Journal of Microbiology

Journal Articles

Identification of avaC from Human Gut Microbial Isolates that Converts 5AVA to 2-Piperidone: Qiudi Zhou, Lihui Feng; J. Microbiol. 2024;62(5):367-379. Published online June 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00141-0

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2-piperidone is a crucial industrial raw material of high-value nylon-5 and nylon-6,5. Currently, a major bottleneck in the biosynthesis of 2-piperidone is the identification of highly efficient 2-piperidone synthases. In this study, we aimed to identify specific strains among 51 human gut bacterial strains capable of producing 2-piperidone and to elucidate its synthetic mechanism. Our findings revealed that four gut bacterial strains, namely Collinsella aerofaciens LFYP39, Collinsella intestinalis LFYP54, Clostridium bolteae LFYP116, and Clostridium hathewayi LFYP18, could produce 2-piperidone from 5-aminovaleric acid (5AVA). Additionally, we observed that 2-piperidone could be synthesized from proline through cross-feeding between Clostridium difficile LFYP43 and one of the four 2-piperidone producing strains, respectively. To identify the enzyme responsible for catalyzing the conversion of 5AVA to 2-piperidone, we utilized a gain-of-function library and identified avaC (5-aminovaleric acid cyclase) in C. intestinalis LFYP54. Moreover, homologous genes of avaC were validated in the other three bacterial strains. Notably, avaC were found to be widely distributed among environmental bacteria. Overall, our research delineated the gut bacterial strains and genes involved in 2-piperidone production, holding promise for enhancing the efficiency of industrial biosynthesis of this compound.

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Metabolite biomarkers of screening neonatal congenital hypothyroidism based on dried blood spot metabolomics
Xingyu Guo, Feng Suo, Yuting Wang, Di Yu, Yi Wang, Bulian Dong, Lingshan Gou, Xinhui Gan, Benjing Wang, Chaowen Yu, Xiaoxiang Xie, Dandan Linghu, Xinyu Liu, Maosheng Gu, Guowang Xu
Analytical and Bioanalytical Chemistry.2025;[Epub] CrossRef

Genetically Engineered CLDN18.2 CAR-T Cells Expressing Synthetic PD1/CD28 Fusion Receptors Produced Using a Lentiviral Vector: Heon Ju Lee, Seo Jin Hwang, Eun Hee Jeong, Mi Hee Chang; J. Microbiol. 2024;62(7):555-568. Published online May 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00133-0

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Abstract: This study aimed to develop synthetic Claudin18.2 (CLDN18.2) chimeric antigen receptor (CAR)-T (CAR-T) cells as a treatment for advanced gastric cancer using lentiviral vector genetic engineering technology that targets the CLDN18.2 antigen and simultaneously overcomes the immunosuppressive environment caused by programmed cell death protein 1 (PD-1). Synthetic CAR T cells are a promising approach in cancer immunotherapy but face many challenges in solid tumors. One of the major problems is immunosuppression caused by PD-1. CLDN18.2, a gastric-specific membrane protein, is considered a potential therapeutic target for gastric and other cancers. In our study, CLDN18.2 CAR was a second-generation CAR with inducible T-cell costimulatory (CD278), and CLDN18.2-PD1/CD28 CAR was a third-generation CAR, wherein the synthetic PD1/CD28 chimeric-switch receptor (CSR) was added to the second-generation CAR. In vitro, we detected the secretion levels of different cytokines and the killing ability of CAR-T cells. We found that the secretion of cytokines such as interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) secreted by three types of CAR-T cells was increased, and the killing ability against CLDN18.2-positive GC cells was enhanced. In vivo, we established a xenograft GC model and observed the antitumor effects and off-target toxicity of CAR-T cells. These results support that synthetic anti-CLDN18.2 CAR-T cells have antitumor effect and anti-CLDN18.2-PD1/CD28 CAR could provide a promising design strategy to improve the efficacy of CAR-T cells in advanced gastric cancer.

