Journal of Microbiology

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Medium Chain Length Polyhydroxyalkanoate Production by Engineered Pseudomonas gessardii Using Acetate-formate as Carbon Sources: Woo Young Kim, Seung-Jin Kim, Hye-Rin Seo, Yoonyong Yang, Jong Seok Lee, Moonsuk Hur, Byoung-Hee Lee, Jong-Geol Kim, Min-Kyu Oh; J. Microbiol. 2024;62(7):569-579. Published online May 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00136-x

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Production of medium chain length polyhydroxyalkanoate (mcl-PHA) was attempted using Pseudomonas gessardii NIBRBAC000509957, which was isolated from Sunchang, Jeollabuk-do, Republic of Korea (35°24'27.7"N, 127°09'13.0"E) and effectively utilized acetate and formate as carbon sources. We first evaluated the utilization of acetate as a carbon source, revealing optimal growth at 5 g/L acetate. Then, formate was supplied to the acetate minimal medium as a carbon source to enhance cell growth. After overexpressing the acetate and formate assimilation pathway enzymes, this strain grew at a significantly higher rate in the medium. As this strain naturally produces PHA, it was further engineered metabolically to enhance mcl-PHA production. The engineered strain produced 0.40 g/L of mcl-PHA with a biomass content of 30.43% in fed-batch fermentation. Overall, this strain can be further developed to convert acetate and formate into valuable products.

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Formate-driven photoautotrophic growth and biopolymer storage in anaerobic purple bacteria
Mohammad Adib Ghazali Abdul Rahman, Bronwyn Laycock, Steven Pratt, Damien J. Batstone
Bioresource Technology.2025; 434: 132753. CrossRef
Sulphide and oleic acid synergism in accelerating mcl-PHA biopolymer production in Pseudomonas aeruginosa MCC 5300 by modulating electron transport system
Raghavendra Paduvari, Divyashree Somashekara
Biochemistry and Biophysics Reports.2025; 44: 102286. CrossRef
Unlocking efficient polyhydroxyalkanoate production by Gram-positive Priestia megaterium using waste-derived feedstocks
Xinyi Bai, Libo Xu, Kang Li, Guangbao Zhang, Mengjun Zhang, Yi Huang
Microbial Cell Factories.2025;[Epub] CrossRef

Sporosarcina jeotgali sp. nov., Sporosarcina oncorhynchi sp. nov., and Sporosarcina trichiuri sp. nov., Isolated from Jeotgal, a Traditional Korean Fermented Seafood: Ah-In Yang, Bora Kim, Sung-Hong Joe, Hae-In Joe, Hanna Choe, Ki Hyun Kim, Min Ok Jun, Na-Ri Shin; J. Microbiol. 2024;62(4):285-296. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00106-3

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Three novel, Gram-stain-positive, obligate aerobic, catalase- and oxidase-positive bacterial strains, designated B2O-1(T), T2O-4(T), and 0.2-SM1T-5(T), were isolated from jeotgal, a traditional Korean fermented seafood. Strains B2O-1(T), T2O-4(T), and 0.2-SM1T-5(T) exhibited distinct colony colors, characterized by pink, yellow, and red opaque circular colonies, respectively. Phylogenetic analysis revealed that three strains formed a paraphyletic clade within the genus Sporosarcina and shared < 99.0% similarity with Sporosarcina aquimarina KCTC 3840(T) and Sporosarcina saromensis KCTC 13119(T) in their 16S rRNA gene sequences. The three strains exhibiting Orthologous Average Nucleotide Identity values < 79.3% and digital DNA-DNA hybridization values < 23.1% within the genus Sporosarcina affirmed their distinctiveness. Strains B2O-1(T), T2O-4(T), and 0.2-SM1T-5(T) contained MK-7 as a sole respiratory menaquinone and A4α type peptidoglycan based on lysine with alanine, glutamic acid, and aspartic acid. The common polar lipids include diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Strain T2O-4(T) contained one unidentified phospholipid, whereas strain 0.2-SM1T-5(T) contained two unidentified phospholipids. Cellular fatty acid profiles, with C(15:0) anteiso as the major fatty acid, supported the affiliation of the three strains to the genus Sporosarcina. Based on the polyphasic characteristics, strains B2O-1(T) (= KCTC 43506(T) = JCM 36032(T)), T2O-4(T) (= KCTC 43489(T) = JCM 36031(T)), and 0.2-SM1T-5(T) (= KCTC 43519(T) = JCM 36034(T)) represent three novel species within the genus Sporosarcina, named Sporosarcina jeotgali sp. nov., Sporosarcina oncorhynchi sp. nov., and Sporosarcina trichiuri sp. nov., respectively.

