Phylogeny of Helicobacter felis sp. nov., Helicobacter mustelae, and related bacteria.

Strain CS1T (T = type strain) is a gram-negative, microaerophilic, urease-positive, spiral-shaped bacterium that was isolated from the gastric mucosa of a cat. Additional strains which possessed biochemical and ultrastructural characteristics similar to those of strain CS1T were isolated from the gastric mucosa of cats and dogs. The guanine-plus-cytosine content of the DNA of strain CS1T was 42.5 mol%. The 16S rRNA sequences of strain CS1T, strain DS3 (a spiral-shaped isolate from a dog), and Helicobacter mustelae were determined by direct RNA sequencing, using a modified Sanger method. These sequences were compared with the 16S rRNA sequences of Helicobacter pylori, "Flexispira rappini," Wolinella succinogenes, and 11 species of campylobacters. A dendrogram was constructed based upon sequence similarities. Strains CS1T and DS3 were very closely related (level of similarity, 99.3%). Two major phylogenetic groups were formed; one group consisted of strains CS1T and DS3, H. mustelae, H. pylori, "F. rappini," and W. succinogenes, and the other group contained the true campylobacters. The average level of similarity between members of these two groups was 84.9%. Within the first group, strains CS1T and DS3, H. pylori, and H. mustelae formed a cluster of organisms with an interspecies similarity level of 94.5%. The phylogenetic positions of W. succinogenes and "F. rappini" were just outside this cluster. On the basis of the results of this study, we believe that strains CS1T (= ATCC 49179T) and DS3 represent a new species of the genus Helicobacter, for which we propose the name Helicobacter felis.     

Lipid profile of Helicobacter spp.: presence of cholesteryl glucoside as a characteristic feature.

The lipid and fatty acid profiles of eight Helicobacter spp. (H. nemestrinae, H. acinonyx, H. canis, Helicobacter sp. strain CLO-3, "H. rappini" [Flexispira rappini], H. pametensis, Helicobacter sp. strain Bird-B, and Helicobacter sp. strain Bird-C) and the fatty acid profiles of five additional species (H. pylori, H. felis, H. muridarum, H. mustelae, and H. fennelliae) were analyzed and compared. A heterologous fatty acid profile was observed among the Helicobacter spp., and on that basis the species could be divided into two groups. Group A had 19-carbon cyclopropane fatty acid (19:0cyc) and tetradecanoic acid (14:0) as the major fatty acids, and group B characteristically lacked the 19:0cyc and had hexadecanoic acid (16:0) and octadecenoic (18:1) acids as the major fatty acids. The species of group A are primarily gastric colonizers, and those of group B are primarily intestinal colonizers. Seven of the eight species studied showed the unusual and characteristic presence of cholesteryl glucosides (CGs), and most of these seven showed a very large amount (9.7 to 27.4% of the weight of total extractable lipid). The types of CGs and their distribution in different species were as follows: cholesteryl-6-O-acyl-alpha-D-glucopyranoside (cholesteryl-6-O-tetradecanoyl-alpha-D-glucopyranoside in H. nemestrinae and mainly cholesteryl-6-O-dodecanoyl-alpha-D-glucopyranoside in "H. rappini"), cholesteryl-alpha-D-glucopyranoside (H. nemestrinae, H. acinonyx, H. canis, Helicobacter sp. strain CLO-3, and "H. rappini"), and cholesteryl-6-O-phosphatidyl-alpha-D-glucopyranoside (H. nemestrinae, H. acinonyx, H. canis, and Helicobacter sp. strain CLO-3). Besides this, we could also detect cholesteryl acyl glucoside in H. acinonyx, cholesteryl glucoside in Helicobacter sp. strains Bird-B and -C, and cholesteryl phosphatidyl glucoside in "H. rappini" and Helicobacter sp. strain Bird-C. A selective accumulation of free cholesterol was observed in the neutral lipid fractions. On the basis of the detection of CGs in 11 of the 13 species studied so far, the presence of CGs appears to be a characteristic feature of the genus Helicobacter. In view of this and also because of a simple and rapid detection method described herein, the CGs can be used as a valuable chemotaxonomic marker.     

Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov.