UACG: Up‑to‑Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction: Seong-In Na , Michael James Bailey , Mauricio Chalita , Jae Hyoung Cho , Jongsik Chun; J. Microbiol. 2023;61(7):683-692. Published online August 11, 2023; DOI: https://doi.org/10.1007/s12275-023-00064-2

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Abstract

In the post-genomic era, phylogenomics is a powerful and routinely-used tool to discover evolutionary relationships between microorganisms. Inferring phylogenomic trees by concatenating core gene sequences into a supermatrix is the standard
method
. The previously released up-to-date bacterial core gene (UBCG) tool provides a pipeline to infer phylogenomic trees using single-copy core genes for the Bacteria domain. In this study, we established up-to-date archaeal core gene (UACG), comprising 128 genes suitable for inferring archaeal phylogenomic trees. To test the gene set, we selected the Haloarcula genus and scrutinized its phylogeny. The phylogeny inferred using the UACG tool was consistent with the orthoANIu dendrogram, whereas the 16S rRNA gene phylogeny showed high intragenomic heterogeneity resulting in phylogenetic discrepancies. The software tool using the UACG set is available at https:// www. ezbio cloud. net/ tools/ uacg.

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Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Raúl Riesco, Martha E. Trujillo
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Physiological roles of catalases Cat1 and Cat2 in Myxococcus xanthus: Kimura Yoshio , Yuri Yoshioka , Kie Toshikuni; J. Microbiol. 2022;60(12):1168-1177. Published online October 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2277-7

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Abstract

Catalases are key antioxidant enzymes in aerobic organisms. Myxococcus xanthus expresses two monofunctional catalases, small-subunit Cat1 and large-subunit Cat2. The Km of H2O2 for recombinant Cat1 and Cat2 were 14.0 and 9.0 mM, respectively, and the catalytic efficiency of Cat2 (kcat/Km = 500 sec-1 mM-1) was 4-fold higher than that of Cat1. The activity ratio of Cat1 to Cat2 in the exponential growth phase of M. xanthus was 1 to 3–4. A Cat1-deficient strain was constructed, whereas a Cat2-deficient strain could not be produced. In H2O2-supplemented medium, the cat1 mutant exhibited marked growth retardation and a longer generation time than the wild-type (wt) strain. After 2 h of incubation in 0.5 mM H2O2-supplemented medium, the catalase activity of the wt strain significantly increased (by 64-fold), but that of the cat1 mutant strain did not. Under starvation-induced developmental conditions, catalase activity was induced by approximately 200-fold in both wt and cat1 strains, although in the mutant the activity increase as well as spore formation occurred one day later, indicating that the induction of catalase activity during starvation was due to Cat2. In wt starved cells, catalase activity was not induced by H2O2. These results suggest that Cat2 is the primary housekeeping catalase during M. xanthus growth and starvation-induced development, whereas Cat1 may have a complementary role, being responsible for the rapid degradation of H2O2 in proliferating vegetative cells subjected to oxidative stress.

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Enzymatic characterization of five thioredoxins and a thioredoxin reductase from Myxococcus xanthus
Ryota Tanifuji, Yoshio Kimura
FEMS Microbiology Letters.2024;[Epub] CrossRef
Overexpression of cat2 restores antioxidant properties and production traits in degenerated strains of Volvariella volvacea
Jianing Zhu, Wenpei Wang, Wanhe Sun, Yuanxi Lei, Qiangfei Tan, Gahong Zhao, Jianmin Yun, Fengyun Zhao
Free Radical Biology and Medicine.2024; 215: 94. CrossRef
Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa
Yerim Park, Wonjae Kim, Yeji Cha, Minkyung Kim, Woojun Park
Harmful Algae.2024; 137: 102680. CrossRef
Cis-3-Indoleacrylic Acid: A Nematicidal Compound from Streptomyces youssoufiensis YMF3.862 as V-ATPase Inhibitor on Meloidogyne incognita
Min Chen, Ying Huang, Li Ma, Jian-Jin Liu, Yi Cao, Pei-Ji Zhao, Ming-He Mo
Journal of Agricultural and Food Chemistry.2024; 72(44): 24347. CrossRef
Broad-spectrum ROS autonomous scavenging polysaccharide-based vehicle to improve the bioactivity of blueberry anthocyanidins through intestinal synergistic mucoadhesion
Jingwen Xu, Yue Zhang, Xiaolin Yao, Sijuan Wang, Guangwen Luo, Kaiqiang Lv, Yongkang Zhang, Guoliang Li
Food Hydrocolloids.2024; 152: 109899. CrossRef
Polyphosphate Plays a Significant Role in the Maturation of Spores in Myxococcus xanthus
Daiki Harita, Hiroka Matsukawa, Yoshio Kimura
Current Microbiology.2024;[Epub] CrossRef
Discovery of 2-Naphthol from the Leaves of Actephila merrilliana as a Natural Nematicide Candidate
Xi Zhang, Zhan Hu, Shuai Wang, Fengman Yin, Yuyang Wei, Jia Xie, Ranfeng Sun
Journal of Agricultural and Food Chemistry.2023; 71(36): 13209. CrossRef

