Journal of Microbiology

Research Article

Comprehensive genomic and functional analysis of Leuconostoc lactic acid bacteria in alcohol and acetaldehyde metabolism: Joo-Han Gwak, Yun Ji Choi, Hina Ayub, Min Kyeong Seol, Hongik Kim, Man-Young Jung; J. Microbiol. 2025;63(2):e2410026. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2410026

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Alcohol consumption can lead to the accumulation of harmful metabolites, such as acetaldehyde, contributing to various adverse health effects, including hangovers and liver damage. This study presents a comprehensive genomic and functional analysis of Leuconostoc suionicum VITA-PB2, a lactic acid bacterial strain isolated from kimchi, to elucidate its role in enhancing alcohol and acetaldehyde metabolism. Genomic characterization revealed key genes encoding alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), providing insights into the metabolic capabilities of strain VITA-PB2. Phylogenomic analyses confirmed its taxonomic classification and genetic similarity to other Leuconostoc species. Functional validation through in vitro and in vivo experiments demonstrated superior ethanol and acetaldehyde decomposition abilities of strain VITA-PB2, with significant reductions in blood ethanol and acetaldehyde levels observed in rats administered with the strain. Further analysis indicated that while hepatic ADH activity did not significantly increase; however, ALDH expression was elevated. This suggests that the microbial ADH of strain VITA-PB2 contributed to ethanol breakdown, while both microbial and host ALDH facilitated acetaldehyde detoxification. These findings highlight the potential of strain VITA-PB2 as a functional probiotic for mitigating the toxic effects of alcohol consumption.

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Microorganisms: The Key Regulators of Wine Quality
Hechao Zhao, Shiyuan Liu, Lixian Zhu, Yanhua Wang
Comprehensive Reviews in Food Science and Food Safety.2025;[Epub] CrossRef

Journal Articles

Investigation of Bottleneck Enzyme Through Flux Balance Analysis to Improve Glycolic Acid Production in Escherichia coli: Jungyeon Kim, Ye-Bin Kim, Ju-Young Kim, Min-Ju Seo, Soo-Jin Yeom, Bong Hyun Sung; J. Microbiol. 2024;62(11):1023-1033. Published online October 28, 2024; DOI: https://doi.org/10.1007/s12275-024-00175-4

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Abstract: Amid rising environmental concerns, attempts have been made to produce glycolic acid (GA) using microbial processes with renewable carbon resources instead of using chemicals. The Dahms pathway for GA production uses xylose as a substrate and consists of relatively simple enzymatic steps. However, employing it leads to a decrease in cell growth and GA productivity. Systematically identifying and addressing metabolic bottlenecks in the Dahms pathway are essential for efficient glycolic acid (GA) production have not yet been performed. Through metabolic flux balance analysis, we found that insufficient aldehyde dehydrogenase (AldA) activity lowers GA production and negatively affects cell growth due to reduced energy production. Thus, we discovered a novel AldA isolated from Buttiauxella agrestis (BaAldA) demonstrated a 1.69-fold lower K_M and a 1.49-fold higher turnover rate (k_cat/K_M) than AldA from Escherichia coli (EcAldA). GA production in E. coli harboring BaAldA was 1.59 times higher than in the original strain. Fed-batch fermentation of E. coli harboring BaAldA produced 22.70 g/L GA with a yield of 0.497 g/g_xylose (98.2% of the theoretical maximum yield in the Dahms pathway), showing a higher final yield for GA than previously reported in E. coli. Our novel BaAldA enzyme shows great potential for the production of GA using microorganisms or enzymes. Furthermore, our approach to identifying metabolic bottlenecks using flux balance analysis could be utilized to enhance the microbial production of various desirable products in future studies.

