Journal of Microbiology

Volume 60(7); July 2022

Journal Articles

[Protocol] Development of DNA aptamers specific for small therapeutic peptides using a modified SELEX method: Jaemin Lee , Minkyung Ryu , Dayeong Bae , Hong-Man Kim , Seong-il Eyun , Jeehyeon Bae , Kangseok Lee; J. Microbiol. 2022;60(7):659-667. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2235-4

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Aptamers are short single-stranded DNA or RNA oligonucleotides capable of binding with high affinity and specificity to target molecules. Because of their durability and ease of synthesis, aptamers are used in a wide range of biomedical fields, including the diagnosis of diseases and targeted delivery of therapeutic agents. The aptamers were selected using a process called systematic evolution of ligands by exponential enrichment (SELEX), which has been improved for various research purposes since its development in 1990. In this protocol, we describe a modified SELEX method that rapidly produces high aptamer screening yields using two types of magnetic beads. Using this method, we isolated an aptamer that specifically binds to an antimicrobial peptide. We suggest that by conjugating a small therapeutic-specific aptamer to a gold nanoparticle-based delivery system, which enhances the stability and intracellular delivery of peptides, aptamers selected by our method can be used for the development of therapeutic agents utilizing small therapeutic peptides.

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Recent approaches in the application of antimicrobial peptides in food preservation
Satparkash Singh, Bhavna Jha, Pratiksha Tiwari, Vinay G. Joshi, Adarsh Mishra, Yashpal Singh Malik
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Design and application of microfluidics in aptamer SELEX and Aptasensors
Shikun Zhang, Yingming Zhang, Zhiyuan Ning, Mengxia Duan, Xianfeng Lin, Nuo Duan, Zhouping Wang, Shijia Wu
Biotechnology Advances.2024; 77: 108461. CrossRef
Nanogenosensors based on aptamers and peptides for bioelectrochemical cancer detection: an overview of recent advances in emerging materials and technologies
Babak Mikaeeli Kangarshahi, Seyed Morteza Naghib
Discover Applied Sciences.2024;[Epub] CrossRef
Recent progress of SELEX methods for screening nucleic acid aptamers
Chao Zhu, Ziru Feng, Hongwei Qin, Lu Chen, Mengmeng Yan, Linsen Li, Feng Qu
Talanta.2024; 266: 124998. CrossRef
Aptamer-conjugated gold nanoparticles platform as the intracellular delivery of antibodies for cancer therapy
Ji-Hyun Yeom, Eunkyoung Shin, Hanyong Jin, Haifeng Liu, Yongyang Luo, Youngwoo Nam, Minkyung Ryu, Wooseok Song, Heeyoun Chi, Jeongkyu Kim, Kangseok Lee, Jeehyeon Bae
Journal of Industrial and Engineering Chemistry.2023; 126: 480. CrossRef
Regulation of transforming growth factor-β signaling as a therapeutic approach to treating colorectal cancer
Jana Maslankova, Ivana Vecurkovska, Miroslava Rabajdova, Jana Katuchova, Milos Kicka, Michala Gayova, Vladimir Katuch
World Journal of Gastroenterology.2022; 28(33): 4744. CrossRef

Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons): Qian Liu , Guoying Fan , Kui Wu , Xiangning Bai , Xi Yang , Wentao Song , Shengen Chen , Yanwen Xiong , Haiying Chen; J. Microbiol. 2022;60(7):668-677. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2089-9

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Abstract

Two novel Gram-positive, non-spore-forming, facultatively anaerobic, non-motile, and short rods to coccoid strains were isolated from the feces of the greater white-fronted geese (Anser albifrons) at Poyang Lake. The 16S rRNA gene sequences of strains 4H37-19T and 3HC-13 shared highest identity to that of Corynebacterium uropygiale Iso10T (97.8%). Phylogenetic and phylogenomic analyses indicated that strains 4H37-19T and 3HC-13 formed an independent clade within genus Corynebacterium and clustered with Corynebacterium uropygiale Iso10T. The average nucleotide identity and digital DNA-DNA hybridization value between strains 4H37-19T and 3HC-13 and members within genus Corynebacterium were all below 95% and 70%, respectively. The genomic G + C content of strains 4H37-19T and 3HC-13 was 52.5%. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidylcholine, and phosphatidyl inositol mannosides (PIM) were the major polar lipids, with C18:1ω9c, C16:0, and C18:0 as the major fatty acids, and MK-8 (H4), MK-8(H2), and MK-9(H2) as the predominant respiratory quinones. The major whole cell sugar was arabinose, and the cell wall included mycolic acids. The cell wall peptidoglycan contained meso-diaminopimelic acid (meso-DAP). The polyphasic taxonomic data shows that these two strains represent a novel species of the genus Corynebacterium, for which the name Corynebacterium poyangense sp. nov. is proposed. The type strain of Corynebacterium poyangense is 4H37-19T (=GDMCC 1.1738T = KACC 21671T).