Reviews

[Minireview]Potential roles of condensin in genome organization and beyond in fission yeast: Kyoung-Dong Kim; J. Microbiol. 2021;59(5):449-459. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1039-2

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Abstract

The genome is highly organized hierarchically by the function of structural maintenance of chromosomes (SMC) complex proteins such as condensin and cohesin from bacteria to humans. Although the roles of SMC complex proteins have been well characterized, their specialized roles in nuclear processes remain unclear. Condensin and cohesin have distinct binding sites and mediate long-range and short-range genomic associations, respectively, to form cell cycle-specific genome organization. Condensin can be recruited to highly expressed genes as well as dispersed repeat genetic elements, such as Pol III-transcribed genes, LTR retrotransposon, and rDNA repeat. In particular, mitotic transcription factors Ace2 and Ams2 recruit condensin to their target genes, forming centromeric clustering during mitosis. Condensin is potentially involved in various chromosomal processes such as the mobility of chromosomes, chromosome territories, DNA reannealing, and transcription factories. The current knowledge of condensin in fission yeast summarized in this review can help us understand how condensin mediates genome organization and participates in chromosomal processes in other organisms.

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Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes
Debayan Chakraborty, Balaka Mondal, D. Thirumalai
Journal of Chemical Theory and Computation.2024; 20(3): 1398. CrossRef
Contributions of transcriptional noise to leukaemia evolution: KAT2A as a case-study
Cristina Pina
Philosophical Transactions of the Royal Society B: Biological Sciences.2024;[Epub] CrossRef
Viral remodeling of the 4D nucleome
Kyoung-Dong Kim, Paul M. Lieberman
Experimental & Molecular Medicine.2024; 56(4): 799. CrossRef
BiFCo: visualizing cohesin assembly/disassembly cycle in living cells
Emilio González-Martín, Juan Jiménez, Víctor A Tallada
Life Science Alliance.2023; 6(7): e202301945. CrossRef

[MINIREVIEW]Bacterial bug-out bags: outer membrane vesicles and their proteins and functions: Kesavan Dineshkumar , Vasudevan Aparna , Liang Wu , Jie Wan , Mohamod Hamed Abdelaziz , Zhaoliang Su , Shengjun Wang , Huaxi Xu; J. Microbiol. 2020;58(7):531-542. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-0026-3

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Abstract

Among the major bacterial secretions, outer membrane vesicles (OMVs) are significant and highly functional. The proteins and other biomolecules identified within OMVs provide new insights into the possible functions of OMVs in bacteria. OMVs are rich in proteins, nucleic acids, toxins and virulence factors that play a critical role in bacteria-host interactions. In this review, we discuss some proteins with multifunctional features from bacterial OMVs and their role involving the mechanisms of bacterial survival and defence. Proteins with moonlighting activities in OMVs are discussed based on their functions in bacteria. OMVs harbour many other proteins that are important, such as proteins involved in virulence, defence, and competition. Overall, OMVs are a power-packed aid for bacteria, harbouring many defensive and moonlighting proteins and acting as a survival kit in
case
of an emergency or as a defence weapon. In summary, OMVs can be defined as bug-out bags for bacterial defence and, therefore, survival.