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Notification of changes in taxonomic opinion previously published outside the IJSEM. List of Changes in Taxonomic Opinion no. 41
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Brevibacterium koreense sp. nov., a moderately halophilic bacterium isolated from jogae-jeotgal, a Korean fermented seafood
Sohee Nam, Yujin Kim, Min Ji Lee, Yeon Bee Kim, Jeong Ui Yun, Mi-Ja Jung, Hye Seon Song, Se Hee Lee, Seok-Jun Kim, Tae Woong Whon
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov., isolated from human feces, and the reclassification of Bacteroides koreensis Shin et al. 2017 and Bacteroides kribbi Shin et al. 2017 as later heterotypic synonyms of Bacteroides ovatus Egg
Ah-In Yang, Bora Kim, Woorim Kang, Hae-In Joe, Na-Ri Shin
Journal of Microbiology.2025; 63(6): e2502006. CrossRef
Validation List no. 220. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp: Juseok Kim , Joon Yong Kim , Hye Seon Song , In-Tae Cha , Seong Woon Roh , Se Hee Lee; J. Microbiol. 2019;57(6):444-449. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8704-8

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A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA- 4604T was observed at 10–40°C (optimum, 37°C), pH 6.0–10.0 (optimum, pH 7.0), and in the presence of 0–8.0% (w/v) NaCl (optimum, 0–2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA- 4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).

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Bacteroides faecium sp. nov. isolated from human faeces
Juseok Kim, Hye Seon Song, Joon Yong Kim, Tae Woong Whon, Won-Hyong Chung, Young-Do Nam, Yoon-E Choi, Seong Woon Roh
International Journal of Systematic and Evolutionary Microbiology.2023;[Epub] CrossRef
ODFM, an omics data resource from microorganisms associated with fermented foods
Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
Scientific Data.2021;[Epub] CrossRef
Flaviflexus ciconiae sp. nov., isolated from the faeces of the oriental stork, Ciconia boyciana
Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2020; 70(10): 5439. CrossRef
Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa
Anusha Rai, Smita N, Suresh G, Shabbir A, Deepshikha G, Sasikala Ch, Ramana Ch.V
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1720. CrossRef
Pectin Degradation is an Important Determinant for Alfalfa Silage Fermentation through the Rescheduling of the Bacterial Community
Bing Wang, Zhiqiang Sun, Zhu Yu
Microorganisms.2020; 8(4): 488. CrossRef
Iodobacter ciconiae sp. nov., a bacterium isolated from feces of oriental stork, Ciconia boyciana
Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2019; 69(9): 2948. CrossRef

Research Support, Non-U.S. Gov't

NOTE] Halomonas jeotgali sp. nov., a New Moderate Halophilic Bacterium Isolated from a Traditional Fermented Seafood: Min-Soo Kim , Seong Woon Roh , Jin-Woo Bae; J. Microbiol. 2010;48(3):404-410. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-0032-y