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Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023
Erik Munson, Claire R. Burbick, Sara D. Lawhon, Trinity Krueger, Elena Ruiz-Reyes, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Keratokonjunktivitisli bir tavuktan Corynebacterium spp. ve Arcanobacterium spp. izolasyonu
Hüban GÖÇMEN, Banur BOYNUKARA
Veteriner Hekimler Derneği Dergisi.2023; 94(2): 161. CrossRef

Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.: Yujin Kim , Yeon Bee Kim , Juseok Kim , Joon Yong Kim , Tae Woong Whon , Won-Hyong Chung , Eun-Ji Song , Young-Do Nam , Se Hee Lee , Seong Woon Roh; J. Microbiol. 2022;60(7):678-688. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-1581-6

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Abstract

Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104T and CBA3105T, were isolated from kimchi. Strain CBA3104T and CBA3105T grew at 10–35°C (optimum, 25°C and 30°C, respectively), at pH 6.0–8.5 (optimum, pH 6.5), and in the presence of 0–15% (w/v) NaCl (optimum, 5%). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBA3104T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105T was closely positioned with Brachybacterium halotolerans MASK1Z-5T. The 16S rRNA gene sequence similarity between strains CBA3104T and CBA3105T was 99.9%, but ANI and dDDH values between strains CBA3104T and CBA3105T were 93.61% and 51.5%, respectively. Strain CBA3104T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium, however, strain CBA3105T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5T. Among biochemical analysis results, strain CBA3104T could uniquely utilize bromo-succinic acid whereas only strain CBA3105T was positive for alkaline phosphatase and α-fucosidase among two novel strains, closely related strains, and type species of the genus Brachybacterium. Compared with strain CBA3105T and Brachybacterium halotolerans JCM 34339T, strain CBA3105T was differentially positive for acid production of D-arabinose, D-adonitol, and potassium 5-ketogluconate and enzyme activity of β-glucuronidase. Both strains contained menaquinone-7 as the dominant quinone. The cell-wall peptidoglycan of two novel strains contained meso-diaminopimelic acid. The major fatty acids of strains CBA3104T and CBA3105T were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54–62 tRNAs). Both the CBA3104T and CBA3105T strain harbored various oxidoreductase, transferase, hydrolase, and lyase as strain-specific functional genes compared to closely related strains and Brachybacterium type species. The results of biochemical/physiological, chemotaxonomic, and genomic analyses demonstrated that strains CBA3104T and CBA3105T represent a novel species of the genus Brachybacterium and a novel subspecies of B. halotolerans, respectively, for which the names Brachybacterium kimchii sp. nov. and B. halotolerans subsp. kimchii subsp. nov. are proposed. The type strains of the novel species and the novel subspecies are CBA3104T (= KCCM 43417T = JCM 34759T) and CBA3105T (= KCCM 43418T = JCM 34760T), respectively.

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Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
Alexander G. Elcheninov, Kseniya S. Zayulina, Alexandra A. Klyukina, Mariia K. Kremneva, Ilya V. Kublanov, Tatiana V. Kochetkova
Microorganisms.2023; 12(1): 16. CrossRef
Validation List no. 208. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Complete Genome Sequence of Brachybacterium sp. Strain NBEC-018, Isolated from Nematode-Infected Potatoes
Ling Chen, Yueying Wang, Nanxi Liu, Lei Zhu, Yong Min, Yimin Qiu, Yuxi Tian, Xiaoyan Liu, David Rasko
Microbiology Resource Announcements.2022;[Epub] CrossRef

Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny: Wanderson Marques Da Silva , Mariano Larzabal , Flavia Figueira Aburjaile , Nahuel Riviere , Luisina Martorelli , James Bono , Ariel Amadio , Angel Cataldi; J. Microbiol. 2022;60(7):689-704. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-1616-z