Hybridization experiments were carried out between DNAs from more than 70 strains of Campylobacter spp. and related taxa and either 3H-labeled 23S rRNAs from reference strains belonging to Campylobacter fetus, Campylobacter concisus, Campylobacter sputorum, Campylobacter coli, and Campylobacter nitrofigilis, an unnamed Campylobacter sp. strain, and a Wolinella succinogenes strain or 3H- or 14C-labeled 23S rRNAs from 13 gram-negative reference strains. An immunotyping analysis of 130 antigens versus 34 antisera of campylobacters and related taxa was also performed. We found that all of the named campylobacters and related taxa belong to the same phylogenetic group, which we name rRNA superfamily VI and which is far removed from the gram-negative bacteria allocated to the five rRNA superfamilies sensu De Ley. There is a high degree of heterogeneity within this rRNA superfamily. Organisms belonging to rRNA superfamily VI should be reclassified in several genera. We propose that the emended genus Campylobacter should be limited to Campylobacter fetus, Campylobacter hyointestinalis, Campylobacter concisus, Campylobacter mucosalis, Campylobacter sputorum, Campylobacter jejuni, Campylobacter coli, Campylobacter lari, and "Campylobacter upsaliensis." Wolinella curva and Wolinella recta are transferred to the genus Campylobacter as Campylobacter curvus comb. nov. and Campylobacter rectus comb. nov., respectively. Bacteroides gracilis and Bacteroides ureolyticus are generically misnamed and are closely related to the genus Campylobacter. Campylobacter nitrofigilis, Campylobacter cryaerophila, and an unnamed Campylobacter sp. strain constitute a new genus, for which the name Arcobacter is proposed; this genus contains two species, Arcobacter nitrofigilis comb. nov. (type species) and Arcobacter cryaerophilus comb. nov. Wolinella succinogenes so far is the only species of the genus Wolinella. The genus Helicobacter is also emended; Campylobacter cinaedi and Campylobacter fennelliae are included in this genus as Helicobacter cinaedi comb. nov. and Helicobacter fennelliae comb. nov., respectively. The genus "Flexispira," with "Flexispira rappini" as the only species, is closely related to the genus Helicobacter. The free-living, sulfur-reducing campylobacters do not belong to any of these genera; they probably constitute a distinct genus within rRNA superfamily VI.     

Detection of non-pylori Helicobacter species in "Helicobacter heilmannii"-infected humans

BACKGROUND: A small proportion of patients suffering from chronic active gastritis are diagnosed with gastric Helicobacter species other than Helicobacter pylori. Circumstantial evidence has suggested that these bacteria, also referred to as "Helicobacter heilmannii"-like organisms (HHLO), may be transmitted through animals. The isolation of a Helicobacter bizzozeronii strain from a human patient confirmed this hypothesis. It was the aim of the present study to assess the presence of animal Helicobacter species and H. pylori in humans infected with HHLO, as diagnosed by histology. METHODS: Paraffin-embedded gastric biopsy specimens of 108 HHLO-infected patients (42 women and 66 men) from three clinical centers were screened for the presence of animal gastric Helicobacter species by polymerase chain reaction (PCR), using assays targeting the 16S rDNA region of the three known canine and feline helicobacters (H. bizzozeronii, H. salomonis and H. felis), "Candidatus H. suis", and "Candidatus H. bovis". In addition, the presence of H. pylori was evaluated by multiplex PCR analysis. RESULTS: In 63.4% of the stomachs (64/101) classification of the Helicobacter infection into the above mentioned groups was achieved. Non-pylori Helicobacter species commonly colonizing the stomachs of cats and dogs were found in 48.5% (49/101) of the patients. Fourteen (13.9%) samples tested positive for "Candidatus H. suis", and "Candidatus H. bovis" was demonstrated in 1 (0.9%) patient. The presence of H. pylori was established in 13 patients (12.9%). Eleven stomachs (10.9%) were infected with at least two different Helicobacter species. CONCLUSIONS: This study identifies animal Helicobacter species in the stomach of a large series of HHLO-infected patients, which may have clinical implications in a subset of patients with gastric disease.     

Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev.