Those Nematode‑Trapping Fungi That are not Everywhere: Hints Towards Soil Microbial Biogeography: Wei Deng , Fa Zhang , Davide Fornacca , Xiao-Yan Yang , Wen Xiao; J. Microbiol. 2023;61(5):511-523. Published online April 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00043-7

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Abstract

The existence of biogeography for microorganisms is a raising topic in ecology and researchers are employing better distinctions between single species, including the most rare ones, to reveal potential hidden patterns. An important volume of evidence supporting heterogeneous distributions for bacteria, archaea and protists is accumulating, and more recently a few efforts have targeted microscopic fungi. We propose an insight into this latter kingdom by looking at a group of soil nematode-trapping fungi whose species are well-known and easily recognizable. We chose a pure culture approach because of its reliable isolation procedures for this specific group. After morphologically and molecularly identifying all species collected from 2250 samples distributed in 228 locations across Yunnan province of China, we analyzed occurrence frequencies and mapped species, genera, and richness. Results showed an apparent cosmopolitan tendency for this group of fungi, including species richness among sites. However, only four species were widespread across the region, while nonrandom heterogeneous distributions were observed for the remaining 40 species, both in terms of statistical distribution of species richness reflected by a significant variance-to-mean ratio, as well as in terms of visually discernible spatial clusters of rare species and genera on the map. Moreover, several species were restricted to only one location, raising the question of whether endemicity exists for this microbial group. Finally, environmental heterogeneity showed a marginal contribution in explaining restricted distributions, suggesting that other factors such as geographical isolation and dispersal capabilities should be explored. These findings contribute to our understanding of the cryptic geographic distribution of microorganisms and encourage further research in this direction.

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Linking watershed formation with the phylogenetic distribution of a soil microscopic fungus in Yunnan Province, China
Davide Fornacca, Wei Deng, Yaoquan Yang, Fa Zhang, Xiaoyan Yang, Wen Xiao
BMC Microbiology.2024;[Epub] CrossRef
Analysis of Nuclear Dynamics in Nematode-Trapping Fungi Based on Fluorescent Protein Labeling
Liang Zhou, Zhiwei He, Keqin Zhang, Xin Wang
Journal of Fungi.2023; 9(12): 1183. CrossRef

Adaptation of Pseudomonas helmanticensis to fat hydrolysates and SDS: fatty acid response and aggregate formation: Ilya N. Zubkov , Anatoly P. Nepomnyshchiy , Vadim D. Kondratyev , Pavel N. Sorokoumov , Konstantin V. Sivak , Edward S. Ramsay , Sergey M. Shishlyannikov; J. Microbiol. 2021;59(12):1104-1111. Published online October 26, 2021; DOI: https://doi.org/10.1007/s12275-021-1214-5

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Abstract

An essential part of designing any biotechnological process is examination of the physiological state of producer cells in different phases of cultivation. The main marker of a bacterial cell’s state is its fatty acid (FA) profile, reflecting membrane lipid composition. Consideration of FA composition enables assessment of bacterial responses to cultivation conditions and helps biotechnologists understand the most significant factors impacting cellular metabolism. In this work, soil SDS-degrading Pseudomonas helmanticensis was studied at the fatty acid profile level, including analysis of rearrangement between planktonic and aggregated forms. The set of substrates included fat hydrolysates, SDS, and their mixtures with glucose. Such media are useful in bioplastic production since they can help incrementally lower overall costs. Conventional gas chromatography-mass spectrometry was used for FA analysis. Acridine orange-stained aggregates were observed by epifluorescence microscopy. The bacterium was shown to change fatty acid composition in the presence of hydrolyzed fats or SDS. These changes seem to be driven by the depletion of metabolizable substrates in the culture medium. Cell aggregation has also been found to be a defense strategy, particularly with anionic surfactant (SDS) exposure. It was shown that simple fluidity indices (such as saturated/ unsaturated FA ratios) do not always sufficiently characterize a cell's physiological state, and morphological examination is essential in cases where complex carbon sources are used.