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Abstract

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen capable of causing illness in humans. In a previous study, our group showed that a STEC isolate belonging to O22:H8 serotype (strain 154) can interfere with STEC O157:H7 colonization both in vitro and in vivo. Using whole-genome sequencing and genomic comparative, we predicted a subset of genes acquired by O22:H8 strain 154 through horizontal gene transfer that might be responsible for the phenotype previously described by our group. Among them were identified genes related to the pathogenesis of non-LEE (locus of enterocyte effacement) STEC, specific metabolic processes, antibiotic resistance and genes encoding for the T6SS-1 that is related to inter-bacterial competition. In addition, we showed that this strain carries stx1c and stx2dact, a mucus-inducible variant. The results obtained in this study provide insights into STEC genomic plasticity and the importance of genomic islands in the adaptation and pathogenesis of this pathogen.

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MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
Nathalie Bonin, Enrique Doster, Hannah Worley, Lee J Pinnell, Jonathan E Bravo, Peter Ferm, Simone Marini, Mattia Prosperi, Noelle Noyes, Paul S Morley, Christina Boucher
Nucleic Acids Research.2023; 51(D1): D744. CrossRef
Genomes-based MLST, cgMLST, wgMLST and SNP analysis of Salmonella Typhimurium from animals and humans
Shigan Yan, Zhaoxu Jiang, Wencheng Zhang, Zhenhai Liu, Xiaorui Dong, Donghui Li, Zijun Liu, Chengyu Li, Xu Liu, Liping Zhu
Comparative Immunology, Microbiology and Infectious Diseases.2023; 96: 101973. CrossRef
Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition
Margaret D. Weinroth, Michael L. Clawson, Gregory P. Harhay, Mark Eppinger, Dayna M. Harhay, Timothy P. L. Smith, James L. Bono
Frontiers in Microbiology.2023;[Epub] CrossRef
Occurrence and genetic characterization of Shiga toxin-producing Escherichia coli on bovine and pork carcasses and the environment from transport trucks
Rocío Colello, Manuela Baigorri, Felipe Del Canto, Juliana González, Ariel Rogé, Claudia van der Ploeg, Federico Sánchez Chopa, Mónica Sparo, Analía Etcheverría, Nora Lía Padola
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef

Yeast polyubiquitin unit regulates synaptonemal complex formation and recombination during meiosis: Min-Kyung Jo , Kiwon Rhee , Keun Pil Kim , Soogil Hong; J. Microbiol. 2022;60(7):705-714. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-2204-y

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Abstract

Ubiquitin is highly conserved in most eukaryotes and involved in diverse physiological processes, including cell division, protein quality control, and protein degradation mediated by the ubiquitin-proteasome system after heat shock, glucose-starvation, and oxidative stress. However, the role of the ubiquitin gene UBI4, which contains five consecutive head-to-tail ubiquitin repeats, in meiosis has not been investigated. In this study, we show that the Saccharomyces cerevisiae polyubiquitin precursor gene, UBI4, is required to promote synaptonemal complex (SC) formation and suppress excess doublestrand break formation. Moreover, the proportion of Zip1 polycomplexes, which indicate abnormal SC formation, in cells with a mutation in UBI4 (i.e., ubi4Δ cells) is higher than that of wild-type cells, implying that the UBI4 plays an important role in the early meiotic prophase I. Interestingly, although ubi4Δ cells rarely form full-length SCs in the pachytene stage of prophase I, the Zip3 foci are still seen, as in wild-type cells. Moreover, ubi4Δ cells proficiently form crossover and noncrossover products with a slight delay compared to wild-type cells, suggesting that UBI4 is dispensable in SCcoupled recombination. Our findings demonstrate that UBI4 exhibits dual functions that are associated with both positive and negative roles in SC formation and recombination during meiosis.

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The deubiquitinase Usp7 in Drosophila melanogaster is required for synaptonemal complex maintenance
Cathleen M. Lake, Jennifer Gardner, Salam Briggs, Zulin Yu, Grace McKown, R. Scott Hawley
Proceedings of the National Academy of Sciences.2024;[Epub] CrossRef

Isolation of a novel Lactiplantibacillus plantarum strain resistant to nitrite stress and its transcriptome analysis: Chae Young Kwon , Kyoung Jin Choi , Dongeun Yong , Ji-Eun Kim , Sang Sun Yoon; J. Microbiol. 2022;60(7):715-726. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-2221-x

