Journal of Microbiology

Protocol

Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates: Yeong-Jun Park, Jae Kyu Lim, Yeon-Ju Lee, Kae Kyoung Kwon; J. Microbiol. 2025;63(9):e2507003. Published online September 30, 2025; DOI: https://doi.org/10.71150/jm.2507003

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Abstract PDF: Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts’ immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.

Full articles

Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., isolated from Korean coastal surface seawater: Jisoo Han, Yeonjung Lim, Mirae Kim, Jang-Cheon Cho; J. Microbiol. 2025;63(8):e2504017. Published online August 13, 2025; DOI: https://doi.org/10.71150/jm.2504017

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Abstract PDF Supplementary Material: Two Gram-stain-negative, obligately aerobic, non-motile, short rod-shaped bacteria, designated IMCC43871^T and IMCC45206^T, were isolated from coastal surface seawater collected from the Yellow Sea and the South Sea of Korea, respectively. The two strains shared 99.2% 16S rRNA gene sequence similarity with each other and exhibited ≤ 98.4% similarity to three described Rubrivirga species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between IMCC43871^T and IMCC45206^T were 88.5% and 36.3%, respectively, confirming that they represent two distinct species. Their ANI (≤ 77.7%) and dDDH (≤ 21.4%) values relative to the type strains of the genus Rubrivirga further supported the recognition of strains IMCC43871^T and IMCC45206^T as two novel species within the genus. The complete genomes of IMCC43871^T (4.17 Mb, 71.8% G + C content) and IMCC45206^T (4.17 Mb, 72.8% G + C content) fall within the known genomic range of the genus. Cellular fatty acid, quinone, and polar lipid profiles were consistent with the chemotaxonomic features of the genus Rubrivirga, supporting their affiliation with the genus. Based on phylogenetic, genomic, and phenotypic evidence, strains IMCC43871^T and IMCC45206^T are proposed as two novel species, Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., respectively. The type strains are IMCC43871^T (= KCTC 102072^T = NBRC 116463^T) and IMCC45206^T (= KCTC 92925^T = NBRC 116172^T = CCTCC AB 2023136^T).

Phycobium rhodophyticola gen. nov., sp. nov. and Aliiphycobium algicola gen. nov., sp. nov., isolated from the phycosphere of marine red algae: Jeong Min Kim, Woonhee Baek, Byeong Jun Choi, Hülya Bayburt, Jae Kyeong Lee, Sung Chul Lee, Che Ok Jeon; J. Microbiol. 2025;63(6):e2503014. Published online June 30, 2025; DOI: https://doi.org/10.71150/jm.2503014

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Abstract PDF Supplementary Material

Two Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacteria, designated D3-12ᵀ and G2-2ᵀ, were isolated from the phycosphere of marine red algae. Both strains exhibited catalase- and oxidase-positive activities. Strain D3-12ᵀ grew optimally at 30°C, pH 7.0, and 2.0–3.0% (w/v) NaCl, while strain G2-2ᵀ showed optimal growth at 30°C, pH 7.0, and 2.0% NaCl. Ubiquinone-10 was the sole respiratory quinone in both strains. The major fatty acids (> 5%) in strain D3-12ᵀ were feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), 11-methyl-C_18:1 ω7c, and C_16:0, while strain G2-2ᵀ contained summed feature 8 and C_16:0. The predominant polar lipids in strain D3-12ᵀ were phosphatidylcholine, phosphatidylglycerol, and phosphatidylethanolamine, whereas strain G2-2ᵀ contained phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G + C content was 59.9% for strain D3-12ᵀ and 60.2% for strain G2-2ᵀ. Phylogenetic analyses based on 16S rRNA and whole-genome sequences placed both strains into distinct lineages within the family Roseobacteraceae, separate from previously described genera. Genome-based relatedness metrics, including average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity, and percentage of conserved proteins, further confirmed that these strains represent novel genera. Based on phenotypic, chemotaxonomic, and molecular characteristics, strains D3-12ᵀ and G2-2ᵀ are proposed as novel genera: Phycobium rhodophyticola gen. nov., sp. nov. (D3-12ᵀ = KACC 22712ᵀ = JCM 35528ᵀ) and Aliiphycobium algicola gen. nov., sp. nov. (G2-2ᵀ = KACC 22602ᵀ = JCM 35752ᵀ). Additionally, metabolic features relevant to interactions with marine algae, including genes associated with carbohydrate-active enzymes, vitamin biosynthesis, phenylacetic acid production, and bacterioferritin synthesis, were bioinformatically investigated.