Citations

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Bacterial membrane vesicles in the pathogenesis and treatment of inflammatory bowel disease
Chinasa Valerie Olovo, Dickson Kofi Wiredu Ocansey, Ying Ji, Xinxiang Huang, Min Xu
Gut Microbes.2024;[Epub] CrossRef
Glycosylphosphatidylinositol-anchored proteins as non- DNA matter of inheritance: from molecular to cell to philosophical biology
Günter Müller
Academia Molecular Biology and Genomics.2024;[Epub] CrossRef
Microbe-host interactions: structure and functions of Gram-negative bacterial membrane vesicles
Min Xiao, Guiding Li, Hefeng Yang
Frontiers in Microbiology.2023;[Epub] CrossRef
Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition
Houssein Zhour, Fabrice Bray, Israa Dandache, Guillaume Marti, Stéphanie Flament, Amélie Perez, Maëlle Lis, Llorenç Cabrera-Bosquet, Thibaut Perez, Cécile Fizames, Ezekiel Baudoin, Ikram Madani, Loubna El Zein, Anne-Aliénor Véry, Christian Rolando, Hervé
International Journal of Molecular Sciences.2022; 23(23): 15248. CrossRef
Tiny but mighty: Possible roles of bacterial extracellular vesicles in gut‐liver crosstalk for non‐alcoholic fatty liver disease
Li Shao, Junping Shi, Xiaohui Fan
Clinical and Translational Discovery.2022;[Epub] CrossRef
Extracellular membrane vesicles from Limosilactobacillus reuteri strengthen the intestinal epithelial integrity, modulate cytokine responses and antagonize activation of TRPV1
Yanhong Pang, Ludwig Ermann Lundberg, Manuel Mata Forsberg, David Ahl, Helena Bysell, Anton Pallin, Eva Sverremark-Ekström, Roger Karlsson, Hans Jonsson, Stefan Roos
Frontiers in Microbiology.2022;[Epub] CrossRef
Streptomyces coelicolor Vesicles: Many Molecules To Be Delivered
Teresa Faddetta, Giovanni Renzone, Alberto Vassallo, Emilio Rimini, Giorgio Nasillo, Gianpiero Buscarino, Simonpietro Agnello, Mariano Licciardi, Luigi Botta, Andrea Scaloni, Antonio Palumbo Piccionello, Anna Maria Puglia, Giuseppe Gallo, Gladys Alexandre
Applied and Environmental Microbiology.2022;[Epub] CrossRef
Novel devices for isolation and detection of bacterial and mammalian extracellular vesicles
Shiana Malhotra, Zarinah M. Amin, Garima Dobhal, Sophie Cottam, Thomas Nann, Renee V. Goreham
Microchimica Acta.2021;[Epub] CrossRef
Tracing the origins of extracellular DNA in bacterial biofilms: story of death and predation to community benefit
Davide Campoccia, Lucio Montanaro, Carla Renata Arciola
Biofouling.2021; 37(9-10): 1022. CrossRef
The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages
Leah M. Smith, Simon A. Jackson, Lucia M. Malone, James E. Ussher, Paul P. Gardner, Peter C. Fineran
Nature Microbiology.2021; 6(2): 162. CrossRef
Role of extracellular vesicles in liver diseases and their therapeutic potential
Enis Kostallari, Shantha Valainathan, Louise Biquard, Vijay H. Shah, Pierre-Emmanuel Rautou
Advanced Drug Delivery Reviews.2021; 175: 113816. CrossRef

Journal Articles

Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of Thioclava electrotropha Chang et al. 2018: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(12):1048-1055. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9260-y

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Abstract

A Gram-stain-negative, strictly aerobic, marine bacterium, designated GH2-2T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) in Gangwha Island, the Republic of Korea. The cells of the organism were oxidase- positive, catalase-positive, flagellated, short rods that grew at 10–40°C, pH 4–10, and 0–13% (w/v) NaCl. The predominant ubiquinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The major fatty acid is C18:1. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed an independent lineage at the base of the radiation encompassing members of the genus Thioclava, except for Thioclava arenosa. The closest relatives were T. nitratireducens (96.03% sequence similarity) and T. dalianensis (95.97%). The genome size and DNA G+C content were 3.77 Mbp and 59.6 mol%, respectively. Phylogenomic analysis supported phylogenetic distinctness based on 16S rRNA gene sequences. Average nucleotide identity values were 73.6–74.0% between the novel strain and members of the genus Thioclava. On the basis of data obtained from a polyphasic approach, the strain GH2-2T (= KCTC 62124T = DSM 105743T) represents a novel species of a new genus for which the name Hahyoungchilella caricis gen. nov., sp. nov. is proposed. Moreover, the transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava gen. nov. as Pseudothioclava arenosa comb. nov. is also proposed. Finally, Thioclava electrotropha Chang et al. 2018 is proposed to be a later heterosynonym of Thioclava sediminum Liu et al. 2017.

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Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat
Zhaobin Huang, Meiqin Li, Aharon Oren, Qiliang Lai
Frontiers in Microbiology.2024;[Epub] CrossRef
Sustainable agricultural management of saline soils in arid and semi-arid Mediterranean regions through halophytes, microbial and soil-based technologies
Salvadora Navarro-Torre, Pedro Garcia-Caparrós, Amaia Nogales, Maria Manuela Abreu, Erika Santos, Ana Lúcia Cortinhas, Ana Delaunay Caperta
Environmental and Experimental Botany.2023; 212: 105397. CrossRef
Notification of changes in taxonomic opinion previously published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4061. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef

Kinetic characterization of laccase from Bacillus atrophaeus, and its potential in juice clarification in free and immobilized forms: Lokesh Kumar Narnoliya , Neera Agarwal , Satya N. Patel , Sudhir P. Singh; J. Microbiol. 2019;57(10):900-909. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9170-z