Two new species of aerobic, gram-negative, peritrichously flagellated or nonmotile marine bacteria usually forming star-shaped aggregates were isolated from northeastern Atlantic Ocean bottom sediments. These organisms resembled eight star-shaped-aggregate-forming bacterial species from the Baltic Sea originally ascribed to the genus Agrobacterium but not included on the Approved Lists of Bacterial Names because of their questionable relationships to true agrobacteria. These two sets of star-shaped-aggregate-forming bacteria were compared by means of phenotypic data, DNA base compositions, DNA-DNA relatedness, and one-dimensional electrophoretic analysis of low-molecular-weight RNAs (5S rRNA and tRNA). According to the results of genotyping, the northeastern Atlantic Ocean isolates and three of the Baltic Sea species formed a group of closely related bacteria that could not be excluded from the genus Agrobacterium with certainty. Until more genotypic data are available, these five marine species are regarded as a distinct subdivision of the genus Agrobacterium consisting of Agrobacterium atlanticum sp. nov. (type strain, 1480T = DSM 5823T), A. meteori sp. nov. (type strain, 1513T = DSM 5824T), A. ferrugineum sp. nov. nom. rev. emend. (type strain, ATCC 25652T), A. gelatinovorum sp. nov. nom. rev. emend. (type strain, ATCC 25655T), and A. stellulatum sp. nov. nom. rev. emend. (type strain, ATCC 15215T). "A. aggregatum" proved to be a later subjective synonym of A. stellulatum, which had priority. The remaining four Baltic Sea species, "A. agile," "A. kieliense," "A. luteum," and "A. sanguineum," could not be placed in the new subdivision of Agrobacterium.     

实验树鼩肠道螺杆菌属细菌特征分析

近年来,树鼩(Tupaia belangeri)作为一种新型的实验动物被广泛应用于生物医学研究的各个领域。本研究组前期的研究结果显示,螺杆菌属(Helicobacter)是树鼩肠道微生物群落中相对丰度最高的一类细菌,但其具体的细菌种类和结构特征仍然不清楚。因此,本研究将开展实验树鼩肠道中螺杆菌属细菌的分布种类和特征分析,为后续实验研究工作提供资料。通过系统采集72只树鼩的粪便样本,提取核酸后采用巢氏PCR法应用属特异性引物扩增螺杆菌属特异性片段,再分别采用7个种特异性引物对属特异性阳性样本扩增螺杆菌种特异性片段,包括肝螺杆菌(H.hepaticus)、家鼠螺杆菌(H.muridarum)、胆汁螺杆菌(H. bilis)、啮齿类螺杆菌(H. rodentium)、弯曲螺杆菌(Flexispira rappini)、鼩螺杆菌(H. suncus)和盲肠螺杆菌(H. typhlonius)。属特异性引物扩增阳性但种引物扩增阴性的样本进行核酸序列测定和BLAST比对分析,确认其最终所属的螺杆菌种类。结果显示,72份树鼩粪便样本中,属特异性引物扩增阳性有18份,总体阳性率为25.0%。其中,盲肠...     

Plasmids of enterotoxigenic Escherichia coli H10407: evidence for two heat-stable enterotoxin genes and a conjugal transfer system

Three species of plasmids, associated with virulence and conjugal transfer, were identified in a clinically isolated enterotoxigenic Escherichia coli strain, H10407 (serotype O78:H11). pCS1, a non-self-transmissible plasmid species with a molecular weight of 62 X 10(6) and a 47 mol% guanine-plus-cytosine content, specified colonization factor antigen I and heat-stable enterotoxin (ST) production, as reported by others previously. A second non-self-transmissible plasmid species, designated pJY11, with a molecular weight of 42 X 10(6) and a 51 mol% guanine-plus-cytosine content, specified ST and heat-labile enterotoxin production and manifested T5/T6 phage restriction. The third plasmid species, pTRA1, also had a molecular weight of 42 X 10(6) and had a guanine-plus-cytosine content of 51 mol%; this species was self-transmissible and promoted transfer of both pCS1 and pJY11 to other bacterial cells. pCS1 may have originated from species of bacteria with a lower guanine-plus-cytosine content than E. coli. Finally, although demonstrating some heterogeneity with each other, both STs encoded by pCS1 and pJY11 belonged to the STa group.     