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Aquimarina rhodophyticola sp. nov. and Aquimarina besae sp. nov., Isolated from Marine Red Algae
Jeong Min Kim, Byeong Jun Choi, Hülya Bayburt, Dong Min Han, Che Ok Jeon
Current Microbiology.2025;[Epub] CrossRef
Carotenoid-Producing Qipengyuania algicola sp. nov. and Qipengyuania rhodophyticola sp. nov., Isolated from Marine Algae, and Emended Description of the Genus Qipengyuania Xu et al. 2020
Jae Kyeong Lee, Min Woo Lee, Chae Yeong Moon, Jeong Min Kim, Hülya Bayburt, Byeong Jun Choi, Che Ok Jeon
Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef

Journal Article

Synthesis of pinene in the industrial strain Candida glycerinogenes by modification of its mevalonate pathway: Tengfei Ma , Hong Zong , Xinyao Lu , Bin Zhuge; J. Microbiol. 2022;60(12):1191-1200. Published online October 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2344-0

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Abstract PDF

Terpenes have many applications and are widely found in nature, but recent progress in synthetic biology has enabled the use of microorganisms as chassis cells for the synthesis of these compounds. Candida glycerinogenes (C. glycerinogenes) is an industrial strain that may be developed as a chassis for the synthesis of terpenes since it has a tolerance to hyperosmolality and high sugar, and has a complete mevalonate (MVA) pathway. However, monoterpenes such as pinene are highly toxic, and the tolerance of C. glycerinogenes to pinene was investigated. We also measured the content of mevalonate and squalene to evaluate the strength of the MVA pathway. To determine terpene synthesis capacity, a pathway for the synthesis of pinene was constructed in C. glycerinogenes. Pinene production was improved by overexpression, gene knockdown and antisense RNA inhibition. Pinene production was mainly enhanced by strengthening the upstream MVA pathway and inhibiting the production of by-products from the downstream pathway. With these strategies, yield could be increased by almost 16 times, to 6.0 mg/L. Overall, we successfully constructed a pinene synthesis pathway in C. glycerinogenes and enhanced pinene production through metabolic modification.

Citations

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Recent advances in genome mining and synthetic biology for discovery and biosynthesis of natural products
Mingpeng Wang, Lei Chen, Zhaojie Zhang, Qinhong Wang
Critical Reviews in Biotechnology.2025; 45(1): 236. CrossRef
Engineering a complete mevalonate pathway in Chlamydomonas reinhardtii for enhanced isoprenoid production
Jingkai Wang, Muhammad Anwar, Jiancheng Li, Lin Dan, Bin Jia, Zhangli Hu
Algal Research.2025; 88: 103987. CrossRef
Two-Phase Fermentation Systems for Microbial Production of Plant-Derived Terpenes
Tuo Li, Ximeng Liu, Haoyu Xiang, Hehua Zhu, Xuan Lu, Baomin Feng
Molecules.2024; 29(5): 1127. CrossRef
Acetic acid stress and utilization synergistically enhance squalene biosynthesis in Candida glycerinogenes
Zhenzhen You, Xueqing Du, Hong Zong, Xinyao Lu, Bin Zhuge
Biochemical Engineering Journal.2024; 210: 109413. CrossRef
Recent developments in enzymatic and microbial biosynthesis of flavor and fragrance molecules
Roman M. Dickey, Madan R. Gopal, Priyanka Nain, Aditya M. Kunjapur
Journal of Biotechnology.2024; 389: 43. CrossRef
Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica
Dong-Xun Li, Qi Guo, Yu-Xin Yang, Shun-Jie Jiang, Xiao-Jun Ji, Chao Ye, Yue-Tong Wang, Tian-Qiong Shi
ACS Synthetic Biology.2024; 13(6): 1647. CrossRef
Gene Editing of Candida glycerinogenes by Designed Toxin–Antitoxin Cassette
Wen Lv, Xinyao Lu, Bin Zhuge, Hong Zong
ACS Synthetic Biology.2024; 13(3): 816. CrossRef
Candida glycerinogenes-Promoted α-Pinene and Squalene Co-production Strategy Based on α-Pinene Stress
Tengfei Ma, Hong Zong, Xinyao Lu, Bin Zhuge
Journal of Agricultural and Food Chemistry.2023; 71(13): 5250. CrossRef

