Journal of Microbiology

Journal Articles

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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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

Review

[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

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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The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum
Cheng-Shan Jiang, Chun Yan Li, Chun Tao Gu
Current Microbiology.2024;[Epub] CrossRef
Bifidobacterium apicola sp. nov., isolated from the gut of honeybee (Apis mellifera)
Ting-Yu Wang, Hao Wang, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Bifidobacterium apis sp. nov., isolated from the gut of honeybee (Apis mellifera)
Cheng-Shan Jiang, Chun Yan Li, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Bifidobacterium favimelis sp. nov., isolated from black comb honey
Yu Li, Qiujie Song, Haizhu Yang, Yue Wei, Bilege Menghe, Wenjun Liu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Antibacterial Activity of Rainbow Trout Plasma: In Vitro Assays and Proteomic Analysis
Toita Mizaeva, Kalimat Alieva, Eldar Zulkarneev, Stanislav Kurpe, Kseniya Isakova, Svetlana Matrosova, Ekaterina Borvinskaya, Irina Sukhovskaya
Animals.2023; 13(22): 3565. CrossRef
Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera)
Ting Ting Li, Hong Xia Zhang, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
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
Jiří Killer, Chahrazed Mekadim, Věra Bunešová, Jakub Mrázek, Zuzana Hroncová, Eva Vlková
Folia Microbiologica.2020; 65(1): 143. CrossRef
Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics
Chahrazed Mekadim, Věra Bunešová, Eva Vlková, Zuzana Hroncová, Jiří Killer
Antonie van Leeuwenhoek.2019; 112(12): 1785. CrossRef
Prebiotic potential of natural gums and starch for bifidobacteria of variable origins
Nikol Modrackova, Marie Makovska, Chahrazed Mekadim, Eva Vlkova, Vaclav Tejnecky, Petra Bolechova, Vera Bunesova
Bioactive Carbohydrates and Dietary Fibre.2019; 20: 100199. CrossRef

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.

Citations

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Amycolatopsis mongoliensis sp. nov., a novel actinobacterium with antifungal activity isolated from a coal mining site in Mongolia
Bilguun Oyuntsetseg, Hyang Burm Lee, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Amycolatopsis nalaikhensis sp. nov. and Amycolatopsis carbonis sp. nov., two novel actinobacteria with antimicrobial activity isolated from a coal mining site in Mongolia
Bilguun Oyuntsetseg, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes
Munisamy Prathaban, Ragothaman Prathiviraj, Mythili Ravichandran, Sharmila Devi Natarajan, Murugesan Sobanaa, S. Hari Krishna Kumar, Varadharaju Chandrasekar, Joseph Selvin
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Quorum Quenching Potential of Reyranella sp. Isolated from Riverside Soil and Description of Reyranella humidisoli sp. nov.
Dong Hyeon Lee, Seung Bum Kim
Journal of Microbiology.2024; 62(6): 449. CrossRef
Mycovorax composti gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from button mushroom compost
Meghann Thai, Tina L. Bell, Michael A. Kertesz
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Description of Chryseobacterium fluminis sp. nov., a keratinolytic bacterium isolated from a freshwater river
Moonsoo Kim, Eun Tak Oh, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Shewanella metallivivens sp. nov., a deep-sea hydrothermal vent tube worm endobiont capable of dissimilatory anaerobic metalloid oxyanion reduction
Chris Maltman, Steven B. Kuzyk, John A. Kyndt, George Lengyel, Vladimir Yurkov
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Flavobacterium humidisoli sp. nov., isolated from riverside soil
Jun Sik Ra, Eun Tak Oh, Ji-Hye Han, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description of Microcella humidisoli sp. nov. and Microcella daejeonensis sp. nov., isolated from riverside soil, reclassification of Marinisubtilis pacificus as Microcella pacifica comb. nov., and emended description of the genus Microcella
Katya Michelle Molina Ayala, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Comparing 16S rRNA gene similarity with simple polar lipids profiling amongst Salmonella isolates
IM T Fadlalla, ME Hamid, AG A Rahim, ED M Elamin
Nigerian Journal of Health Sciences.2023; 23(1): 10. CrossRef
Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes
Gary R. Hix, Muhammad S. Khan, Mikayla T. Miller, Elisha C. Napier, Allison L. O'Brien, Roger P. White, Stephen F. Baron
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Micromonospora antibiotica sp. nov. and Micromonospora humidisoli sp. nov., two new actinobacterial species exhibiting antimicrobial potential
Dong Hyeon Lee, Jun Sik Ra, Min Ji Kim, Seung Bum Kim
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Colwellia maritima sp. nov. and Polaribacter marinus sp. nov., isolated from seawater
Sylvia Kristyanto, Jaejoon Jung, Jeong Min Kim, Keunpil Kim, Mi-hwa Lee, Lujiang Hao, Che Ok Jeon
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Chryseobacterium pennae sp. nov., isolated from poultry feather waste
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Kannan Asha, Punyasloke Bhadury
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Hye Su Jung, Byung Hee Chun, Hyung Min Kim, Che Ok Jeon
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Ciceribacter ferrooxidans sp. nov., a nitrate-reducing Fe(II)-oxidizing bacterium isolated from ferrous ion-rich sediment
Tongchu Deng, Youfen Qian, Xingjuan Chen, Xunan Yang, Jun Guo, Guoping Sun, Meiying Xu
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Paenibacillus piri sp. nov., isolated from urban soil
Ngoc Hoang Trinh, Jaisoo Kim
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Jun Young Choi, Pyung Cheon Lee
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Tuan Manh Nguyen, Jaisoo Kim
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Flavobacterium ureilyticum sp. nov., a novel urea hydrolysing bacterium isolated from stream bank soil
Ram Hari Dahal, Jaisoo Kim
Antonie van Leeuwenhoek.2018; 111(11): 2131. CrossRef
Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae
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Characterization of Flavobacterium aquimarinum sp. nov., a halotolerant bacterium isolated from seawater
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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.

