related) and the human ehrlichiosis agent (Ehrlichia chaffeensis) (98.1% related); all other species in the genus were found to be phylogenetically much more distant. Our results, coupled with previous serologic data, provide conclusive evidence that the canine granulocytic ehrlichiosis agent is a new species of the genus Ehrlichia that is related to, but is distinct from, E. canis and all other members of the genus. We propose the name Ehrlichia ewingii sp. nov.; the Stillwater strain is the type strain.

We propose the name Rickettsia japonica sp. nov. (with type strain YH [= ATCC VR-1363]) for a serologically specific species of spotted fever group rickettsiae that are pathogenic for humans (J. Infect. Dis. 159:1122-1126, 1989; J. Clin. Microbiol. 28:1177-1180, 1990). The biologic and genomic characteristics of the organism (G+C content, 31.2 ± 0.7 mol%) are essentially the same as those of other pathogenic spotted fever group rickettsiae, although the R. japonica isolates cause a persistent infection in Vero cells for many subcultures.

Chlamydia pecorum sp. nov. is proposed as the fourth species of the genus Chlamydia on the basis of the results of a genetic analysis of Chlamydia strains that were isolated from cattle and sheep which had various diseases, including sporadic encephalitis, infectious polyarthritis, pneumonia, and diarrhea. The levels of DNA-DNA homology between C. pecorum and strains of C. psittaci, Chlamydia pneumoniae, and Chlamydia trachomatis were less than 10%. Several DNA probes were used to identify C. pecorum. The C. pecorum strains were distinguished from C. psittaci strains by the results of immunological assays, including an immunofluorescence antibody assay performed with monoclonal antibodies and an immunoblot analysis of the immunological specificity of the major outer membrane protein. Species identification was based on results obtained from DNA analyses and serology. The type strain of C. pecorum is strain ATCC VR628.

Xanthobacter flavus 301T (T = type strain) and other strains, including H4-14, both of which were previously described as nonmotile, were reproducibly motile and peritrichously flagellated during the log phase when they were cultured in medium lacking tricarboxylic acid cycle intermediates. Therefore, the species description is emended to include motility and flagellation. Similarly, Xanthobacter autotrophicus was found to be flagellated and motile, but this finding was not consistently reproducible and was mainly found with the mutant strain Fe-s.

Clostridium perfringens, the first pathogenic clostridium examined, was placed in the nonmycoplasma subgroup of the low-dG+dC-content gram-positive cluster on the basis of the results of a phylogenetic analysis in which we used 16S rRNA comparisons. The closest relative that has been identified to date is Clostridium pasteurianum.