Meta-Analysis

Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets: Hyun-Seok Oh , Uigi Min , Hyejin Jang , Namil Kim , Jeongmin Lim , Mauricio Chalita , Jongsik Chun; J. Microbiol. 2022;60(5):533-549. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1526-0

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Abstract PDF

The disruption of the human gut microbiota has been linked to host health conditions, including various diseases. However, no reliable index for measuring and predicting a healthy microbiome is currently available. Here, the sequencing data of 1,663 Koreans were obtained from three independent studies. Furthermore, we pooled 3,490 samples from public databases and analyzed a total of 5,153 fecal samples. First, we analyzed Korean gut microbiome covariates to determine the influence of lifestyle on variation in the gut microbiota. Next, patterns of microbiota variations across geographical locations and disease statuses were confirmed using a global cohort and disease data. Based on comprehensive comparative analysis, we were able to define three enterotypes among Korean cohorts, namely, Prevotella type, Bacteroides type, and outlier type. By a thorough categorization of dysbiosis and the evaluation of microbial characteristics using multiple datasets, we identified a wide spectrum of accuracy levels in classifying health and disease states. Using the observed microbiome patterns, we devised an index named the gut microbiome index (GMI) that could consistently predict health conditions from human gut microbiome data. Compared to ecological metrics, the microbial marker index, and machine learning approaches, GMI distinguished between healthy and non-healthy individuals with a higher accuracy across various datasets. Thus, this study proposes a potential index to measure health status of gut microbiome that is verified from multiethnic data of various diseases, and we expect this model to facilitate further clinical application of gut microbiota data in future.

Citations

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Methodology for Assessing Patient Centricity and Data Integrity in Clinical Trials With Decentralized Elements: A Pilot Trial on Mastic Gum
Jiyeon Park, Ki Young Huh, Jae‐Yong Chung, Kyung‐Sang Yu
Clinical and Translational Science.2025;[Epub] CrossRef
A comparison of the prevalence of respiratory pathogens and opportunistic respiratory pathogenic profile of ‘clean’ and ‘unclean’ removable dental prostheses
Tong Wah Lim, Shi Huang, Yufeng Zhang, Michael Francis Burrow, Colman McGrath
Journal of Dentistry.2024; 145: 104968. CrossRef
Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing
Tong Wah Lim, Shi Huang, Yuesong Jiang, Yufeng Zhang, Michael Francis Burrow, Colman McGrath
Journal of Oral Microbiology.2024;[Epub] CrossRef
Gut microbial signatures in clinically stable ulcerative colitis according to the mucosal state and associated symptoms
Soyoung Kim, Yeonjae Jung, Seung Bum Lee, Hyun‐Seok Oh, Sung Noh Hong
Journal of Gastroenterology and Hepatology.2024; 39(2): 319. CrossRef
Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease
Don Gueu Park, Woorim Kang, In-Ja Shin, Mauricio Chalita, Hyun-Seok Oh, Dong-Wook Hyun, Hyun Kim, Jongsik Chun, Young-Sil An, Eun Jeong Lee, Jung Han Yoon
Neurobiology of Disease.2024; 201: 106655. CrossRef
Should Routine Diagnostics Implement Gut Microbiota Analysis?
Giuseppe Guido Maria Scarlata, Ludovico Abenavoli
The International Journal of Gastroenterology and Hepatology Diseases.2024;[Epub] CrossRef
Feasibility study for a fully decentralized clinical trial in participants with functional constipation symptoms
Ki Young Huh, Woo Kyung Chung, Jiyeon Park, SeungHwan Lee, Min‐Gul Kim, Jaeseong Oh, Kyung‐Sang Yu
Clinical and Translational Science.2023; 16(11): 2177. CrossRef
Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health
Car Reen Kok, Devin Rose, Robert Hutkins
Annual Review of Food Science and Technology.2023; 14(1): 157. CrossRef
Effects of the multidomain intervention with nutritional supplements on cognition and gut microbiome in early symptomatic Alzheimer’s disease: a randomized controlled trial
Eun Hye Lee, Geon Ha Kim, Hee Kyung Park, Hae Jin Kang, Yoo Kyoung Park, Hye Ah Lee, Chang Hyung Hong, So Young Moon, Woorim Kang, Hyun-Seok Oh, Hai-Jeon Yoon, Seong Hye Choi, Jee Hyang Jeong
Frontiers in Aging Neuroscience.2023;[Epub] CrossRef
Fecal microbial signatures of healthy Han individuals from three bio-geographical zones in Guangdong
Litao Huang, Liting Deng, Changhui Liu, Enping Huang, Xiaolong Han, Cheng Xiao, Xiaomin Liang, Huilin Sun, Chao Liu, Ling Chen
Frontiers in Microbiology.2022;[Epub] CrossRef

