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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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.

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.

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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11 Citations

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.

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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9 Citations

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.

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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22 Citations

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.

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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5 Citations

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.

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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