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Effect of different diet composition on the fat profile of two different black soldier fly larvae populations
M. Tognocchi, L. Abenaim, C. Adamaki-Sotiraki, G.C. Athanassiou, I.C. Rumbos, M. Mele, B. Conti, G. Conte
animal.2024; 18(7): 101205. CrossRef
Earth to Mars: A Protocol for Characterizing Permafrost in the Context of Climate Change as an Analog for Extraplanetary Exploration
Kimberley R. Miner, Joseph Razzell Hollis, Charles E. Miller, Kyle Uckert, Thomas A. Douglas, Emily Cardarelli, Rachel Mackelprang
Astrobiology.2023; 23(9): 1006. CrossRef
Preparation of polyhydroxyalkanoates using Pseudomonas helmanticensis in non-sterile media containing glycerol and sodium dodecyl sulfate
I. N. Zubkov, Yu. S. Bukin, P. N. Sorokoumov, S. M. Shishlyannikov
Proceedings of Universities. Applied Chemistry and Biotechnology.2022; 12(3): 479. CrossRef

Characterization of a novel phage depolymerase specific to Escherichia coli O157:H7 and biofilm control on abiotic surfaces: Do-Won Park , Jong-Hyun Park; J. Microbiol. 2021;59(11):1002-1009. Published online October 6, 2021; DOI: https://doi.org/10.1007/s12275-021-1413-0

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Abstract

The increasing prevalence of foodborne diseases caused by Escherichia coli O157:H7 as well as its ability to form biofilms poses major threats to public health worldwide. With increasing concerns about the limitations of current disinfectant treatments, phage-derived depolymerases may be used as promising biocontrol agents. Therefore, in this study, the characterization, purification, and application of a novel phage depolymerase, Dpo10, specifically targeting the lipopolysaccharides of E. coli O157, was performed. Dpo10, with a molecular mass of 98 kDa, was predicted to possess pectate lyase activity via genome analysis and considered to act as a receptor- binding protein of the phage. We confirmed that the purified Dpo10 showed O-polysaccharide degrading activity only for the E. coli O157 strains by observing its opaque halo. Dpo10 maintained stable enzymatic activities across a wide range of temperature conditions under 55°C and mild basic pH. Notably, Dpo10 did not inhibit bacterial growth but significantly increased the complement-mediated serum lysis of E. coli O157 by degrading its O-polysaccharides. Moreover, Dpo10 inhibited the biofilm formation against E. coli O157 on abiotic polystyrene by 8-fold and stainless steel by 2.56 log CFU/coupon. This inhibition was visually confirmed via fieldemission scanning electron microscopy. Therefore, the novel depolymerase from E. coli siphophage exhibits specific binding and lytic activities on the lipopolysaccharide of E. coli O157 and may be used as a promising anti-biofilm agent against the E. coli O157:H7 strain.

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Application of phage-derived enzymes for enhancing food safety
Junhwan Kim, Xinyu Liao, Song Zhang, Tian Ding, Juhee Ahn
Food Research International.2025; 209: 116318. CrossRef
Effect of Bacteriophages against Biofilms of Escherichia coli on Food Processing Surfaces
Ana Brás, Márcia Braz, Inês Martinho, João Duarte, Carla Pereira, Adelaide Almeida
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Bacteriophage–Host Interactions and the Therapeutic Potential of Bacteriophages
Leon M. T. Dicks, Wian Vermeulen
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Current Strategies for Combating Biofilm-Forming Pathogens in Clinical Healthcare-Associated Infections
Rashmita Biswas, Bhawana Jangra, Ganapathy Ashok, Velayutham Ravichandiran, Utpal Mohan
Indian Journal of Microbiology.2024; 64(3): 781. CrossRef
Phage Adsorption to Gram-Positive Bacteria
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Journal of Microbiology.2023; 61(12): 1063. CrossRef
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Siyu Liu, Hongyun Lu, Shengliang Zhang, Ying Shi, Qihe Chen
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Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments: Shengxiang Pei , Siwen Niu , Fuquan Xie , Wenjing Wang , Shuang Zhang , Gaiyun Zhang; J. Microbiol. 2021;59(10):898-910. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1235-0

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Abstract

During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5– 99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2T, YB235T, and WO024T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235T, WO024T, and o2T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains’ ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2T, YB235T and WO024T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2T = JCM 33844T = MCCC 1A09961T), Brevibacterium pigmenatum sp. nov. (type strain YB235T = JCM 33843T = MCCC 1A09842T) and Brevibacterium atlanticum sp. nov. (type strain WO024T = JCM 33846T = MCCC 1A16743T) are proposed.

