Hsp60 Gene Sequence Analysis Research Articles

Dialister hominis sp. nov., isolated from human faeces.

An obligately anaerobic, Gram-stain-negative, rod or coccobacilli organism was isolated from a faecal sample of a healthy Japanese woman. In the 16S rRNA gene sequence analysis, strain 5BBH33T showed the highest 16S rRNA gene sequence similarity to Dialister succinatiphilus YIT 11850T (95.9 %), Dialister propionicifaciens ADV 1053.03T (94.3 %), Dialister micraerophilus DSM 19965T (93.1 %), Dialister invisus DSM 15470T (92.5 %) and Dialister pneumosintes ATCC 33048T (91.4 %). The hsp60 gene sequence analysis also revealed strain 5BBH33T had relatively low hsp60 gene sequence similarities (74.4-85.3 %) to other Dialister species. Strain 5BBH33T showed 21.8-23.9 % in silico DNA-DNA hybridization values with other Dialister species. In addition, the average nucleotide identity values between strain 5BBH33T and other Dialister species ranged from 68.7-74.2 %, indicating that this strain should be considered as new species based on whole-genome relatedness. Strain 5BBH33T was asaccharolytic and largely unreactive for commercial kit. However, its growth was enhanced by adding 1 % (w/v) succinate to the medium; strain 5BBH33T was able to decarboxylate succinate to propionate. The strain 5BBH33T genome contained the enzymes involved in succinate utilization. These results improve our understanding of succinate-utilizing bacteria. On the basis of the collected data, strain 5BBH33T represents a novel species in the genus Dialister, for which the name Dialister hominis sp. nov. is proposed. The type strain of D. hominis is 5BBH33T (=JCM 33369T=DSM 109768T).

Toxoplasma gondii Strains: Bioinformatic Analysis of Heat shock protein 60 Gene in Experimentally Infected Mice

Background and study aim: There is a need for more detailed characterisation of T. gondii strains to determine the level of genetic variability which is useful in effective diagnosis, treatment and control of toxoplasmosis. This work aimed to assess the difference between the two sequences of Hsp60 gene of both RH and ME 49 strains of T. gondii and to investigate its role in the virulence of the parasite. Materials and Methods: Two strains of T. gondii parasite RH and ME-49 were used for experimental infection of mice groups which were divided into group I (infected with RH strain), group II (infected with ME-49), and group III (non-infected non treated group). Results: Histopathological examination showed that there was a statistically significant increase in the intensity of infection in liver and spleen of group I and in kidney and brain of group II, with no difference between both groups organs. Molecular and Bioinformatics studies included Primers design using primer 3 program, primer 2 (P2) was selected and used in PCR amplification according to its highest product size 247 bp. The results of Insilico PCR amplification program that was carried out to amplify Hsp60 gene theoretically using primer 2 (P2) showed higher number of positive samples that detected in group II than group I, there was significant statistical increase in frequency of brain infection in group II. Conclusion: Our results showed that PCR was a highly sensitive, specific and rapid technique for detecting T. gondii. It revealed higher positive results in chronic strain (ME49) especially in brain tissue than acute strain (RH) but it may show false negative results in some samples. Both PCR technique and histopathological examination showed that the preferred tissue for detection of T. gondii in experimentally infected mice was liver & spleen in acute strain (RH) and brain & kidney in chronic strain (ME49). Bioinformatic analysis of Hsp60 gene sequences of both (RH & ME 49) strains of T. gondii showed that there was a polymorphism in some nucleotides between the 2 sequences.

Parolsenella catena gen. nov., sp. nov., isolated from human faeces.

Strain 2CBEGH3T, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a healthy Japanese man. The 16S rRNA gene sequence analysis showed that strain 2CBEGH3T represented a member of the family Atopobiaceae and formed a monophyletic cluster with Olsenella uli DSM 7084T (93.6 % sequence similarity), Olsenella umbonata strain lac31T (93.0 %), Olsenella profusa JCM 14553T (92.7 %) and Olsenella scatoligenes strain SK9K4T (92.7 %) as closest neighbours and Atopobium species. The hsp60 gene sequence analysis supported the phylogenetic relationships based on the 16S rRNA gene sequences, with sequence similarity values of 82.1-84.7 % to the four species described above. A unique three-base (one amino acid residue) insertion was found in the alignment regions of the hsp60 gene sequence of strain 2CBEGH3T. The major end products from d-glucose were d- and l-lactic acids produced at the ratio of 75 : 25, while four species of the genus Olsenella produced d- and l-lactic acids at ratios of 94-98 : 2-6. The isolate formed characteristic crater-like colonies on Eggerth-Gagnon agar plates. The major cellular fatty acids were C18 : 1ω9c, C18 : 1ω9c dimethyl acetal (DMA) and C16 : 0 DMA. The G+C content of the genomic DNA was 68.4 mol%. On the basis of these data, strain 2CBEGH3T represents a novel species in a novel genus of the family Atopobiaceae, for which the name Parolsenella catena gen. nov., sp. nov. is proposed. The type strain of P. catena is 2CBEGH3T (=JCM 31932T=DSM 105194T).

Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.

Two bacterial strains, designated EGH7T and TSAH33, were isolated from human faeces and characterized by using a polyphasic taxonomic approach that included analysis of morphology, phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic position based on 16S rRNA and hsp60 gene sequence analyses. The results of 16S rRNA gene sequence analysis indicated that these strains represented members of the family Lachnospiraceae and formed a monophyletic cluster near Eubacterium contortum JCM 6483T (95 % sequence similarity), Ruminococcus gnavus JCM 6515T (95 %), Clostridium oroticum JCM 1429T (95 %), Eubacterium fissicatena JCM 31501T (95 %) and Clostridium nexile JCM 31500T (94 %). The results of a hsp60 gene sequence analysis supported the phylogenetic tree based on the 16S rRNA gene sequence, with a sequence similarity value of between 77.9 and 84.8 % to the five strains listed above. The novel strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive cocco-bacilli. The strains formed characteristic umbilicated colonies on EG agar plates. The major cellular fatty acids were C18 : 1ω9c, C16 : 0 and C18 : 1ω9c dimethyl acetal (DMA). EGH7T and TSAH33 have DNA G+C contents of 46.9 and 45.5 mol%, respectively. On the basis of these data, strains EGH7T and TSAH33 represent a novel species of a novel genus, for which the name Faecalimonas umbilicata gen. nov., sp. nov. is proposed. The type strain of F. umbilicata is EGH7T (=JCM 30896T=DSM 103426T).

Porphyromonas pasteri sp. nov., isolated from human saliva.

A bacterial strain, designated KUFDS01T, isolated from human saliva was characterized using a polyphasic taxonomic approach that included analysis of physiological and biochemical features, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. Cells of the strain were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. Growth of the strain was inhibited on medium containing 20% bile. The 16S rRNA gene sequence analysis showed that the strain was a member of the genus Porphyromonas. Strain KUFDS01T was closely related to Porphyromonas catoniae JCM 13863T (96.6% sequence similarity). An hsp60 gene sequence analysis indicated that strain KUFDS01T was different from P. catoniae JCM 13863T, with a sequence similarity value of 87.8%. The major cellular fatty acids of strain KUFDS01T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0, C18 : 2ω6, 9c and C18 : 1ω9c. The DNA G+C content of strain KUFDS01T was 57.7 ± 0.66 mol%. On the basis of these data, strain KUFDS01T represents a novel species of the genus Porphyromonas, for which the name Porphyromonas pasteri sp. nov. is proposed. The type strain of P. pasteri is KUFDS01T ( = JCM 30531T = CCUG 66735T).

Parabacteroides faecis sp. nov., isolated from human faeces

A bacterial strain, designated 157(T), isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20% (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157(T) was closely related to Parabacteroides gordonii JCM 15724(T) (96% sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157(T) was different from P. gordonii JCM 15724(T), with a hsp60 gene sequence similarity of 96.1%. The major cellular fatty acids of strain 157(T) were anteiso-C(15 : 0), iso-C(17 : 0) 3-OH, C(18 : 1)ω9c and anteiso-C(17 : 0) 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157(T) was 41.8 mol%. On the basis of these data, strain 157(T) represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157(T) ( = JCM 18682(T) = CCUG 66681(T)).

Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces

Strains of Gram-stain-negative, anaerobic, rod-shaped bacteria were isolated from chinchilla (Chinchilla lanigera) faeces, and strain ST166(T) was investigated taxonomically. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain ST166(T) belonged to the genus Parabacteroides. Strain ST166(T) formed a distinct line of descent, and the highest sequence similarity to ST166(T) was found with Parabacteroides merdae JCM 9497(T) (95.6%) and Parabacteroides johnsonii JCM 13406(T) (95.0%). Analysis of hsp60 gene sequences also supported these relationships. Based on the phenotypic and phylogenetic characteristics, the novel species Parabacteroides chinchillae sp. nov. is proposed. The type strain of P. chinchillae sp. nov. is ST166(T) ( = JCM 17104(T) =CCUG 62154(T)).

Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus)

An obligately anaerobic, non-pigmented, non-spore-forming, Gram-staining-negative, rod-shaped bacterium, designated strain Rs-03(T), was isolated from the gut of the subterranean termite Reticulitermes speratus. The taxonomic position of the novel strain was determined by following a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Rs-03(T) was a member of the genus Bacteroides and was most closely related to Bacteroides thetaiotaomicron JCM 5827(T) (95.0 % sequence similarity), Bacteroides faecis JCM 16478(T) (94.8 %) and Bacteroides xylanisolvens JCM 15633(T) (94.3 %). The results of hsp60 gene sequence analysis indicated that the novel strain was different from established members of the genus Bacteroides. Strain Rs-03(T) was saccharolytic and produced succinic and acetic acids, with small amounts of propionic acid, as metabolic end products. The major cellular fatty acids of strain Rs-03(T) were anteiso-C(15 : 0), C(18 : 1)ω9c and iso-C(17 : 0) 3-OH. The major menaquinones were MK-10 and MK-9 and the genomic DNA G+C content was 44.9 mol%. Based on these data, strain Rs-03(T) represents a novel species in the genus Bacteroides, for which the name Bacteroides reticulotermitis sp. nov. is proposed. The type strain is Rs-03(T) ( = JCM 10512(T) = CCUG 62153(T)).

Porphyromonas crevioricanis is an earlier heterotypic synonym of Porphyromonas cansulci and has priority

A DNA-DNA hybridization experiment was carried out to clarify the relationship between Porphyromonas crevioricanis and Porphyromonas cansulci. The taxonomic standing of these two species was unclear so far because of the high 16S rRNA gene sequence similarity value (99.9 %). The DNA-DNA relatedness values between P. crevioricanis JCM 15906(T) and P. cansulci JCM 13913(T) were above 91 % (91-99 %). In addition, P. crevioricanis JCM 15906(T) exhibited high hsp60 gene sequence similarity with P. cansulci JCM 13913(T) (100 %). The hsp60 gene sequence analysis and the DNA-DNA relatedness values demonstrated that P. crevioricanis JCM 15906(T) and P. cansulci JCM 13913(T) are a single species. Based on these data, we propose Porphyromonas cansulci as a later heterotypic synonym of Porphyromonas crevioricanis.

Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority

Strains of the recently proposed species Bacteroides chinchillae share more than 99.4 % 16S rRNA gene sequence similarity with the type strain of Bacteroides sartorii although these two species do not appear to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of both species to clarify their taxonomic position. B. chinchillae JCM 16497(T) exhibited high hsp60 gene sequence similarity with B. sartorii JCM 17136(T) (100 %) as well as B. chinchillae JCM 16498 (100 %). The hsp60 gene sequence analysis and levels of DNA-DNA relatedness observed demonstrated B. sartorii JCM 17136(T), B. chinchillae JCM 16497(T), and B. chinchillae JCM 16498 are members of a single species. Based on these data, we propose Bacteroides chinchillae as a later heterotypic synonym of Bacteroides sartorii. An emended description of B. sartorii is provided.

Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces

Strains of gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces, and three strains, ST161(T), ST33 and ST37(T), were investigated taxonomically. Based on phylogenetic analyses and specific phenotypic characteristics, the three strains were allocated to the genus Bacteroides. Phylogenetic analyses of their 16S rRNA gene sequences revealed that strain ST161(T) formed a distinct line of descent, with highest sequence similarity to strain ST33 (98.7 %) and Bacteroides oleiciplenus JCM 16102(T) (97.7 %). High levels of DNA-DNA relatedness (79-89 %) were found between strains ST161(T) and ST33, but low levels were found between strain ST161(T) and B. oleiciplenus JCM 16102(T) (33-37 %) and between strain ST33 and B. oleiciplenus JCM 16102(T) (33-37 %). These data clearly indicated that strains ST161(T) and ST33 represent a single novel species. 16S rRNA gene sequence analyses showed that strain ST37(T) also formed a distinct line of descent, with highest sequence similarity to Bacteroides acidifaciens JCM 10556(T) (96.5 %) and Bacteroides caccae JCM 9498(T) (95.6 %). Analysis of hsp60 gene sequences also supported these relationships. Based on phenotypic and phylogenetic characteristics, two novel species, Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., are thus proposed. The type strains of B. stercorirosoris and B. faecichinchillae are ST161(T) ( = JCM 17103(T) = CCUG 60872(T)) and ST37(T) ( = JCM 17102(T) = CCUG 60873(T)), respectively. The DNA G+C contents of strains ST161(T) and ST37(T) were 45.7 and 41.0 mol%, respectively.

