International journal of systematic and evolutionary microbiology最新文献

Three aerobic, pink-pigmented, Gram-negative, motile and rod-shaped bacterial strains, designated SD21^T, SI9^T and SB2^T, were isolated from the phyllosphere of healthy litchis collected from three main producing sites of Guangdong Province, PR China. The 16S rRNA gene analysis showed that strains SD21^T and SI9^T belonged to the genus Methylobacterium (Mtb.) with the highest similarity to Mtb. komagatae DSM 19563^T (98.7%) and Mtb. phyllosphaerae CBMB27^T (99.8%), respectively, while strain SB2^T belonged to the genus Methylorubrum (Mtr.) and showed the highest similarity to Mtr. suomiense DSM 14458^T (98.6%). Phylogenomic analysis based on 92 core genes clearly showed that the most closely related type strains of SD21^T, SI9^T and SB2^T were Mtb. komagatae DSM 19563^T, Mtb. phyllostachyos ICMP 17619^T and Mtr. salsuginis CGMCC 1.6474^T, respectively. The ANI and dDDH values between the three isolates and their most closely related type strains were 85.6‒90.1% and 29.5‒40.4%, respectively, much below the threshold values for species delimitation. The isolates showed clear differences from their closely related type strains in terms of growth conditions, enzyme activities, substrates assimilation and contents of the major fatty acids. They all took summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) as the major fatty acid, ubiquinone 10 as the predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as the major polar lipids. The phenotypic, phylogenetic and chemotaxonomic analyses with genome comparison strongly support that the isolates represent three distinct novel species within the genera of Methylobacterium and Methylorubrum, for which the names Methylobacterium litchii sp. nov., Methylobacterium guangdongense sp. nov. and Methylorubrum subtropicum sp. nov. are proposed, with SD21^T (=GDMCC 1.4327^T=KCTC 8300^T), SI9^T (=GDMCC 1.4329^T=KCTC 8298^T) and SB2^T (=GDMCC 1.4328^T=KCTC 8299^T) as the type strains, respectively.

Objective: The aim of the current clinical study was to reveal whether harvesting of a temporalis fascia graft would be associated with a higher incidence of temporomandibular joint (TMJ) internal derangement.

Methods: The study group involved 104 patients who had middle-ear operations, 67 of which involved harvesting of temporalis fascia and 37 that did not. The TMJs were clinically examined in each group.

Results: The total incidence of internal derangement of the TMJ was significantly higher in the group that had temporalis fascia harvesting (79.1%), compared to the group that did not have temporalis fascia harvesting (29.7%), (p= 0.001).

Conclusion: Harvesting of temporalis fascia probably alters mandibular kinematics and predisposes to internal derangement of the TMJs.

A novel strain of the genus Holzapfeliella, named He02^T, was isolated from flowers of Satureja montana L. in a survey for lactic acid bacteria associated with wild and cultivated plants in the metropolitan area of Valencia, Spain. Partial 16S rRNA gene sequencing revealed a similarity of 99% to Holzapfeliella floricola DSM 23037^T=Ryu1-2^T. Strain He02^T cells are Gram-stain-positive, catalase-negative non-motile rods, usually occurring in pairs. Cells show a pale yellow pigmentation when pelleted. As H. floricola, strain He02^T utilized a narrow range of carbohydrates, namely, glucose and fructose, homofermentatively. However, genome sequencing and estimation of average nucleotide identity (ANI) revealed an ANI value of 87.44 with H. floricola DSM 23037^T, the only H. floricola strain sequenced to date. A value of 30.5% for digital DNA-DNA hybridization was estimated with the Type Strain Genome Server tool when He02^T was compared with strain DSM 23037^T. These results indicate that strain He02^T constitutes a novel species, for which the name Holzapfeliella saturejae sp. nov. with He02^T (=CECT 31001^T=DSM 117324^T=CCM 9395^T) as type strain is proposed.