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Brevibacterium litoralis sp. nov., a cellulose-degrading strain isolated from marine surface sediment
Quan Yang, Aolin Zhao, Haifei Liu, Jiawei Li, Shujing Wu, Ying Huang, Jie Weng, Mingguo Jiang, Yi Jiang
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Comparative analysis of bacterial communities and environmental interactions in seawater and saline-alkali aquaculture ponds for Scylla paramamosain in northern China
Dongping Zhou, Yuanyuan Fu, Lei Liu, Weichuan Lin, Zhibin Lu, Yangfang Ye, Minglei Zhang
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Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan
Sadia Manzoor, Saira Abbas, Sobia Zulfiqar, Hong-Chuan Wang, Min Xiao, Wen-Jun Li, Muhammad Arshad, Iftikhar Ahmed
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Saxibacter everestensis gen. nov., sp. nov., A Novel Member of the Family Brevibacteriaceae, Isolated from the North Slope of Mount Everest
Mao Tian, Shiyu Wu, Wei Zhang, Gaosen Zhang, Xue Yu, Yujie Wu, Puchao Jia, Binglin Zhang, Tuo Chen, Guangxiu Liu
Journal of Microbiology.2024; 62(4): 277. CrossRef
Omics-Based Approaches in Research on Textile Dye Microbial Decolorization
Anna Jasińska, Aleksandra Walaszczyk, Katarzyna Paraszkiewicz
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Fajar Hidayaturohman, Aninditia Sabdaningsih, Diah Ayuningrum
Asia Pacific Journal of Molecular Biology and Biotechnology.2024; : 101. CrossRef
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Larissa Caló Zitelli, Gabriela Merker Breyer, Mariana Costa Torres, Luiza de Campos Menetrier, Ana Paula Muterle Varela, Fabiana Quoos Mayer, Cláudio Estêvão Farias Cruz, Franciele Maboni Siqueira
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Mimi Zhang, Qianqian Song, Jin Sang, Zhiyong Li
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
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Andrés Cumsille, Néstor Serna-Cardona, Valentina González, Fernanda Claverías, Agustina Undabarrena, Vania Molina, Francisco Salvà-Serra, Edward R.B. Moore, Beatriz Cámara
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Marat Tafkilevich Lutfullin, Guzel Fanisovna Lutfullina, Dasha Sergeevna Pudova, Yaw Abayie Akosah, Elena Ilyasovna Shagimardanova, Semyon Germanovich Vologin, Margarita Rashidovna Sharipova, Ayslu Mirkasymovna Mardanova
3 Biotech.2022;[Epub] CrossRef
Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
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Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food: Young Joon Oh , Joon Yong Kim , Hee Eun Jo , Hyo Kyeong Park , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi; J. Microbiol. 2020;58(5):387-394. Published online April 11, 2020; DOI: https://doi.org/10.1007/s12275-020-9507-7

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Abstract

Two bacterial strains designated NKC220-2T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5–9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3–99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3T (97.4–97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1- 9T (79.5–79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC- 220-2T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains. The major cellular fatty acids of the strains were anteiso-C15:0 and anteiso- C17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2T (= KACC 21232T = JCM 33390T).