Identification of enterohepatic Helicobacter species by restriction fragment-length polymorphism analysis of the 16S rRNA gene

Background. Restriction fragment-length polymorphism (RFLP) analysis of a 1,200-bp polymerase chain reaction–amplified DNA fragment of gene coding for 16S rRNA was used to generate restriction profiles of 11 enterohepatic Helicobacter spp. isolated from various animals and humans.
Methods. The amplicon from each Helicobacter sp. was digested with four restriction endonucleases: Alu I, Hinf I, Hha I, and Dde I. Alu I digestion produced five patterns that were useful for initial differentiation.
Results. Most Helicobacter spp. isolated from rodents had the same RFLP profiles by Alu I digestion (except H. rodentium and H. cholecystus ), but they had different RFLP profiles by Hha I digestion. Only H. bilis and " H. rappini" mouse isolates could not be readily distinguished by the polymerase chain reaction-RFLP method. However, these two species can be distinguished using H. bilis specific primers. Some of the Helicobacter spp. have an intervening sequence in their 16S rRNA gene, which changes the RFLP patterns; in these cases, sequencing is the preferred method to make an appropriate diagnosis.
Conclusions. The RFLP method used in this study was straightforward and rapid and should prove useful as an adjunct for identification and classification of multiple enterohepatic Helicobacter spp.     

Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit

Phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. The unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an Eubacterium species. Comparative 16S rRNA gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from Eubacterium limosum (the type species of the genus Eubacterium) and related organisms. Phylogenetically, the unknown species displayed a close association with an uncultured organism from human subgingival plaque and formed an unknown sub-line within a cluster of organisms which includes Alloioccoccus otitis, Alkalibacterium olivoapovliticus, Allofustis seminis, Dolosigranulum pigrum, and related organisms, within the low mol% G+C Gram-positive bacteria. Sequence divergence values of >8% with all known taxonomically recognised taxa, however, clearly indicates the novel bacterium represents a hitherto unknown genus. Based on both phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig manure be classified in a new genus and species, as Atopostipes suicloacale gen. nov., sp. nov. The type strain of Atopostipes suicloacale is PPC79(T)=NRRL 23919(T)=DSM 15692(T).     

Hansschlegelia plantiphila gen. nov. sp. nov., a new aerobic restricted facultative methylotrophic bacterium associated with plants

A new genus, Hansschlegelia, and a new species, Hansschlegelia plantiphila, are proposed for three strains of methanol-utilizing bacteria isolated from lilac buds (strain S(1)(T)), linden buds (strain S(2)) and blue spruce needles (strain S(4)), which were selected in winter at -17 degrees C. These bacteria are aerobic, Gram-negative, colorless, non-motile short rods that multiply by binary fission and employ the ribulose bisphosphate (RuBP) and the serine pathways for C(1) assimilation. The strains have a limited number of growth substrates and use methanol, methylamine, formate, CO(2)/H(2) and glycerol as carbon and energy sources. Only strain S(1)(T) grows with ethanol and inulin. The strains are neutrophilic and mesophilic, and synthesize phytohormones (auxins and cytokinins) and vitamin B(12). Their major cellular fatty acids are saturated C(16:0), straight-chain, unsaturated C(18:1)(omega)(7) and cyclopropane C(19 cyc) acids. The main ubiquinone is ubiquinone-10 (Q-10). The dominant phospholipids are phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol (cardiolipin). The DNA G+C content is 68.5+/-0.2 mol%. The strains share almost identical 16S rRNA gene sequences, a high DNA-DNA hybridization value (72-86%) and represent a novel lineage of autotrophic methanol-utilizing bacteria within the Alphaproteobacteria. Collectively, these strains comprise a new genus and species H. plantiphila gen. nov., sp. nov., with strain S(1)(T) (VKM B-2347(T), NCIMB 14035(T)) as the type strain.     

Isolation and characterization of a Helicobacter sp. from the gastric mucosa of dolphins, Lagenorhynchus acutus and Delphinus delphis

Gastric ulcerations in dolphins have been reported for decades. Some of these lesions were associated with parasitic infections. However, cases of nonparasitic gastric ulcers with no clearly defined etiology also have been reported in wild and captive dolphins. Considerable speculation exists as to whether dolphins have Helicobacter-associated gastritis and peptic ulcer disease. The stomachs of seven stranded Atlantic white-sided dolphins, Lagenorhynchus acutus, and 1 common dolphin, Delphinus delphis, were assessed for the presence of Helicobacter species. Novel Helicobacter species were identified by culture in the gastric mucosa of two of the eight dolphins studied and by PCR in seven of the eight dolphins. The gram-negative organisms were urease, catalase, and oxidase positive. Spiral to fusiform bacteria were detected in gastric mucosa by Warthin Starry staining. Histopathology revealed mild to moderate diffuse lymphoplasmacytic gastritis within the superficial mucosa of the main stomach. The pyloric stomach was less inflamed, and bacteria did not extend deep into the glands. The lesions parallel those observed in Helicobacter pylori-infected humans. Bacteria from two dolphins classified by 16S rRNA analysis clustered with gastric helicobacters and represent a novel Helicobacter sp. most closely related to H. pylori. These findings suggest that a novel Helicobacter sp. may play a role in the etiopathogenesis of gastritis and gastric ulcers in dolphins. To our knowledge this represents the first isolation and characterization of a novel Helicobacter sp. from a marine mammal and emphasizes the wide host distribution and pathogenic potential of this increasingly important genus.     

