Journal of Microbiology

Jeong-Seon Kim

4 Articles

Comparative genomics of Lactobacillus species as bee symbionts and description of Lactobacillus bombintestini sp. nov., isolated from the gut of Bombus ignitus: Jun Heo , Soo-Jin Kim , Jeong-Seon Kim , Seung-Beom Hong , Soon-Wo Kwon; J. Microbiol. 2020;58(6):445-455. Published online March 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9596-3

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The Lactobacillus genus is widely used for fermentation of plant materials and dairy products. These species are typically found in highly specialized environments, with the bee gut serving as one of the niche locations in which Lactobacillus is detected. Lactobacillus species isolated from the bee gut and bee-related habitats were phylogenetically classified into three distinct groups, Lactobacillus kunkeei, Firm-4, and Firm-5. The L. kunkeei group was clearly differentiated from other members of the Lactobacillus buchneri group isolated from non-bee habitats. In comparison with non-bee members of the L. buchneri group, three bee-symbiotic Lactobacillus groups had a small-sized genome with low G + C content and showed a sharp reduction in the number of genes involved in energy production, carbohydrate transport and metabolism, and amino acid transport and metabolism. In addition, all three groups lacked the mutY gene, which encodes A/G-specific adenine glycosylase. The phylogenetic dendrogram based on the presence or absence of 1,199 functional genes indicated that these bee-symbiotic groups experienced convergent evolution. The occurrence of convergent evolution is thought to stem from the three bee-symbiotic groups sharing a similar habitat, i.e., the bee gut. The causative factor underlying genomic reduction was postulated to be mutY, which was absent in all three groups. Here, a novel strain, BHWM-4T, isolated from the gut of Bombus ignites was studied using polyphasic taxonomy and classified as a new member of the L. kunkeei group. The strain was Gram-positive, facultative anaerobic, and rod-shaped. The 16S ribosomal RNA gene sequence and genome analysis revealed that strain BHWM-4T was clustered into the L. kunkeei group, forming a compact cluster with L. kunkeei and Lactobacillus apinorum. Biochemical, chemotaxonomic, and genotypic data of strain BHWM-4T supports the proposal of a novel species, Lactobacillus bombintestini sp. nov., whose type strain is BHWM-4T (= KACC 19317T = NBRC 113067T).

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Paraflavitalea soli gen. nov., sp. nov., isolated from greenhouse soil: Jun Heo , Hang-Yeon Weon , Hayoung Cho , Seung-Beom Hong , Jeong-Seon Kim , Soo-Jin Kim , Soon-Wo Kwon; J. Microbiol. 2020;58(1):17-23. Published online November 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9236-y

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Abstract PDF

A bacterial strain designated 5GH32-13T was isolated from greenhouse soil in Yongin-city, Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, motile rods of two different shapes. The strain was catalase-positive and oxidasenegative. Flexirubin-like pigments were not detected. β-Carotene was produced. The strain grew in the range of 10–37°C (optimum of 28–30°C) and pH 6–8 (optimum of pH 7) and tolerated up to 1% (w/v) NaCl (optimum of 0%). According to the 16S rRNA gene sequence comparison, strain 5GH32- 13T shared a sequence similarity of less than 96.0% with all validly named taxa, having the highest sequence similarity with Pseudoflavitalea soli KIS20-3T (95.8%), Pseudoflavitalea rhizosphaerae T16R-265T (95.4%), Flavitalea gansuensis JCN-23T (95.3%), Pseudobacter ginsenosidimutans Gsoil 221T (95.3%), and Flavitalea populi HY-50RT (95.2%). A phylogenetic tree showed that strain 5GH32-13T was not grouped consistently into any specific genus. Its only polyamine was homospermidine, and its major fatty acids (> 10% of total fatty acids) were iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. The strain’s only respiratory quinone was MK-7, and its polar lipids were phosphatidylethanolamine, one unidentified phospholipid, six unidentified aminolipids and four unidentified lipids. Its DNA G + C content was 47.5 mol%. The results from chemotaxonomic, phenotypic and phylogenetic analyses indicated that strain 5GH32-13T represents a novel species of a novel genus of the family Chitinophagaceae, and the name Paraflavitalea soli gen. nov., sp. nov. is proposed. The type strain is 5GH32-13T (= KACC 17331T = JCM 33061T).

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Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter: Soo-Jin Kim , Hayoung Cho , Jae-Hyung Ahn , Hang-Yeon Weon , Jae-Ho Joa , Jeong-Seon Kim , Soon-Wo Kwon; J. Microbiol. 2019;57(10):836-841. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9118-3

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A Gram-stain-positive, rod-shaped, non-endospore-forming, motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13arT was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4–35°C (optimum, 28–30°C), pH 5.0–9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13arT belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88T (98.5%), Paenibacillus hordei RH-N24T (98.4%) and Paenibacillus nicotianae YIM h-19T (98.1%). The major fatty acid was anteiso-C15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13arT represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13arT (= KACC 18728T = NBRC 112013T).

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Chujaibacter soli gen. nov., sp. nov., isolated from soil: Soo-Jin Kim , Jae-Hyung Ahn , Hang-Yeon Weon , Seung-Beom Hong , Soon-Ja Seok , Jeong-Seon Kim , Soon-Wo Kwon; J. Microbiol. 2015;53(9):592-597. Published online August 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5136-y

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A Gram-staining-negative, aerobic, non-flagellated, rod-shaped bacterial strain, KIS55-21T, was isolated from a soil sample from Chuja Island, Jeju Province, Republic of Korea. Strain KIS55-21T grew optimally at pH 7.0, at 28–30°C and in the presence of 0% (w/v) NaCl. Neighbor-joining and maximum-likelihood trees based on the 16S rRNA gene sequences revealed that strain KIS55-21T fell within the family Xanthomonadaceae and was closely related to Metallibacterium scheffleri DKET. Strain KIS55-21T exhibited the highest 16S rRNA gene sequence similarity (92.6%) to that of M. scheffleri DKET, with similarities of less than 92.0% to those of the genera Dokdonella, Rhodanobacter, Aquimonas, and Frateuria. Strain KIS55-21T contained ubiquinone-8 (Q-8) as the predominant ubiquinone, iso-C17:0, summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl), anteiso-C17:0 and C16:0 as the major fatty acids, and phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylmonomethylethanolamine as the main polar lipids. The DNA G+C content of strain KIS55-21T was 65.9 mol%. Differential phenotypic and chemotaxonomic properties and phylogenetic data of strain KIS55-21T demonstrated that this strain is distinguishable from closely related genera within the family Xanthomonadaceae. On the basis of the data presented, strain KIS55-21T is considered to represent a novel genus and species, for which the name Chujaibacter soli gen. nov., sp. nov. is proposed. The type strain is KIS55-21T (=KACC 16971T =DSM 28578T).

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