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Identification of Roseomonas xinghualingensis sp. nov. isolated from hospital air
Zhiming Kang, Wenjing Lei, Ji Pu, Lijun Zhao, Guowen Min, Yufeng Liu, Wenjuan Chang, Yuqian Gao, Kui Dong, Bin Sun
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
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Cansu Çelik Doğan, Hafize Tuğba Yüksel Dolgun, Serkan İkiz, Şükrü Kırkan, Uğur Parın
Foods.2023; 12(19): 3538. CrossRef
Lentibacillus daqui sp. nov., isolated from high-temperature Daqu, a starter for production of Chinese Jiang-flavour Baijiu
Yuan Liang, Zhen-Ming Lu, Wei Shi, Lin-Huan Wu, Li-Juan Chai, Xiao-Juan Zhang, Su-Yi Zhang, Song-Tao Wang, Cai-Hong Shen, Zheng-Hong Xu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
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Marina Ghislaine Abré, Clémentine Amenan Kouakou-Kouamé, Florent Kouadio N’guessan, Corinne Teyssier, Didier Montet
Folia Microbiologica.2023; 68(2): 257. CrossRef
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Qian Liu, Guoying Fan, Kui Wu, Xiangning Bai, Xi Yang, Wentao Song, Shengen Chen, Yanwen Xiong, Haiying Chen
Journal of Microbiology.2022; 60(7): 668. CrossRef
Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
Ji-Ho Yoo, Jeong Eun Han, June-Young Lee, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Hojun Sung, Euon Jung Tak, Hyun Sik Kim, Pil Soo Kim, Jee-Won Choi, Do-Yeon Kim, In Chul Jeong, Do-Hun Gim, Seo Min Kang, Jin-Woo Bae
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Yun Wang, Gang-Qiang Jiang, Hong-Ping Lin, Peng Sun, Hong-Yan Zhang, Dong-Mei Lu, Li-Yun Wang, Chang-Jin Kim, Shu-Kun Tang
Archives of Microbiology.2021; 203(2): 621. CrossRef
Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. CrossRef
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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
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List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
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Review

[MINIREVIEW] Alanine dehydrogenases in mycobacteria: Ji-A Jeong , Jeong-Il Oh; J. Microbiol. 2019;57(2):81-92. Published online January 31, 2019; DOI: https://doi.org/10.1007/s12275-019-8543-7

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Abstract

Since NAD(H)-dependent L-alanine dehydrogenase (EC 1.1.4.1; Ald) was identified as one of the major antigens present in culture filtrates of Mycobacterium tuberculosis, many studies on the enzyme have been conducted. Ald catalyzes the reversible conversion of pyruvate to alanine with concomitant oxidation of NADH to NAD+ and has a homohexameric quaternary structure. Expression of the ald genes was observed to be strongly upregulated in M. tuberculosis and Mycobacterium smegmatis grown in the presence of alanine. Furthermore, expression of the ald genes in some mycobacteria was observed to increase under respiration-inhibitory conditions such as oxygen-limiting and nutrient-starvation conditions. Upregulation of ald expression by alanine or under respiration-inhibitory conditions is mediated by AldR, a member of the Lrp/AsnC family of transcriptional regulators. Mycobacterial Alds were demonstrated to be the enzymes required for utilization of alanine as a nitrogen source and to help mycobacteria survive under respiration-inhibitory conditions by maintaining cellular NADH/NAD+ homeostasis. Several inhibitors of Ald have been developed, and their application in combination with respiration-inhibitory antitubercular drugs such as Q203 and bedaquiline was recently suggested.

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Chiara Della Bella, Marco Antonio Motisi, Elisabetta Venturini, Sofia D’Elios, Evangelia Asvestopoulou, Agnese Maria Tamborino, Luisa Galli, Mario Milco D’Elios, Elena Chiappini
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Alanine dehydrogenases from four different microorganisms: characterization and their application in L-alanine production
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Pragya Anand, Yusuf Akhter
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Alanine synthesized by alanine dehydrogenase enables ammonium-tolerant nitrogen fixation in Paenibacillus sabinae T27
Qin Li, Haowei Zhang, Yi Song, Minyang Wang, Chongchong Hua, Yashi Li, Sanfeng Chen, Ray Dixon, Jilun Li
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Moxi Yu, Yachen Hou, Meiling Cheng, Yongshen Liu, Caise Ling, Dongshen Zhai, Hui Zhao, Yaoyao Li, Yamiao Chen, Xiaoyan Xue, Xue Ma, Min Jia, Bin Wang, Pingan Wang, Mingkai Li
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Anna Egorova, Elena G. Salina, Vadim Makarov
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Journal Articles

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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Abstract