Taxonomic and phylogenetic studies on a new taxon of budding, hyphal Proteobacteria, Hirschia baltica gen. nov., sp. nov

Four strains of budding, hyphal bacteria, which had very similar chemotaxonomic properties, were isolated from the Baltic Sea. The results of DNA-DNA hybridization experiments, indicated that three of the new isolates were closely related, while the fourth was only moderately related to the other three. Sequence signature and higher-order structural detail analyses of the 16S rRNA of strain IFAM 1418T (T = type strain) indicated that this isolate is related to the alpha subclass of the class Proteobacteria. Although our isolates resemble members of the genera Hyphomicrobium and Hyphomonas in morphology, assignment to either of these genera was excluded on the basis of their markedly lower DNA guanine-plus-cytosine contents. We propose that these organisms should be placed in a new genus, Hirschia baltica is the type species of this genus, and the type strain of H. baltica is strain IFAM 1418 (= DSM 5838).     

Rhodovulum phaeolacus sp. nov. a phototrophic alphaproteobacterium isolated from a brown pond

Two strains of oval-rod shaped, Gram-negative, phototrophic, purple non-sulfur bacteria designated JA580(T) and JA595 were isolated from a sediment sample collected from a brown pond. Strain JA580(T) was designated as the type strain, while strain JA595 as an additional strain has similar characteristics to the type strain. Strain JA580(T) was non-motile and grew photoheterotrophically with a number of organic compounds serving as carbon source/electron donor. Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids of the spheroidene series were present as the major photosynthetic pigments. Strain JA580(T) requires yeast extract for growth. Strain JA580(T) has an obligate requirement for sulfide or thiosulfate for growth. C(18:1)ω7c, C(18:0), C(18:1)ω9c were the predominant components of cellular fatty acids. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA580(T) clustered with species of the genus Rhodovulum of the family Rhodobacteraceae and is most closely related to the type strains of Rhodovulum adriaticum, Rhodovulum iodosum (96.5%), Rhodovulum robiginosum (96%), Rhodovulum imhoffii (95.6%) and other members of the genus Rhodovulum (<95%). On the basis of phenotypic and molecular genetic evidence, it is proposed that strain JA580(T) should be classified as a novel species of the genus Rhodovulum of the family Rhodobacteraceae, with the species name Rhodovulum phaeolacus sp. nov. The type strain of the species is JA580(T) (=NBRC 107612(T) =KCTC 5963(T)).     

Modification of Salmonella Typhimurium motility by the probiotic yeast strain Saccharomyces boulardii

Background

Motility is an important component of Salmonella enterica serovar Typhimurium (ST) pathogenesis allowing the bacteria to move into appropriate niches, across the mucus layer and invade the intestinal epithelium. In vitro, flagellum-associated motility is closely related to the invasive properties of ST. The probiotic yeast Saccharomyces boulardii BIOCODEX (S.b-B) is widely prescribed for the prophylaxis and treatment of diarrheal diseases caused by bacteria or antibiotics. In case of Salmonella infection, S.b-B has been shown to decrease ST invasion of T84 colon cell line. The present study was designed to investigate the impact of S.b-B on ST motility.

Methodology/Principal Findings

Experiments were performed on human colonic T84 cells infected by the Salmonella strain 1344 alone or in the presence of S.b-B. The motility of Salmonella was recorded by time-lapse video microscopy. Next, a manual tracking was performed to analyze bacteria dynamics (MTrackJ plugin, NIH image J software). This revealed that the speed of bacterial movement was modified in the presence of S.b-B. The median curvilinear velocity (CLV) of Salmonella incubated alone with T84 decreased from 43.3 µm/sec to 31.2 µm/sec in the presence of S.b-B. Measurement of track linearity (TL) showed similar trends: S.b-B decreased by 15% the number of bacteria with linear tract (LT) and increased by 22% the number of bacteria with rotator tract (RT). Correlation between ST motility and invasion was further established by studying a non-motile flagella-deficient ST strain. Indeed this strain that moved with a CLV of 0.5 µm/sec, presented a majority of RT and a significant decrease in invasion properties. Importantly, we show that S.b-B modified the motility of the pathogenic strain SL1344 and significantly decreased invasion of T84 cells by this strain.