Journal Articles

Spot 42 RNA regulates putrescine catabolism in Escherichia coli by controlling the expression of puuE at the post-transcription level: Xin Sun , Ruyan Li , Guochen Wan , Wanli Peng , Shuangjun Lin , Zixin Deng , Rubing Liang; J. Microbiol. 2021;59(2):175-185. Published online February 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0421-4

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Abstract PDF

Putrescine, a typical polyamine compound important for cell growth and stress resistance, can be utilized as an energy source. However, the regulation of its catabolism is unclear. Here the small RNA (sRNA) Spot 42, an essential regulator of carbon catabolite repression (CCR), was confirmed to participate in the post-transcriptional regulation of putrescine catabolism in Escherichia coli. Its encoding gene spf exclusively exists in the γ-proteobacteria and contains specific binding sites to the 5􍿁-untranslated regions of the puuE gene, which encodes transaminase in the glutamylated putrescine pathway of putrescine catabolism converting γ-aminobutyrate (GABA) into succinate semialdehyde (SSA). The transcription of the spf gene was induced by glucose, inhibited by putrescine, and unaffected by PuuR, the repressor of puu genes. Excess Spot 42 repressed the expression of PuuE significantly in an antisense mechanism through the direct and specific base-pairing between the 51–57 nt of Spot 42 and the 5􍿁- UTR of puuE. Interestingly, Spot 42 mainly influenced the stability of the puuCBE transcript. This work revealed the regulatory role of Spot 42 in putrescine catabolism, in the switch between favorable and non-favorable carbon source utilization, and in the balance of metabolism of carbon and nitrogen sources.

Citations

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Regulation of TCA cycle genes by srbA sRNA: Impacts on Pseudomonas aeruginosa virulence and survival
Piyali Saha, Samir Kumar Mukherjee, Sk Tofajjen Hossain
Biochemical and Biophysical Research Communications.2024; 737: 150520. CrossRef
Rational Design of High-Efficiency Synthetic Small Regulatory RNAs and Their Application in Robust Genetic Circuit Performance Through Tight Control of Leaky Gene Expression
Jun Ren, Nuong Thi Nong, Phuong N. Lam Vo, Hyang-Mi Lee, Dokyun Na
ACS Synthetic Biology.2024; 13(10): 3256. CrossRef

Comparative genomic analysis of selenium utilization traits in different marine environments: Muhammad Farukh; J. Microbiol. 2020;58(2):113-122. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9250-0

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Abstract PDF

Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.