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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Functional characterization of the cutI gene for the transcription of carbon monoxide dehydrogenase genes in Mycobacterium sp. strain JC1 DSM 3803: Jae Ho Lee , Sae Woong Park , Young Min Kim , Jeong-Il Oh; J. Microbiol. 2017;55(1):31-36. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6572-7

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Abstract

Carbon monoxide dehydrogenase (CO-DH) in Mycobacterium sp. strain JC1 is a key enzyme for the carboxydotrophic growth, when carbon monoxide (CO) is supplied as a sole source of carbon and energy. This enzyme is also known to act as nitric oxide dehydrogenase (NO-DH) for the detoxification of NO. Several accessory genes such as cutD, cutE, cutF, cutG, cutH, and cutI, are clustered together with two copies of the CO-DH structural genes (cutB1C1A1 and cutB2C2A2) in Mycobacterium sp. strain JC1 and are well conserved in carboxydotrophic mycobacteria. Transcription of the CO-DH structural and accessory genes was demonstrated to be increased significantly by acidified sodium nitrate as a source of NO. A cutI deletion (ΔcutI) mutant of Mycobacterium sp. strain JC1 was generated to identity the function of CutI. Lithoautotrophic growth of the ΔcutI mutant was severely affected in mineral medium supplemented with CO, while the mutant grew normally with glucose. Western blotting, CO-DH activity staining, and CO-DH-specific enzyme assay revealed a significant decrease in the cellular level of CO-DH in the ΔcutI mutant. Northern blot analysis and promoter assay showed that expression of the cutB1 and cutB2 genes was significantly reduced at the transcriptional level in the ΔcutI mutant, compared to that of the wildtype strain. The ΔcutI mutant was much more susceptible to NO than was the wild type.

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Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide
Gonzalo Durante-Rodríguez, Sofía de Francisco-Polanco, José Luis García, Eduardo Díaz
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Identification of D-amino acid dehydrogenase as an upstream regulator of the autoinduction of a putative acyltransferase in Corynebacterium glutamicum: Jung-Hoon Lee , Yong-Jae Kim , Hee-Sung Shin , Heung-Shick Lee , Shouguang Jin , Un-Hwan Ha; J. Microbiol. 2016;54(6):432-439. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6046-3

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Abstract

Expression of a putative acyltransferase encoded by NCgl- 0350 of Corynebacterium glutamicum is induced by cell-free culture fluids obtained from stationary-phase growth of both C. glutamicum and Pseudomonas aeruginosa, providing evidence for interspecies communication. Here, we further confirmed that such communication occurs by showing that acyltransferase expression is induced by culture fluid obtained from diverse Gram-negative and -positive bacterial strains, including Escherichia coli, Salmonella Typhimurium, Bacillus subtilis, Staphylococcus aureus, Mycobacterium sp. strain JC1, and Mycobacterium smegmatis. A homologous acyltransferase encoded by PA5238 of P. aeruginosa was also induced by fluids obtained from P. aeruginosa as well as other bacterial strains, as observed for NCgl0350 of C. glutamicum. Because C. glutamicum is difficult to study using molecular approaches, the homologous gene PA5238 of P. aeruginosa was used to identify PA5309 as an upstream regulator of expression. A homologous D-amino acid dehydrogenase encoded by NCgl- 2909 of C. glutamicum was cloned based on amino acid similarity to PA5309, and its role in the regulation of NCgl0350 expression was confirmed. Moreover, NCgl2909 played positive roles in growth of C. glutamicum. Thus, we identified a D-amino acid dehydrogenase as an upstream regulator of the autoinduction of a putative acyltransferase in C. glutamicum.

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Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source
Takeshi Naganuma, Yoshiakira Iinuma, Hitomi Nishiwaki, Ryota Murase, Kazuo Masaki, Ryosuke Nakai
Frontiers in Microbiology.2018;[Epub] CrossRef

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

Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii: Hackwon Do , Chang Woo Lee , Sung Gu Lee , Hara Kang , Chul Min Park , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee; J. Microbiol. 2016;54(2):114-121. Published online February 2, 2016; DOI: https://doi.org/10.1007/s12275-016-5549-2

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Abstract

The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NADdependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH.