Citations

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A report on 22 unrecorded Actinomycetota species isolated from freshwater environments in the Republic of Korea
Soo-Yeong Lee, Jaeduk Goh, Ahyoung Choi
Environmental Biology Research.2024; 42(3): 288. CrossRef
Impact of eight widely consumed antibiotics on the growth and physiological profile of natural soil microbial communities
María Rosa Pino-Otín, Natalia Ferrando, Diego Ballestero, Elisa Langa, Francisco J. Roig, Eva M. Terrado
Chemosphere.2022; 305: 135473. CrossRef
Microbial Community and Atrazine-Degrading Genetic Potential in Deep Zones of a Hypersaline Lake-Aquifer System
Yolanda Espín, Giuliana Aranzulla, Manuel Álvarez-Ortí, Juan José Gómez-Alday
Applied Sciences.2020; 10(20): 7111. CrossRef
Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds
Zothanpuia, Ajit Kumar Passari, Vincent Vineeth Leo, Preeti Chandra, Brijesh Kumar, Chandra Nayak, Abeer Hashem, Elsayed Fathi Abd_Allah, Abdulaziz A. Alqarawi, Bhim Pratap Singh
Microbial Cell Factories.2018;[Epub] CrossRef
Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea
Chi Nam Seong, Joo Won Kang, Ji Hee Lee, So Yeon Seo, Jung Jae Woo, Chul Park, Kyung Sook Bae, Mi Sun Kim
Journal of Microbiology.2018; 56(1): 1. CrossRef

Lipid analysis of streptomycetes isolated form volcanic soil: Kim, Seung Bum , Kim, Min Young , Seong, Chi Nam , Kang Sa Ouk , Hah, Yung Chil; J. Microbiol. 1996;34(2):184-191.

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Abstract: The cellular fatty acids and quinones of streptomycetes isolated from volcanic soils were analysed. The strains contained fatty acids of 14 to 17 carbon chains, and 12-methyltetradecanoic acid and 14 methylpentadecanoic acid were dominant in most strains. The total profiles consisted of 74% branched fatty acid family, 16.8% linear family and 8.2% unsaturated family. The largest cluster of grey spore masses defined by numerical classification was separated from the remainders in the principal component analysis, but the other clusters were overlapped with one another. In the analysis of respiratory quinones, all of the strains contained either the menaquinone of 9 isoprene units with 6 hydrogenations of 8 hydrogenations as the major species. The distribution of menaquinones among the clusters could provide an important key in the chemotaxonomy of streptomycetes.

Characterization of Isolated Lactobacillus spp. and Classification by RAPD-PCR Analysis: Oh-Sik Kwon; J. Microbiol. 2000;38(3):137-144.

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Abstract: The genetic relationships of six Lactobacillus strains and five laboratory isolates from fermented milk were determined by a random amplified polymorphic DNA (RAPD)-Polymease chan reaction (PCR) method. With 42 random primers, the results were analyzed by using the NTSYS-PC software for phenetic analysis. It revealed that all tested bacteria were divided into three distinct clusters. The clusters implied three subgenuses existed for the genus Lactobacillus, which were previously proposed by Rogosa and Sharpe. From the results, it was also possible to determine that the isolated Lactobacillus strains from fermented milk were grouped into L. acidophilus or L. bulgaricus. Interestingly, the three tested L. casei strains were divided into different clusters implying different subgenuses, i.e., Thermobacterium (L. casei YIT 9018) and Strepto-bacterium (L. casei CHR. Hansen and L. casei ATCC 4646). According to the distance matrix generated by an UPGMA program, the isolated bacteria LT01 and LT02 were determined as a subspecies of L. bulgaricus. The HK01, HK02 and HK03 were very closely related to either L. acidophilus or L. casei YIT 9018. Hence, RAPD-PCR appears to be a very practical method to determine the genetic relationships of the Lactobacillus species and to characterize the unknown Lactobacillus strains at the subspecies level.

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