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The selenophosphate synthetase family: A review
Bruno Manta, Nadezhda E Makarova, Marco Mariotti
Free Radical Biology and Medicine.2022; 192: 63. CrossRef
Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective
Yan Zhang, Jiao Jin, Biyan Huang, Huimin Ying, Jie He, Liang Jiang
Biomolecules.2022; 12(7): 917. CrossRef
Uses of Selenium Nanoparticles in the Plant Production
Iqra Bano, Sylvie Skalickova, Hira Sajjad, Jiri Skladanka, Pavel Horky
Agronomy.2021; 11(11): 2229. CrossRef

Overexpression and characterization of a novel cold-adapted and salt-tolerant GH1 β-glucosidase from the marine bacterium Alteromonas sp. L82: Jingjing Sun , Wei Wang , Congyu Yao , Fangqun Dai , Xiangjie Zhu , Junzhong Liu , Jianhua Hao; J. Microbiol. 2018;56(9):656-664. Published online August 23, 2018; DOI: https://doi.org/10.1007/s12275-018-8018-2

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Abstract PDF

A novel gene (bgl) encoding a cold-adapted β-glucosidase was cloned from the marine bacterium Alteromonas sp. L82. Based on sequence analysis and its putative catalytic conserved region, Bgl belonged to the glycoside hydrolase family 1. Bgl was overexpressed in E. coli and purified by Ni2+ affinity chromatography. The purified recombinant β- glucosidase showed maximum activity at temperatures between 25°C to 45°C and over the pH range 6 to 8. The enzyme lost activity quickly after incubation at 40°C. Therefore, recombinant β-glucosidase appears to be a cold-adapted enzyme. The addition of reducing agent doubled its activity and 2 M NaCl did not influence its activity. Recombinant β-glucosidase was also tolerant of 700 mM glucose and some organic solvents. Bgl had a Km of 0.55 mM, a Vmax of 83.6 U/mg, a kcat of 74.3 s-1 and kcat/Km of 135.1 at 40°C, pH 7 with 4-nitrophenyl-β-D-glucopyranoside as a substrate. These properties indicate Bgl may be an interesting candidate for biotechnological and industrial applications.

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Aiguo Li, Wenlu Liu, Xuehua Yu, Rui Han, Xinyu Xiong, Bo Guan, Youzhen Hu, Yongqin Ni, Jun Zeng
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International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
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Jinjian He, Jiajing Duan, Pinglian Yu, Yuying Li, Mansheng Wang, Xiu Zhang, Zishu Chen, Pengjun Shi
Current Research in Food Science.2024; 8: 100777. CrossRef
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Anna N Khusnutdinova, Hai Tran, Saloni Devlekar, Marco A Distaso, Ilya V Kublanov, Tatiana Skarina, Peter Stogios, Alexei Savchenko, Manuel Ferrer, Olga V Golyshina, Alexander F Yakunin, Peter N Golyshin
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Zeynep Gül Aytaş, Münir Tunçer, Çağrı Seda Kul, Sümeyye Cilmeli, Nurayan Aydın, Tuğrul Doruk, Ali Osman Adıgüzel
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Lichuang Cao, Ran Chen, Xin Huang, Shuifeng Li, Sufang Zhang, Xiangpeng Yang, Zongmin Qin, Wei Kong, Wei Xie, Yuhuan Liu
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The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT: Thinh-Phat Cao , Jin Myung Choi , Si Wouk Kim , Sung Haeng Lee; J. Microbiol. 2018;56(4):246-254. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7483-y

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The first crystal structure of a pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) from a marine methylotrophic bacterium, Methylophaga aminisulfidivorans MPT (MDHMas), was determined at 1.7 Å resolution. The active form of MDHMas (or MDHIMas) is a heterotetrameric α2β2, where each β-subunit assembles on one side of each of the α-subunits, in a symmetrical fashion, so that two β-subunits surround the two PQQ-binding pockets on the α-subunits. The active site consists of a PQQ molecule surrounded by a β-propeller fold for each α-subunit. Interestingly, the PQQ molecules are coordinated by a Mg2+ ion, instead of the Ca2+ ion that is commonly found in the terrestrial MDHI, indicating the efficiency of osmotic balance regulation in the high salt environment. The overall interaction of the β-subunits with the α-subunits appears tighter than that of terrestrial homologues, suggesting the efficient maintenance of MDHIMas integrity in the sea water environment to provide a firm basis for complex formation with MxaJMas or Cyt cL. With the help of the features mentioned above, our research may enable the elucidation of the full molecular mechanism of methanol oxidation by taking advantage of marine bacterium-originated proteins in the methanol oxidizing system (mox), including MxaJ, as the attainment of these proteins from terrestrial bacteria for structural studies has not been successful.