Three strains of actinobacteria, designated as B-S-A6^T, B-S-A8^T and B-S-A12^T, were isolated from soil samples collected in the Phu Pha Phet Cave located in the Satun UNESCO Global Geopark, Satun Province, Thailand. A comprehensive polyphasic approach was used to describe these strains. Strains B-S-A6^T, B-S-A8^T and B-S-A12^T were identified within the genus Streptomyces based on a comparative examination of 16S rRNA gene sequences. Strains B-S-A8^T and B-S-A12^T showed a high genetic similarity to Streptomyces spectabilis NBRC 13424^T (99.0%, for both) and to Streptomyces deserti C63^T (98.6 and 98.7 %, respectively). Meanwhile, strain B-S-A6^T exhibited 98.6% sequence similarity with S. spectabilis NBRC 13424^T and Streptomyces koyangensis VK-A6 ^T. However, upon further comparison, the 16S rRNA gene sequence of strain B-S-A6^T showed a similarity of 99.6% to B-S-A8^T and 99.7% to B-S-A12^T. Contrastingly, B-S-A8^T showed a very high similarity of 99.8% with B-S-A12^T. The use of digital DNA-DNA hybridization, along with the analysis of average nt identities and aa identities, comparing the three strains to their closest known type strains, validated that each of these strains represents a new and distinct species. Three newly identified strains exhibited phenotypic characteristics and chemotaxonomic properties consistent with the members of the genus Streptomyces. The primary menaquinones identified in these strains were MK-9(H₆) and MK-9(H₈). The major fatty acids were iso-C_15 : 0 and anteiso-C_15 : 0. Their polar lipid profiles included diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The comprehensive phenotypic and genomic analyses of the Streptomyces strains strongly suggest that strains B-S-A6^T, B-S-A8^T and B-S-A12^T represent three new species for which the names Streptomyces cavernicola sp. nov. (type strain B-S-A6^T =TBRC 17074^T =NBRC 116118^T), Streptomyces solicavernae sp. nov. (type strain B-S-A8^T =TBRC 17072^T =NBRC 116117^T) and Streptomyces luteolus sp. nov. (type strain B-S-A12^T =TBRC 17060^T =NBRC 116116^T) are proposed.

An obligately anaerobic, Gram-stain-negative, non-spore-forming and non-motile rod (strain LPYR103-Pre^T) was isolated from a two-phase methane fermentation system. Using 16S rRNA gene sequence-based phylogenetic analysis, strain LPYR103-Pre^T was classified in the genus Segatella. The 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization between strain LPYR103-Pre^T and its phylogenetically nearest species - Segatella cerevisiae JCM 30867^T - were 94.4, 77.9 and 23.4%, respectively. The genome size of strain LPYR103-Pre^T was 3 326 733 bp, and its genomic DNA G+C content was 44.05%. The most abundant cellular fatty acid was anteiso-C_15 : 0. The growth of strain LPYR103-Pre^T was stimulated by the addition of pectin, d-galacturonate and d-glucuronate; in contrast, the strain exhibited poor growth in the presence of common sugars, such as glucose. Therefore, strain LPYR103-Pre^T was classified as a pectinophile - a bacterium that shows a preference for pectin and a few related compounds as substrates. Glucose is degraded by type strains of 12 species belonging to the genus Segatella; thus, strain LPYR103-Pre^T is the first described pectinophile belonging to this genus. Strain LPYR103-Pre^T produced succinate and acetate as its major metabolic end products. Based on the differences in the phylogenetic, genomic, physiological and chemotaxonomic characteristics of strain LPYR103-Pre^T and related species, the name Segatella asaccharophila sp. nov. is proposed to accommodate strain LPYR103-Pre^T (= NRIC 0997^T = JCM 37351^T=DSM 118531^T = KCTC 25923^T).

Two mycelium-forming actinobacterial strains, designated as DLS-47 and DLS-62^T, were isolated from volcanic ash collected from the surface of a rock on the peak of Darangshi Oreum (a volcanic cone) in Jeju, Republic of Korea, and their taxonomic positions were investigated by a polyphasic approach. Both of the isolates showed growth at 20-42 °C, pH 6.0-9.0 and 0-1% (w/v) NaCl. Furthermore, DLS-47 was found to grow at 45 °C, while strain DLS-62^T grew at pH 10.0 and 3% (w/v) NaCl. The 16S rRNA gene-based phylogeny showed that both of the isolates belonged to the genus Actinomadura; strain DLS-47 was most closely related to Actinomadura chokoriensis DSM 45346^T (100% sequence identity), while strain DLS-62^T formed a tight cluster with Actinomadura bangladeshensis DSM 45347^T (99.5% sequence similarity). Morphological and chemotaxonomic characteristics supported the affiliation of the two isolates to the genus Actinomadura. Phylogenomic analysis based on 92 core gene sequences showed that both of the isolates were most closely related to A. chokoriensis DSM 45346^T. Strain DLS-47 shared 100% of orthologous average nucleotide identity and digital DNA-DNA hybridization values with A. chokoriensis DSM 45346^T, while strain DLS-62^T showed orthologous average nucleotide identity ≤89.8% and digital DNA-DNA hybridization values ≤39.4% with strain DLS-47 and members of the genus Actinomadura. The results of phenotypic assays and comparison of overall genomic relatedness indices support the conclusion that strain DLS-47 (= KACC 23347=DSM 116423) is a strain of A. chokoriensis, while strain DLS-62^T (= KACC 23345^T = DSM 116424^T) represents a new species of the genus Actinomadura, for which the name Actinomadura monticuli sp. nov. is proposed. Also, Actinomadura glauciflava Lu et al. 2003 is reclassified as a later heterotypic synonym of Actinomadura luteofluorescens (Shinobu 1962) Preobrazhenskaya et al. 1975 (Approved Lists 1980) based on analysis of overall genomic relatedness indices and phenotypic similarity.