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Abstract

In the present study, a laccase gene (BaLc) from a lignin degrading bacterium, Bacillus atrophaeus, has been cloned and expressed in Escherichia coli. The optimal catalytic activity of the protein was achieved at 5.5 pH and 35°C temperature, measured by oxidation of ABTS. The Km and Vmax values were determined as 1.42 mM and 4.16 μmole/min, respectively. To achieve the enzyme recovery, the biocatalyst (BaLc) was covalently attached onto the functionalized iron magnetic-nanoparticles. The nanoparticles were characterized by zeta-potential and FTIR analyses. The immobilized BaLc enzyme was physico-kinetically characterized, exhibiting retention of 60% of the residual activity after ten reaction cycles of ABTS oxidation. The immobilized biocatalyst system was tested for its biotechnological exploitability in plant juice processing, achieving 41–58% of phenol reduction, 41–58% decolorization, 50–59% turbidity reduction in the extracts of banana pseudo-stem and sweet sorghum stalk, and apple fruit juice. This is the first study to demonstrate the use of nanoparticle- laccase conjugate in juice clarification. The findings suggest that B. atrophaus laccase is a potential catalytic tool for plant juice bioprocessing activities.

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Immobilized enzymes: exploring its potential in food industry applications
K. A. Jothyswarupha, Swethaa Venkataraman, Devi Sri Rajendran, S. S. Sakthi Shri, Shivani Sivaprakasam, Tholeti Yamini, P. Karthik, Vaidyanathan Vinoth Kumar
Food Science and Biotechnology.2024;[Epub] CrossRef
Harnessing the power of bacterial laccases for xenobiotic degradation in water: A 10-year overview
Mujeeb ur Rahman, Muhammad Wajid Ullah, Junaid Ali Shah, Sivasamy Sethupathy, Hazart Bilal, Sidikov Akmal Abdikakharovich, Afaq Ullah Khan, Khalid Ali Khan, Noureddine Elboughdiri, Daochen Zhu
Science of The Total Environment.2024; 918: 170498. CrossRef
Laccase-mediated degradation of emerging contaminants: unveiling a sustainable solution
Pooja Thathola, Elda M. Melchor-Martínez, Priyanka Adhikari, Saúl Antonio Hernández Martínez, Anita Pandey, Roberto Parra-Saldívar
Environmental Science: Advances.2024; 3(11): 1500. CrossRef
Biochemical Characteristics of Laccases and Their Practical Application in the Removal of Xenobiotics from Water
Agnieszka Gałązka, Urszula Jankiewicz, Andrzej Szczepkowski
Applied Sciences.2023; 13(7): 4394. CrossRef
Application of Immobilized Enzymes in Juice Clarification
Feng Wang, Hui Xu, Miaomiao Wang, Xiaolei Yu, Yi Cui, Ling Xu, Anzhou Ma, Zhongyang Ding, Shuhao Huo, Bin Zou, Jingya Qian
Foods.2023; 12(23): 4258. CrossRef
Bacterial Laccases as Biocatalysts for the Remediation of Environmental Toxic Pollutants: A Green and Eco-Friendly Approach—A Review
Neha Agarwal, Vijendra Singh Solanki, Amel Gacem, Mohd Abul Hasan, Brijesh Pare, Amrita Srivastava, Anupama Singh, Virendra Kumar Yadav, Krishna Kumar Yadav, Chaigoo Lee, Wonjae Lee, Sumate Chaiprapat, Byong-Hun Jeon
Water.2022; 14(24): 4068. CrossRef
Enzymatic treatment, unfermented and fermented fruit-based products: current state of knowledge
Joanne Yi Hui Toy, Yuyun Lu, Dejian Huang, Keisuke Matsumura, Shao-Quan Liu
Critical Reviews in Food Science and Nutrition.2022; 62(7): 1890. CrossRef
Current research progress on laccase-like nanomaterials
Lulu Lei, Xiaoyu Yang, Yudong Song, Hui Huang, Yongxin Li
New Journal of Chemistry.2022; 46(8): 3541. CrossRef
Poly(vinyl Alcohol)-Alginate Immobilized Trametes versicolor IBL-04 Laccase as Eco-friendly Biocatalyst for Dyes Degradation
Sadia Noreen, Muhammad Asgher, Sarmad Ahmad Qamar, Muhammad Bilal, Hafiz M. N. Iqbal
Catalysis Letters.2022; 152(6): 1869. CrossRef
Recent developments in enzyme immobilization technology for high-throughput processing in food industries
Asghar Taheri-Kafrani, Sara Kharazmi, Mahmoud Nasrollahzadeh, Asieh Soozanipour, Fatemeh Ejeian, Parisa Etedali, Hajar-Alsadat Mansouri-Tehrani, Amir Razmjou, Samaneh Mahmoudi-Gom Yek, Rajender S. Varma
Critical Reviews in Food Science and Nutrition.2021; 61(19): 3160. CrossRef
Laccases in food processing: Current status, bottlenecks and perspectives
Emanueli Backes, Camila Gabriel Kato, Rúbia Carvalho Gomes Corrêa, Regina de Fátima Peralta Muniz Moreira, Rosely Aparecida Peralta, Lillian Barros, Isabel C.F.R. Ferreira, Gisella Maria Zanin, Adelar Bracht, Rosane Marina Peralta
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A novel Bacillus ligniniphilus catechol 2,3-dioxygenase shows unique substrate preference and metal requirement
Peter Adewale, Alice Lang, Fang Huang, Daochen Zhu, Jianzhong Sun, Michael Ngadi, Trent Chunzhong Yang
Scientific Reports.2021;[Epub] CrossRef
Laccases as green and versatile biocatalysts: from lab to enzyme market—an overview
Tatiane Brugnari, Dayane Moreira Braga, Camila Souza Almeida dos Santos, Bruno Henrique Czelusniak Torres, Tatiani Andressa Modkovski, Charles Windson Isidoro Haminiuk, Giselle Maria Maciel
Bioresources and Bioprocessing.2021;[Epub] CrossRef
Extracting flavonoid from Ginkgo biloba using lignocellulolytic bacteria Paenarthrobacter sp. and optimized via response surface methodology
Sihai Han, Chonlong Chio, Tianxiao Ma, Aristide Laurel Mokale Kognou, Sarita Shrestha, Feifei Chen, Wensheng Qin
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Shamraja S. Nadar, Pravin D. Patil, Nanda M. Rohra
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The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria: Ji&# , Chahrazed Mekadim , Radko Pechar , V&# , Eva Vlková; J. Microbiol. 2018;56(10):713-721. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8167-3