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A New record of four Penicillium species isolated from Agarum clathratum in Korea: Myung Soo Park , Seobihn Lee , Young Woon Lim; J. Microbiol. 2017;55(4):237-246. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6405-8

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Agarum clathratum, brown algae, play important ecological roles in marine ecosystem, but can cause secondary environ-ment pollution when they pile up on the beach. In order to resolve the environment problem by A. clathratum, we focus to isolate and identify Penicillium because many species are well known to produce extracellular enzymes. A total of 32 Penicillium strains were isolated from A. clathratum sam-ples that collected from 13 sites along the mid-east coast of Korea in summer. They were identified based on morpho-logical characters and phylogenetic analysis using β-tubulin DNA sequences as well as a combined dataset of β-tubulin and calmodulin. A total of 32 strains were isolated and they were identified to 13 Penicillium species. The commonly iso-lated species were Penicillium citrinum, P. roseomaculatum, and Penicillium sp. Among 13 Penicillium species, four spe-cies – P. bilaiae, P. cremeogriseum, P. madriti, and P. rose-omaculatum – have not been previously recorded in Korea. For these four new species records to Korea, we provide mor-phological characteristics of each strain.

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Research Support, Non-U.S. Gov'ts

Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment: Wonduck Kim , Jung-Hyun Lee , Kae Kyoung Kwon; J. Microbiol. 2016;54(5):347-352. Published online April 20, 2016; DOI: https://doi.org/10.1007/s12275-016-6048-1

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A Gram-staining-negative, thin rod-shaped, anaerobic bacterium designated MCWD3T was isolated from sediment of the deep sea in Ulleung Basin, East Sea, Korea. The ranges of temperature, pH and NaCl for growth of this strain were 15– 40°C (optimum 29°C), 5.0–10.0 (optimum pH 6.5), and 1–5%, respectively. The major fatty acids were iso-C15:0 (30%) and iso-C15:0 dimethyl acetal (17%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipids, phospholipids, and aminolipids. The fermentation product from yeast extract was acetate. Phylogenetic analysis based on 16S rRNA genes indicated that the isolate was related to Sporosalibacterium faouarense (92.8% sequence identity), Clostridiisalibacter paucivorans (92.6%), and Brassicibacter mesophilus (92.4%). However, the isolate was differentiated from these genera by both physiological and chemotaxonomical properties. On the basis of a polyphasic taxonomic analysis, we propose that MCWD3T represents a novel taxon with the name Abyssisolibacter fermentans gen. nov. sp. nov.

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Luteimonas dalianensis sp. nov., an Obligate Marine Bacterium Isolated from Seawater: Yanjuan Xin , Xupeng Cao , Peichun Wu , Song Xue; J. Microbiol. 2014;52(9):729-733. Published online August 2, 2014; DOI: https://doi.org/10.1007/s12275-014-3610-6

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A marine bacterial strain, designated OB44-3T, was isolated from a crude oil-contaminated seawater sample collected near Dalian Bay, China. Cells of strain OB44-3T were Gramnegative, aerobic, rod-shaped, and oxidase- and catalasepositive. The major fatty acids were branched-chain saturated iso-C15:0 (27.9%) and unsaturated iso-C17:1 ω9c (14.8%). The DNA G+C content was 64.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain OB44-3T was a member of the genus Luteimonas (95–96% 16S rRNA gene sequence similarity); its closest neighbors were the type strains of Luteimonas terricola (96% sequence similarity), Luteimonas mephitis (96%), and Luteimonas lutimaris (96%). On the basis of phenotypic, chemotaxonomic, and phylogenetic distinctiveness, strain OB44-3T was considered to represent a novel species of the genus Luteimonas. The name Luteimonas dalianensis sp. nov. is proposed, with strain OB44-3T (=CGMCC 1.12191T =JCM 18136T) as the type strain.