Three yeast strains were isolated from an olive paste sample (CBS 18661) and two samples of olive oil (CBS 18662 and CBS 18660) were collected in two different mills in Verona province, Italy. The sequence comparison of the D1/D2 domains of the LSU rRNA gene and the internal transcribed space (ITS) regions indicated that these strains belonged to the genus Yamadazyma. Phylogenetic analysis of concatenated sequences of the ITS regions and the D1/D2 domains indicated that they represented members of two distinct species. Strain CBS 18661 and CBS 18662 showed sequence divergence of 2.7-2.8% (13-15 nucleotide substitutions) in the D1/D2 domains from the holotype of Yamadazyma luoyangensis, Yamadazyma ovata, Yamadazyma siamensis and Candida kanchanaburiensis and 5.9-6.2% identities (36-38 nucleotide substitutions) in the ITS regions from Yamadazyma akitaenisis and Yamadazyma nakazawae. Strain CBS 18660 showed sequence divergence of 0.75-1.1% (4-6 nucleotide substitutions) from Y. ovata, Candida trypodendri and Candida insectorum and 3.2-4.1% (18-24 nucleotide substitutions) in the ITS regions from Yamadazyma dushanensis, Yamadazyma terventina, Yamadazyma mexicana and C. trypodendri. The strains CBS 18661^T (PP391581-PP375117) and CBS 18662 (PP391582-PP375118) are named Yamadazyma oleae f.a. sp. nov., whereas CBS 18660^T (PP149061-PP130150) is assigned as Yamadazyma molendinolei f.a. sp. nov. The MycoBank numbers are MB 854683 and MB 854684, respectively. In addition, 11 Candida species belonging to the Yamadazyma clade have been reassigned to the genus Yamadazyma with the proposal of the following new combinations: Yamadazyma aaseri comb. nov., Yamadazyma conglobata comb. nov., Yamadazyma dendronema comb. nov., Yamadazyma diddensiae comb. nov., Yamadazyma germanica comb. nov., Yamadazyma insectorum comb. nov., Yamadazyma kanchanaburiensis comb. nov., Yamadazyma naeodendra comb. nov., Yamadazyma pseudoaaseri comb. nov., Yamadazyma trypodendri comb. nov. and Yamadazyma vaughaniae comb. nov.

Three fluorescent bacterial strains, K1, K13 and K18, were obtained from watermelon (Citrullus lanatus) foliage symptomatic of bacterial leaf spot of cucurbits in Florida. The strains underwent phenotypic characterization, including LOPAT (levan production, oxidase activity, pectolytic activity on potato, arginine dihydrolase production and hypersensitive response (HR) on both tobacco and tomato) and pathogenicity testing on watermelon and squash seedlings. Whole-genome sequencing of the isolates was performed, and multi-locus sequence analysis (MLSA) utilizing housekeeping genes gltA, rpoD, gapA and gyrB placed the isolates into two distinct clades within the Pseudomonas genus. Average nucleotide identity based on blast (ANIb) was used to compare the isolates to Pseudomonas reference genomes. Using ANIb, the closest relatives to the novel strains were identified as Pseudomonas wayambapalatensis (K1 : 82.58%; K13 : 83.77%) and Pseudomonas kilonensis (K18 : 87.16%), although ANIb values were below the 95% threshold for species delineation. DNA-DNA hybridization (genome-genome distance calculation method), comparison to the online Type Genome Server, Biolog biochemical profiling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were also unable to identify the isolates as any known species of Pseudomonas. Based on the combination of genetic and phenotypic data, we conclude that these isolates represent two novel Pseudomonas species, for which we propose the names Pseudomonas boreofloridensis sp. nov. (K1, K13^T, NCPPB 4759=LMG 33364) and Pseudomonas citrulli sp. nov. (K18^T, NCPPB 4761=LMG 33365). The specific epithet boreofloridensis was chosen for the geographic location of isolation (northern Florida), while citrulli designates the host of origin (C. lanatus).