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Abstract

In the modern era, molecular genetic techniques are crucial in ecological studies, as well as in the classification, typing, and phylogenetic analysis of prokaryotes. These techniques are mainly aimed at whole genome comparisons and PCRderived experiments, including amplifying the 16S rRNA and other various housekeeping genes used in taxonomy, as well as MLST (multilocus sequence typing) and MLSA (multilocus sequence analysis) of different taxonomic bacterial groups. The gene encoding threonine-tRNA ligase (thrS) is a gene potentially applicable as an identification and phylogenetic marker in bacteria. It is widely distributed in bacterial genomes and is subject to evolutionary selection pressure due to its important function in protein synthesis. In this study, specific primers were used to amplify a thrS gene fragment (~740 bp) in 36 type and 30 wild strains classified under family Bifidobacteriaceae. The full-length gene has not yet been considered as a possible identification, classification, and phylogenetic marker in bifidobacteria. The thrS sequences revealed higher sequence variability (82.7% of pairwise identities) among members of the family than that shown by 16S rRNA gene sequences (96.0%). Although discrepancies were found between the thrS-derived and previously reported whole genome phylogenetic analyses, the main phylogenetic groups of bifidobacteria were properly assigned. Most wild strains of bifidobacteria were better differentiated based on their thrS sequences than on their 16S rRNA gene identities. Phylogenetic confidence of the evaluated gene with respect to other alternative genetic markers widely used in taxonomy of bifidobacteria (fusA, GroELhsp60, pyrG, and rplB genes) was confirmed using the localized incongruence difference - Templeton analysis.

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Current Microbiology.2024;[Epub] CrossRef
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Antibacterial Activity of Rainbow Trout Plasma: In Vitro Assays and Proteomic Analysis
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Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera)
Ting Ting Li, Hong Xia Zhang, Chun Tao Gu
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Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris)
Vera Neuzil-Bunesova, Gabriele Andrea Lugli, Nikol Modrackova, Marie Makovska, Jakub Mrazek, Chahrazed Mekadim, Sarka Musilova, Ivona Svobodova, Roman Spanek, Marco Ventura, Jiri Killer
International Journal of Systematic and Evolutionary Microbiology .2020; 70(9): 5040. CrossRef
Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera
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Variation of cassiicolin genes among Chinese isolates of Corynespora cassiicola: Jun Wu , Xuewen Xie , Yanxia Shi , Ali Chai , Qi Wang , Baoju Li; J. Microbiol. 2018;56(9):634-647. Published online July 27, 2018; DOI: https://doi.org/10.1007/s12275-018-7497-5

