Journal of Microbiology

Journal Article

Description of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fish: Do-Hun Gim , So-Yeon Lee , Jeong Eun Han , Jae-Yun Lee , Seo Min Kang , Jin-Woo Bae; J. Microbiol. 2022;60(11):1061-1069. Published online September 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2250-5

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Three novel strains, (D17T, D13, and D25T) isolated from the gut of the Korean dark sleeper (Odontobutis platycephala), Kumgang fat minnow (Rhynchocypris kumgangensis), and the Korean oily bitterling (Tanakia koreensis) were identified as two novel species. Strains D17T and D13 showed the highest similarities in 16S rRNA gene and complete genome sequences to Deefgea rivuli WB 3.4-79T (98.0% and 97.9%, respectively, of 16S rRNA gene sequence similarity, 77.8% and 77.7%, respectively, of orthologous average nucleotide identity, Ortho- ANI, and 21.9% and 21.9%, respectively, of digital DNA-DNA hybridization, dDDH). Strain D17T showed the highest similarities in 16S rRNA gene and complete genome sequences to D13 (99.9% of 16S rRNA gene sequence similarity, 91.8% of OrthoANI, and 45.1% of dDDH); therefore, strains D17T and D13 were assigned as the same species. Strain D25T showed the highest similarities in 16S rRNA gene and complete genome sequences to D. chitinilytica Nsw-4T (98.2% of 16S rRNA gene sequence similarity, 82.4% of OrthoANI, and 25.1% of dDDH). Strains D17T and D13 were Gram-stain-negative, facultative anaerobes, rod-shaped, non-motile, and non-flagellated. Strain D25T was Gram-stain-negative, facultative anaerobe, rodshaped, and motile by a single polar flagellum. These strains had C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) as the major cellular fatty acids and possessed Q-8 as a major respiratory ubiquinone. All three strains contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. Based on polyphasic taxonomic data, strains D17T, D13, and D25T represent two novel species of the genus Deefgea. We propose the name Deefgea piscis sp. nov. for strains D17T (= KCTC 82958T = JCM 34941T) and D13 (= KCTC 92368), and Deefgea tanakiae sp. nov. for strain D25T (= KCTC 82959T = JCM 34942T).

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Variations of SSU rDNA Group I Introns in Different Isolates of Cordyceps militaris and the Loss of an Intron during Cross-Mating: Tiantian Lian , Tao Yang , Junde Sun , Suping Guo , Huaijun Yang , Caihong Dong; J. Microbiol. 2014;52(8):659-666. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3681-4

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Abstract

Cordyceps militaris, the type species of genus Cordyceps, is one of the most popular mushrooms and a nutraceutical in eastern Asia. It is considered a model organism for the study of Cordyceps species because it can complete its life cycle when cultured in vitro. In the present study, the occurrence and sequence variation of SSU rDNA group I introns, Cmi.S943 and Cmi.S1199, among different isolates of C. militaris were analyzed. Based on the secondary structure predictions, the Cmi.S943 intron has been placed in subgroup IC1, and the Cmi.S1199 intron has been placed in subgroup IE. No significant similarity between Cmi.S943 and Cmi.S1199 suggested different origins. Three genotypes, based on the frequency and distribution of introns, were described to discriminate the 57 surveyed C. militaris strains. It was found that the genotype was related to the stroma characteristics. The stromata of all of the genotype II strains, which possessed only Cmi.S943, could produce perithecium. In contrast, the stromata of all genotype III strains, which had both Cmi.S943 and Cmi.S1199, could not produce perithecium. Cmi.S1199 showed the lowest level of intra-specific variation among the tested strains. Group I introns can be lost during strain cross-mating. Therefore, we presumed that during cross-mating and recombination, intron loss could be driven by positive Darwinian selection due to the energetic cost of transcribing long introns.

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NOTE] Two Novel Talaromyces Species Isolated from Medicinal Crops in Korea: Hyunkyu Sang , Tae-Jin An , Chang Sun Kim , Gyu-Sub Shin , Gi-Ho Sung , Seung Hun Yu; J. Microbiol. 2013;51(5):704-708. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3361-9

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Abstract: Two novel biverticillate Talaromyces species, T. angelicus and T. cnidii, were collected from the medicinal crops Angelica gigas and Cnidium officinale, respectively, in Korea. Phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region and the β-tubulin gene as well as morphological analyses revealed that the two species differ from any known Talaromyces species. Talaromyces angelicus is related to T. flavovirens in the phylogeny of the ITS region, but the new species is grouped together with Penicillium liani and T. pinophilus in terms of its β-tubulin phylogeny, and its growth rate on Czapek yeast autolysate differs from that of T. flavovirens. Talaromyces cnidii is phylogenetically similar to T. siamensis, but exhibits differences in the morphologies of the colony margin, metulae, and conidia.

NOTE] Penicillium daejeonium sp. nov., a New Species Isolated from a Grape and Schisandra Fruit in Korea: Hyunkyu Sang , Tae-Jin An , Chang Sun Kim , Young Phil Choi , Jian-Xin Deng , Narayan Chandra Paul , Gi-Ho Sung , Seung Hun Yu; J. Microbiol. 2013;51(4):536-539. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-3291-6

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Abstract: Two isolates of monoverticillate Penicillium species were collected from a grape and schisandra fruit in Korea. Multigene phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region and genes encoding β-tubulin (benA) and calmodulin (cmd), as well as morphological analyses revealed that the two isolates are members of the P. sclerotiorum complex in Penicillium subgenus Aspergilloides, but different from species of the P. sclerotiorum complex. The isolates are closely related to P. cainii, P. jacksonii, and P. viticola in terms of their multigene phylogeny, but their colony and conidiophore morphologies differ from those of closely related species. The name P. daejeonium is proposed for this unclassified new species belonging to the P. sclerotiorum complex in subgenus Aspergilloides.

Isolation, Characterization, and Evaluation of Wild Isolates of Lactobacillus reuteri from Pig Feces: Deog Yong Lee , Yeon-Soo Seo , Nabin Rayamajhi , Mi Lan Kang , Su In Lee , Han Sang Yoo; J. Microbiol. 2009;47(6):663-672. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0124-8

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Abstract: Lactic acid bacteria (LAB) are a well-used probiotics for health improvements in both humans and animals. Despite of several benefits, non-host-specific LAB showed poor probiotics effects due to difficulty in colonization and competition with normal flora. Therefore, the feasibility of porcine LAB isolates was evaluated as a probiotics. Ten of 49 Lactobacillus spp. isolates harbored 2~10 kb plasmid DNA. Seven strains were selected based on the safety test, such as hemolytic activity, ammonia, indole, and phenylalanine production. After safety test, five strains were selected again by several tests, such as epithelial adherence, antimicrobial activity, tolerance against acid, bile, heat, and cold-drying, and production of acid and hydrogen peroxide. Then, enzyme profiles (ZYM test) and antibiotics resistance were analyzed for further characterization. Five Lactobacillus reuteri isolates from pig feces were selected by safety and functional tests. The plasmid DNA which was able to develop vector system was detected in the isolates. Together with these approaches, pig-specific Lactobacillus spp. originated from pigs were selected. These strains may be useful tools to develop oral delivery system.

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