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Abstract: Nitric oxide (NO) is a reactive nitrogen species (RNS) that plays a vital role in regulating inflammatory processes. Under abnormal conditions, excessive NO levels can promote the oxidation of cellular components, which may cause or exacerbate diseases such as hypertension, cardiovascular dysfunction, and inflammatory bowel disease (IBD). Previous studies have shown that reducing NO levels in the lumen can attenuate the clinical symptoms of IBD. Thus, we aimed to identify bacteria that can reduce RNS and that can be used as valuable probiotics. In this study, we isolated bacteria resistant to nitrite stress from human feces and used 16S and whole-genome sequencing to identify them as Lactiplantibacillus plantarum LP7 (LP7). The ability to survive at high nitrite levels and to decrease them was greater in the LP7 strain than in the reference strain L. plantarum ATCC14917 (ATCC- 14917). To characterize the LP7 genome in more detail, we performed a comparative genome analysis. However, the unique genes that directly confer the ability to withstand nitrite stress were not present in the LP7 genome. Furthermore, we performed transcriptomic analysis of LP7 and ATCC14917 cells treated with nitrite. We found that the expression levels of genes involved in the cell division process were induced in LP7, which showed a more regular rod-shape than ATCC- 14917. This could explain why LP7 can survive better than ATCC14917 under nitrite stress. Based on its ability to survive better in nitrite stress and decrease nitrite concentration, we suggest that LP7 could be a valuable probiotic strain.

Mutational analysis on stable expression and LasB inhibition of LasB propeptide in Pseudomonas aeruginosa: Youngsun Shin , Xi-Hui Li , Cheol Seung Lee , Joon-Hee Lee; J. Microbiol. 2022;60(7):727-734. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-1671-5

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Abstract: Three major proteases, elastase B (LasB), protease IV (PIV), and elastase A (LasA) expressed in Pseudomonas aeruginosa play important roles in infections and pathogeneses. These are activated by a proteolytic cascade initiated by the activation of LasB. In this study, we investigated whether LasB could be inhibited using its propeptide (LasBpp). Although LasA and PIV were inhibited by their propeptides, LasB was not inhibited by purified LasBpp because LasB degraded LasBpp. To address this problem, mutant LasBpp variants were constructed to obtain a mutant LasBpp resistant to LasB degradation. A C-terminal deletion series of LasBpp was tested in vivo, and two positive candidates, T2 and T2-1, were selected. However, both caused growth retardation and were unstably expressed in vivo. Since deleting the C-terminal end of LasBpp significantly affected its stable expression, substitution mutations were introduced at the two amino acids near the truncation site of T2-1. The resulting mutants, LasBppE172D, LasBppG173A, and LasBppE172DG173A, significantly diminished LasB activity when overexpressed in vivo and were stably expressed in MW1, a quorum sensing mutant that does not produce LasB. In vitro analysis showed that purified LasBppE172DG173A inhibited LasB activity to a small extent. Summarizing, Cterminal modification of LasBpp profoundly affected the stable expression of LasBpp, and little enhanced the ability of LasBpp to resist degradation by LasB.

Extracellular vesicles derived from Lactobacillus plantarum restore chemosensitivity through the PDK2-mediated glucose metabolic pathway in 5-FU-resistant colorectal cancer cells: JaeJin An , Eun-Mi Ha; J. Microbiol. 2022;60(7):735-745. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-2201-1

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Abstract

Metabolic abnormalities are one of the main hallmarks of cancer and are associated with chemoresistance. Therefore, targeting the metabolic reprogramming of cancer cells has the potential to overcome chemoresistance. Probiotic-derived extracellular vesicles (EVs) play important roles in biological function and intracellular communication. However, the inhibitory effect of Lactobacillus plantarum-derived EVs (LpEVs) on colorectal cancer (CRC) cells has not yet been elucidated. This study clearly revealed that increased glycolysis in 5-fluorouracil (5-FU)-resistant CRC cells (CRC/5FUR) is directly related to chemoresistance and that the metabolic shift reversed by LpEVs inhibits cancer cell proliferation and eventually leads to apoptosis. Pyruvate dehydrogenase kinase 2 (PDK2), one of the crucial enzymes for enhancing glycolysis, was upregulated in CRC/5FUR cells. In our study, LpEVs sensitized CRC/5FUR cells to 5-FU by attenuating PDK2 expression in p53-p21-dependent metabolic signaling, thereby circumventing 5-FU resistance. We demonstrated the effect of cellular responses to 5-FU by modifying the PDK2 expression level in both 5-FU-sensitive parental CRC and 5- FU resistant CRC cell lines. Finally, we revealed that the PDK2 signaling pathway can potentially be targeted using LpEVs treatment to overcome chemoresistant CRC, thereby providing a potential strategy for CRC treatment by intervening in tumor metabolism.