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A moderate halophilic, Gram-negative, non-motile, rod-shape, and aerobe designated as strain HwaT was isolated from traditional fermented Korean seafood, which presented as a single cell or paired cells. Optimal growth occurred at 25°C in 10% (w/v) salts at pH 7.0-8.0; however, growth occurred in a temperature range of 10-32°C, a salts concentration of 5-25% (w/v) and pH 5.0-10.0. Tests for oxidase and catalase were positive. The cells produced poly-β-hydroxybutyric acid, but not exopolysaccharide. Based on the 16S rRNA gene sequence, not only was there low similarity between strain HwaT and all other species (94.1% similarity with H. subglaciescola DSM 4683T, 94.0% similarity with H. sulfidaeris Esulfide1T, 93.6% similarity with H. cerina SP4T and 93.0% similarity with H. halodurans DSM 5160T), but the phylogenetic analysis revealed that the isolate may be classified as a novel species belonging to the genus Halomonas in the class Gammaproteobacteria. The predominant fatty acids of strain HwaT were C18:1 ω7c, C16:0, C12:0 3-OH and C16:1 ω7c/C15:0 iso 2-OH. The DNA G+C content was calculated as 61.7 mol%. Based on phenotypic, genotypic, and phylogenetic characteristics, it is proposed that the strain designated as HwaT be assigned to the genus Halomonas as Halomonas jeotgali sp. nov. (=KCTC 22487T =JCM 15645T).

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Determination of the safety of Halomonas sp. KM-1-derived d-β-hydroxybutyric acid and its fermentation-derived impurities in mice and Japanese adults
Shohei Katsuya, Yoshikazu Kawata, Masayuki Sugimoto, Taku Nishimura, Jun Tsubota
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Ah-In Yang, Bora Kim, Sung-Hong Joe, Hae-In Joe, Hanna Choe, Ki Hyun Kim, Min Ok Jun, Na-Ri Shin
Journal of Microbiology.2024; 62(4): 285. CrossRef
Halomonas citrativorans sp. nov., Halomonas casei sp. nov. and Halomonas colorata sp. nov., isolated from French cheese rinds
Caroline Isabel Kothe, Christophe Monnet, Françoise Irlinger, Mathieu Virsolvy, Anja Frühling, Meina Neumann-Schaal, Jacqueline Wolf, Pierre Renault
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Genomic attributes and characterization of novel exopolysaccharide-producing bacterium Halomonas piscis sp. nov. isolated from jeotgal
Bora Kim, Ah-In Yang, Hae-In Joe, Ki Hyun Kim, Hanna Choe, Sung-Hong Joe, Min Ok Jun, Na-Ri Shin
Frontiers in Microbiology.2023;[Epub] CrossRef
Halomonas flagellata sp. nov., a halophilic bacterium isolated from saline soil in Xinjiang
Yin Huang, Rashidin Abdugheni, Jinbiao Ma, Rui Wang, Lei Gao, Yonghong Liu, Wenjun Li, Man Cai, Li Li
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A long-awaited taxogenomic investigation of the family Halomonadaceae
Rafael R. de la Haba, David R. Arahal, Cristina Sánchez-Porro, Maria Chuvochina, Stijn Wittouck, Philip Hugenholtz, Antonio Ventosa
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David F. Woods, Iwona M. Kozak, Fergal O'Gara
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Hoang Thi Lan Anh, Yoshikazu Kawata, Luu Thi Tam, Le Thi Thom, Nguyen Cam Ha, Hoang Thi Minh Hien, Ngo Thi Hoai Thu, Pham Quang Huy, Dang Diem Hong
Archives of Microbiology.2020; 202(5): 1043. CrossRef
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Saber Khelaifia, Aurelia Caputo, Claudia Andrieu, Frederique Cadoret, Nicholas Armstrong, Caroline Michelle, Jean-Christophe Lagier, Felix Djossou, Pierre-Edouard Fournier, Didier Raoult
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Louise Vermote, Marko Verce, Luc De Vuyst, Stefan Weckx
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Halomonas nigrificans sp. nov., isolated from cheese
Folarin A. Oguntoyinbo, Margo Cnockaert, Gyu-Sung Cho, Jan Kabisch, Horst Neve, Wilhelm Bockelmann, Mareike Wenning, Charles M. A. P. Franz, Peter Vandamme
International Journal of Systematic and Evolutionary Microbiology .2018; 68(1): 371. CrossRef
Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment
Jae-Chan Lee, Su-Jin Kim, Kyung-Sook Whang
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Woo Yong Jung, Hyo Jung Lee, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology.2016; 66(2): 731. CrossRef
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Guiming Dou, Wei He, Hongcan Liu, Yuchao Ma
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List of new names and new combinations previously effectively, but not validly, published

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