Campylobacter volucris sp. nov., isolated from black-headed gulls (Larus ridibundus)

During a study of the prevalence of Campylobacter jejuni in black-headed gulls (Larus ridibundus) in Sweden, three isolates, strains LMG 24379, LMG 24380T and LMG 24381, were initially identified as Campylobacter lari. Further characterization by both AFLP and whole-cell protein SDS-PAGE analyses revealed that they formed a distinct group in the genus Campylobacter. This unique position was confirmed by phenotypic characterization, 16S rRNA and hsp60 gene sequence analysis and DNA-DNA hybridizations. The combined data confirm that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter volucris sp. nov. is proposed. The type strain is LMG 24380T (=CCUG 57498T).

Prevotella aurantiaca sp. nov., isolated from the human oral cavity

Two anaerobic, pigmented, non-spore-forming, Gram-stain-negative, rod-shaped strains isolated from the human oral cavity, OMA31(T) and OMA130, were characterized by determining their phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the new isolates belonged to a single species of the genus Prevotella. The two isolates showed 100 % 16S rRNA gene sequence similarity with each other and were most closely related to Prevotella intermedia ATCC 25611(T) with 96.4 % 16S rRNA gene sequence similarity; the next most closely related strains to the isolates were Prevotella pallens AHN 10371(T) (96.1 %) and Prevotella falsenii JCM 15124(T) (95.3 %). Phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248(T), P. falsenii JCM 15124(T) and Prevotella nigrescens JCM 12250(T). The isolates could be differentiated from P. pallens JCM 11140( T) by mannose fermentation and alpha-fucosidase activity. Conventional biochemical tests were unable to differentiate the new isolates from P. intermedia, P. falsenii and P. nigrescens. However, hsp60 gene sequence analysis suggested that strain OMA31(T) was not a representative of P. intermedia, P. pallens, P. falsenii or P. nigrescens. Based on these data, a novel species of the genus Prevotella, Prevotella aurantiaca sp. nov., is proposed, with OMA31(T) (=JCM 15754(T)=CCUG 57723(T)) as the type strain.

Novel Campylobacter lari-like bacteria from humans and molluscs: description of Campylobacter peloridis sp. nov., Campylobacter lari subsp. concheus subsp. nov. and Campylobacter lari subsp. lari subsp. nov.

A polyphasic study was undertaken to clarify the taxonomic position of Campylobacter lari-like strains isolated from shellfish and humans. The diversity within the strain collection was initially screened by means of fluorescent amplified fragment length polymorphism analysis and whole-cell protein electrophoresis, revealing the existence of two clusters distinct from C. lari and other Campylobacter species. The divergence of these clusters was confirmed by phenotypic analysis and by 16S rRNA and hsp60 gene sequence analysis. Phylogenetic analysis identified C. lari, Campylobacter jejuni, Campylobacter coli and Campylobacter insulaenigrae as the closest phylogenetic neighbours of both taxa. DNA-DNA hybridizations revealed that one cluster, comprising 10 strains, represented a novel Campylobacter species, for which the name Campylobacter peloridis sp. nov. is proposed, with 2314BVA(T) (=LMG 23910(T) =CCUG 55787(T)) as the type strain. The second cluster, comprising six strains, represents a novel subspecies within the species C. lari, for which the name Campylobacter lari subsp. concheus subsp. nov. is proposed, with 2897R(T) (=LMG 21009(T) =CCUG 55786(T)) as the type strain. The description of C. lari subsp. concheus has the effect of automatically creating the subspecies Campylobacter lari subsp. lari subsp. nov. (type strain LMG 8846(T)=NCTC 11352(T)).

Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov.

In the year 2002, Bifidobacterium longum, Bifidobacterium infantis and Bifidobacterium suis were unified into a single species, Bifidobacterium longum, preserving the former species names through the creation of the three biotypes 'longum', 'infantis' and 'suis'. Consequently, the use of the species names B. infantis and B. suis was to be discontinued. The above taxonomic rearrangement of B. longum was based on DNA-DNA hybridizations and 16S rRNA and HSP60 gene sequence analysis. However, a variety of other genotypic techniques including ribotyping, amplified rDNA restriction analysis (ARDRA), randomly amplified polymorphic DNA (RAPD)-PCR, BOX-PCR, PCR-denaturing gradient gel electrophoresis (DGGE), comparison of the recA, tuf and ldh gene sequences, plasmid profiling and considerable variation in carbohydrate fermentation patterns as well as results of starch and PAGE electrophoresis experiments clearly discriminate former B. longum, B. infantis and B. suis strains. In the present paper we compile this published information and propose the description of Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov. The International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms is in favour of this proposal. The type strains of Bifidobacterium longum subsp. longum subsp. nov., subsp. infantis comb. nov. and subsp. suis comb. nov. are E194b (variant a)T (ATCC 15707T=DSM 20219T), S12T (=ATCC 15697T=DSM 20088T) and Su859T (ATCC 27533T=DSM 20211T), respectively.