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Enhanced Production of Carboxymethylcellulase by a Marine Bacterium, Bacillus velezensis A-68, by Using Rice Hulls in Pilot-scale Bioreactor under Optimized Conditions for Dissolved Oxygen: Wa Gao , Hye-Jin Kim , Chung-Han Chung , Jin-Woo Lee; J. Microbiol. 2014;52(9):755-761. Published online July 30, 2014; DOI: https://doi.org/10.1007/s12275-014-4156-3

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The optimal conditions for the production of carboxymethylcellulase (CMCase) by Bacillus velezensis A-68 at a flask scale have been previously reported. In this study, the parameters involved in dissolved oxygen in 7 and 100 L bioreactors were optimized for the pilot-scale production of CMCase. The optimal agitation speed and aeration rate for cell growth of B. velezensis A-68 were 323 rpm and 1.46 vvm in a 7 L bioreactor, whereas those for the production of CMCase were 380 rpm and 0.54 vvm, respectively. The analysis of variance (ANOVA) implied that the highly significant factor for cell growth was the aeration rate, whereas that for the production of CMCase was the agitation speed. The optimal inner pressures for cell growth and the production of CMCase by B. velezensis A-68 in a 100 L bioreactor were 0.00 and 0.04 MPa, respectively. The maximal production of CMCase in a 100 L bioreactor under optimized conditions using rice hulls was 108.1 U/ml, which was 1.8 times higher than that at a flask scale under previously optimized conditions.

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Chung-Il Park, Jae-Hong Lee, Jianhong Li, Jin-Woo Lee
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Miao Ye, Xiangfang Tang, Ru Yang, Hongfu Zhang, Fangshu Li, Fangzheng Tao, Fei Li, Zaigui Wang
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Paenibacillus marinisediminis sp. nov., a Bacterium Isolated from Marine Sediment: Hae-Won Lee , Seong Woon Roh , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Joon Yong Kim , Dong-Wook Hyun , Daekyung Kim , Jin-Woo Bae; J. Microbiol. 2013;51(3):312-317. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-3198-2

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Abstract PDF: A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35T was most closely related to Paenibacillus taiwanensis G-soil-2-3T (97.2% similarity). The optimal growth conditions for strain LHW35T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C15:0 and C16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified aminohospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35T (=KACC 16317T =JCM 17886T).

Influence of Culture Conditions and Medium Composition on the Production of Antibacterial Compounds by Marine Serratia sp. WPRA3: Mahtab Jafarzade , Nur Ain Yahya , Fatemeh Shayesteh , Gires Usup , Asmat Ahmad; J. Microbiol. 2013;51(3):373-379. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2440-2

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This study was undertaken to investigate the influence of culture conditions and medium components on production of antibacterial compounds by Serratia sp. WPRA3 (JX020764) which was isolated from marine water of Port Dickson, Malaysia. Biochemical, morphological, and molecular characteristics suggested that the isolate is a new candidate of the Serratia sp. The isolate showed strong antimicrobial activity against fungi, Gram-negative and Gram-positive bacteria. This bacterium exhibited optimum antibacterial compounds production at 28°C, pH 7 and 200 rev/min aeration during 72 h of incubation period. Highest antibacterial activity was obtained when sodium chloride (2%), yeast extract (0.5%), and glucose concentration (0.75%) were used as salt, nitrogen, and carbon sources respectively. Different active fractions were obtained by Thin-Layer Chromatography (TLC) and Flash Column Chromatography (FCC) from ethyl acetate crude extracts namely OCE and RCE in different culture conditions, OCE (pH 5, 200 rev/min) and RCE (pH 7/without aeration). In conclusion, the results suggested different culture conditions have a significant impact on the types of secondary metabolites produced by the bacterium.

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