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Abstract

Corynespora cassiicola is a species of fungus that is a plant pathogen of many agricultural crop plants, including severe target spot disease on cucumber. Cassiicolin is an important effector of pathogenicity of this fungus. In this study, we collected 141 Corynespora isolates from eighteen hosts, and the casscolin gene was detected in 82 C. cassiicola strains. The deduced protein sequences revealed that 72 isolates contained the Cas2 gene, two strains from Gynura bicolor harboured the Cas2.2 gene, and 59 isolates without a cassiicolin gene were classified as Cas0. Phylogenetic analyses was performed for the 141 isolates using four loci (ITS, ga4, caa5, and act1) and revealed two genetic clusters. Cluster A is composed of four subclades: subcluster A1 includes all Cas2 isolates plus 18 Cas0 strains, subcluster A2 includes the eight Cas5 isolates and one Cas0 isolate, and subclusters A3 and A4 contain Cas0 strains. Cluster B consists of 21 Cas0 isolates. Twenty-two C. cassiicola strains from different toxin classes showed varying degrees of virulence against cucumber. Cas0 or Cas2 strains induced diverse responses on cucumber, from no symptoms to symptoms of moderate or severe infection, but all Cas5 isolates exhibited avirulence on cucumber.

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The Diseases and Pests of Rubber Tree and Their Natural Control Potential: A Bibliometric Analysis
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Need for disease resistance breeding against Corynespora cassiicola in crops
Edgar Sierra-Orozco, German Sandoya, Seonghee Lee, Gary Vallad, Samuel Hutton
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Comparison and Correlation of Corynespora cassiicola Populations from Kiwifruit and Other Hosts Based on Morphology, Phylogeny, and Pathogenicity
Jing Xu, Guoshu Gong, Yongliang Cui, Yuhang Zhu, Jun Wang, Kaikai Yao, Wen Chen, Cuiping Wu, Rui Yang, Xiaodan Yang, Pan Li, Henan Zhao, Sen Zhong, Yi Luo, Yue Li, Wenfei Liao
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Unraveling the Host-Selective Toxic Interaction of Cassiicolin with Lipid Membranes and Its Cytotoxicity
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The necrosis- and ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola
Thaís Carolina da Silva Dal’Sasso, Vinícius Delgado da Rocha, Hugo Vianna Silva Rody, Maximiller Dal-Bianco Lamas Costa, Luiz Orlando de Oliveira
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Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients: Min Ho Kim , Jeong Seon Jeon , In Kyo Kim , Ji Seon Park , Hosun Park , Ok Sarah Shin , Chan Hee Lee; J. Microbiol. 2017;55(8):665-672. Published online July 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7171-3

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Abstract

Varicella-zoster virus (VZV) is a causative agent of chickenpox in primary infection and shingles after its reactivation from latency. Complete or almost-complete genomic DNA sequences for various VZV strains have been reported. Recently, clinical VZV strains were isolated from Korean patients whose genome was sequenced using high-throughput sequencing technology. In this study, we analyzed single nucleotide polymorphism (SNP) of VZV strains to genetically characterize Korean clinical isolates. Phylogenetic analyses revealed that three Korean strains, YC01, YC02, and YC03, were linked to clade 2. Comprehensive SNP analysis identified 86 sites specific for the 5 VZV clades. VZV strains isolated from Korea did not form a phylogenetic cluster. Rather, YC02 and YC03 clustered strongly with Chinese strain 84-7 within clade 2, more specifically cluster 2a. Signature sequences for the cluster 2a were identified and found to play an important role in the separation of cluster 2a strains from other clade 2 strains, as shown in substitution studies. Further genetic analysis with additional strains isolated from Japan, China, and other Asian countries would provide a novel insight into the significance of two distinct subclades within clade 2.