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Accumulation of Lipid Production in Chlorella minutissima by Triacylglycerol Biosynthesis-Related Genes Cloned from Saccharomyces cerevisiae and Yarrowia lipolytica: Hsin-Ju Hsieh , Chia-Hung Su , Liang-Jung Chien; J. Microbiol. 2012;50(3):526-534. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2041-5

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Abstract

Discovery of an alternative fuel is now an urgent matter because of the impending issue of oil depletion. Lipids synthesized in algal cells called triacylglycerols (TAGs) are thought to be of the most value as a potential biofuel source because they can use transesterification to manufacture biodiesel. Biodiesel is deemed as a good solution to overcoming the problem of oil depletion since it is capable of providing good performance similar to that of petroleum. Expression of several genomic sequences, including glycerol-3-phosphate dehydrogenase, glycerol-3-phosphate acyltransferase, lysophosphatidic acid acyltransferase, phosphatidic acid phosphatase, diacylglycerol acyltransferase, and phospholipid:diacylglycerol acyltransferase, can be useful for manipulating metabolic pathways for biofuel production. In this study, we found this approach indeed increased the storage lipid content of C. minutissima UTEX 2219 up to 2-fold over that of wild type. Thus, we conclude this approach can be used with the biodiesel production platform of C. minutissima UTEX 2219 for high lipid production that will, in turn, enhance productivity.

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Role of Hydrogen Generation by Klebsiella pneumoniae in the Oral Cavity: Tomoko Kanazuru , Eisuke F. Sato , Kumiko Nagata , Hiroshi Matsui , Kunihiko Watanabe , Emiko Kasahara , Mika Jikumaru , June Inoue , Masayasu Inoue; J. Microbiol. 2010;48(6):778-783. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0149-z

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Abstract

Some gastrointestinal bacteria synthesize hydrogen (H2) by fermentation. Despite the presence of bactericidal factors in human saliva, a large number of bacteria also live in the oral cavity. It has never been shown that oral bacteria also produce H2 or what role H2 might play in the oral cavity. It was found that a significant amount of H2 is synthesized in the oral cavity of healthy human subjects, and that its generation is enhanced by the presence of glucose but inhibited by either teeth brushing or sterilization with povidone iodine. These observations suggest the presence of H2-generating bacteria in the oral cavity. The screening of commensal bacteria in the oral cavity revealed that a variety of anaerobic bacteria generate H2. Among them, Klebsiella pneumoniae (K. pneumoniae) generated significantly large amounts of H2 in the presence of glucose. Biochemical analysis revealed that various proteins in K. pneumoniae are carbonylated under standard culture conditions, and that oxidative stress induced by the presence of Fe++ and H2O2 increases the number of carbonylated proteins, particularly when their hydrogenase activity is inhibited by KCN. Inhibition of H2 generation markedly suppresses the growth of K. pneumoniae. These observations suggest that H2 generation and/or the reduction of oxidative stress is important for the survival and growth of K. pneumoniae in the oral cavity.

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Cloning and Sequence Analysis of a Glyceraldehyde-3-phosphate Dehydrogenase Gene from Ganoderma lucidum: Xu Fei , Ming Wen Zhao , Yu Xiang Li; J. Microbiol. 2006;44(5):515-522.; DOI: https://doi.org/2446 [pii]

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Abstract: A cDNA library of Ganoderma lucidum has been constructed using a Zap Express cloning vector. A glyceraldehyde-3-phosphate dehydrogenase gene (gpd) was isolated from this library by hybridization of the recombinant phage clones with a gpd-specific gene probe generated by PCR. By comparison of the cDNA and the genomic DNA sequences, it was found that the complete nucleotide sequence encodes a putative polypeptide chain of 338 amino acids interrupted by 6 introns. The predicted amino acid sequence of this gene shows a high degree of sequence similarity to the GPD proteins from yeast and filamentous fungi. The promoter region contains a CT-rich stretch, two CAAT boxes, and a consensus TATA box. The possibility of using the gpd promoter in the construction of new transformation vectors is discussed.

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