Conclusions

This study reveals that S.b-B modifies Salmonella''s motility and trajectory which may account for the modification of Salmonella''s invasion.     

Helicobacter nemestrinae sp. nov., a spiral bacterium found in the stomach of a pigtailed macaque (Macaca nemestrina)

A new microaerophilic, spirally curved, rod-shaped bacterium was isolated from the gastric mucosa of a pigtailed macaque (Macaca nemestrina). The gram-negative cells of this bacterium are oxidase, catalase, and urease positive and strongly resemble Helicobacter pylori (Campylobacter pylori) cells. Like H. pylori, this organism does not metabolize glucose, does not reduce nitrate or produce indole, does not produce H2S from triple sugar iron agar, does not hydrolyze hippurate or esculin, and does not grow in the presence of 1% glycine, 1.5% salt, or 1% bile. Also like H. pylori, it is resistant to nalidixic acid and susceptible to cephalothin. However, unlike H. pylori, the colorless colonies are flat and have irregular edges. This organism has a unique cellular fatty acid composition, forming a new gas-liquid chromatography group, group K, and a distinctive DNA content (24 mol% guanine plus cytosine). It exhibits less than 10% DNA-DNA homology (as determined by the nylon filter blot method at 65 degrees C) with other members of the genus Helicobacter. Although the levels of DNA relatedness between previously described Helicobacter species and the new organism are low (less than 10%) and the difference in guanine-plus-cytosine content is large (24 versus 36 to 41 mol%), the genus Helicobacter is the only genus in which it is logical to include the organism at this time. We propose that our single strain represents a new species, Helicobacter nemestrinae, and we designate strain T81213-NTB (= ATCC 49396) as the type strain.     

Proposal of Mycobacterium peregrinum sp. nov., nom. rev., and elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to species status: Mycobacterium abscessus comb. nov.

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 M. chelonae subsp. abscessus ATCC 19977T is genetically different from M. chelonae subsp. chelonae NCTC 946T on 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.     

Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat

A new species of purple nonsulfur bacteria isolated from an Antarctic microbial mat is described. The organism, designated strain ANT.BR, was mildly psychrophilic, growing optimally at 15-18 degrees C with a growth temperature range of 0-25 degrees C. Cells of strain ANT.BR were highly motile curved rods and spirals, contained bacteriochlorophyll a, and showed a multicomponent in vivo absorption spectrum. A specific phylogenetic relationship was observed between strain ANT.BR and the purple bacterium Rhodoferax fermentans FR2T, and the two organisms shared several physiological and other phenotypic properties, with the notable exception of growth temperature optimum. Tests of genomic DNA hybridization, however, showed Rfx. fermentans FR2T and strain ANT.BR to be genetically distinct bacteria. Because of its unique set of properties, especially its requirement for low growth temperatures, we propose to recognize strain ANT.BR as a new species of the genus Rhodoferax, Rhodoferax antarcticus, named for its known habitat, the Antarctic.     

Cryptococcus foliicola sp. nov. and Cryptococcus taibaiensis sp. nov., novel basidiomycetous yeast species from plant leaves

A molecular taxonomic investigation performed on basidiomycetous yeast strains isolated from plant leaves collected in two areas of China revealed two novel species, Cryptococcus foliicola sp. nov. (type strain HS 23.3(T) = AS 2.2471(T) = CBS 9920(T)) and Cryptococcus taibaiensis sp. nov. (type strain ST 7.9(T) = AS 2.2444(T) = CBS 9919(T)), among the non ballistoconidium-forming strains producing cream-colored colonies. These new species differed markedly from closely related species in the internal transcribed spacer (ITS) and 26S rRNA D1/D2 region sequences. They clustered in a strongly supported clade represented by Cryptococcus victoriae in the Tremellales group in the phylogenetic trees drawn from ITS and D1/D2 sequences.