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Cross-reactive humoral immunity of clade 2 Oka and MAV/06 strain-based varicella vaccines against different clades of varicella–zoster virus
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Assessment of attenuation of varicella‐zoster virus vaccines based on genomic comparison
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Immunological characteristics of MAV/06 strain of varicella-zoster virus vaccine in an animal model
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Uliginosibacterium flavum sp. nov. isolated from an artificial lake: Ji Young Kang , Jeesun Chun , Kwang Yeop Jahng; J. Microbiol. 2017;55(8):595-599. Published online July 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7002-6

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Abstract

A Gram-negative, facultative anaerobic, rod-shaped, motile by means of a polar flagellum, greenish-yellow-pigmented bacterial strain (designated strain JJ3220T) was isolated from an artificial lake in South Korea and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain JJ3220T indicated that the isolate belongs to the family Rhodocyclaceae, and that it exhibits 96.4% similarity to Uliginosibacterium paludis KBP-13T. The major cellular fatty acids of the novel strain were C14:0, C16:0, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). Strain JJ3220T had flexirubin-type pigments. The DNA G+C content of the strain was 62.8%. The major respiratory quinone and major polar lipid of strain JJ3220T were ubiquinone-8 and phosphatidylethanolamine, respectively. Based on the morphological and physiological properties and biochemical evidence presented, it can be concluded that strain JJ3220T represents a novel species of the genus Uliginosibacterium. The type strain Uliginosibacterium flavum is JJ3220T (=KACC 17644T =JCM 19465T).

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Decay experiments and microbial community analysis of water lily leaf biofilms: Sediment effects on leaf preservation potential
Brianne Palmer, Sabina Karačić, Shook Ling Low, Kathrin Janssen, Harald Färber, Moritz Liesegang, Gabriele Bierbaum, Carole T. Gee, Przemysław Mroczek
PLOS ONE.2024; 19(12): e0315656. CrossRef
Uliginosibacterium aquaticum sp. nov., Isolated from a Freshwater Lake
Jaeho Song, Mirae Kim, Miri S. Park, Yochan Joung, Ilnam Kang, Jang-Cheon Cho
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Notification of changes in taxonomic opinion previously published outside the IJSEM
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A rapid and simple method for identifying bacterial polar lipid components in wet biomass: Tuan Manh Nguyen , Jaisoo Kim; J. Microbiol. 2017;55(8):635-639. Published online July 4, 2017; DOI: https://doi.org/10.1007/s12275-017-7092-1

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Abstract

There are marked differences between wet and freeze-dried cells with regard to the identification of polar lipid components. The determination of the polar lipid composition of freeze-dried cells is well established. However, several approaches to identifying polar lipid components in wet cells have met with limited success owing to the presence of non-polar compounds in the extracts, resulting in a lipid composition with a narrow scope. In this study, we surveyed the lipid profiles of the wet biomasses of three Gram-positive (Microbacterium lacticum, Rhodococcus koreensis, and Streptomyces longwoodensis) and two Gram-negative (Pseudomonas aeruginosa and Novosphingobium capsulatum) bacteria; the results were comparable in quality to those obtained using a standard freeze-dried approach. Moreover, our improved method ensures simple lipid extraction. Overall, the results of the analysis showed minor lipid profile differences between the two approaches with regard to quantity, and lipid identification was consistent in both methods for all species.

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Viridibacterium curvum gen. nov., sp. nov., isolated from freshwater: Ji Young Kang , Jeesun Chun , Young Cheol Jung , Kwang Yeop Jahng; J. Microbiol. 2017;55(7):514-519. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7003-5

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Abstract

A Gram stain-negative, yellowish green-pigmented, facultatively anaerobic, motile, curved rod-shaped bacterium designated as strain JJ016T was isolated from an artificial lake in South Korea, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain JJ016T indicated that the isolate belonged to the family Rhodocyclaceae and exhibited 95.0% identity to Uliginosibacterium gangwonense 5YN10-9T. The major cellular fatty acids of the novel strain were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:0, C14:0, and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The DNA G+C content of strain JJ016T was 61.9 mol%. The major respiratory quinone and major polar lipid of strain JJ016T were ubiquinone-8 and phosphatidylethanolamine, respectively. Based on the morphological and physiological properties and the biochemical evidence presented, we concluded that strain JJ016T represents a novel species of a new genus in the family Rhodocyclaceae, for which the name Viridibacterium curvum gen. nov., sp. nov. is proposed. The type strain is JJ016T (=KACC 16899T =JCM 18715T).

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Niveibacterium microcysteis sp. nov., isolated from a cyanobacterial bloom sample
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International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef

Review

MINIREVIEW] Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria: Kyung Sook Bae , Mi Sun Kim , Ji Hee Lee , Joo Won Kang , Dae In Kim , Ji Hee Lee , Chi Nam Seong; J. Microbiol. 2016;54(12):789-795. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6446-4

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Abstract

To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.

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