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Effect of probiotic extracellular vesicles and their applications on health and disease
Guangzhao Wang, Yang Wang, Kangliang Sheng, Yongzhong Wang
Journal of the Science of Food and Agriculture.2025;[Epub] CrossRef
Incorporation of recombinant proteins into extracellular vesicles by Lactococcus cremoris
Tina Vida Plavec, Kristina Žagar Soderžnik, Giulia Della Pelle, Špela Zupančič, Robert Vidmar, Aleš Berlec
Scientific Reports.2025;[Epub] CrossRef
The benefits of Lactiplantibacillus plantarum: From immunomodulator to vaccine vector
Joshua Tobias, Stefan Heinl, Kristina Dendinovic, Ajša Ramić, Anna Schmid, Catherine Daniel, Ursula Wiedermann
Immunology Letters.2025; 272: 106971. CrossRef
Interconnections within the tumor microenvironment: extracellular vesicles as critical players of metabolic reprogramming in tumor cells
Carol Costa Encarnação, Giselle Marianne Faria, Victor Aguiar Franco, Luiz Gabriel Xavier Botelho, João Alfredo Moraes, Mariana Renovato-Martins
Journal of Cancer Metastasis and Treatment.2024;[Epub] CrossRef
Review of METTL3 in colorectal cancer: From mechanisms to the therapeutic potential
Lexuan Zhang, Zhenwei Mao, Kai Yin, Shengjun Wang
International Journal of Biological Macromolecules.2024; 277: 134212. CrossRef
Extracellular Vesicles from Lacticaseibacillus Paracasei PC-H1 Inhibit HIF-1α-Mediated Glycolysis of Colon Cancer
Yangqian Shi, Chunliang Zhang, Wanyu Cao, Luyi Li, Kaili Liu, Hanyue Zhu, Fikadu Balcha, Yong Fang
Future Microbiology.2024; 19(3): 227. CrossRef
Role of probiotic extracellular vesicles in inter-kingdom communication and current technical limitations in advancing their therapeutic utility
Rahul Sanwlani, Kyle Bramich, Suresh Mathivanan
Extracellular Vesicles and Circulating Nucleic Acids.2024; : 609. CrossRef
Beneficial microbiome and diet interplay in early-onset colorectal cancer
Zhengyuan Zhou, Linda Kleis, Ana Depetris-Chauvin, Stefanie Jaskulski, Victoria Damerell, Karin B Michels, Biljana Gigic, Ute Nöthlings, Gianni Panagiotou
EMBO Molecular Medicine.2024; 17(1): 9. CrossRef
Deciphering the role of host-gut microbiota crosstalk via diverse sources of extracellular vesicles in colorectal cancer
Yun Song, Min Shi, Yugang Wang
Molecular Medicine.2024;[Epub] CrossRef
Targeting the gut and tumor microbiome in cancer treatment resistance
Sona Ciernikova, Aneta Sevcikova, Michal Mego
American Journal of Physiology-Cell Physiology.2024; 327(6): C1433. CrossRef
Lactobacillus plantarum Metabolites Elicit Anticancer Effects by Inhibiting Autophagy-Related Responses
Sihyun Jeong, Yuju Kim, Soyeong Park, Doyeon Lee, Juho Lee, Shwe Phyu Hlaing, Jin-Wook Yoo, Sang Hoon Rhee, Eunok Im
Molecules.2023; 28(4): 1890. CrossRef
Extracellular Vesicles of Probiotics: Shedding Light on the Biological Activity and Future Applications
Paweł Krzyżek, Beatrice Marinacci, Irene Vitale, Rossella Grande
Pharmaceutics.2023; 15(2): 522. CrossRef
Isolation and Characterization of Cow-, Buffalo-, Sheep- and Goat-Milk-Derived Extracellular Vesicles
Monisha Samuel, Rahul Sanwlani, Mohashin Pathan, Sushma Anand, Ella L. Johnston, Ching-Seng Ang, Maria Kaparakis-Liaskos, Suresh Mathivanan
Cells.2023; 12(20): 2491. CrossRef
Gut microbiota in colorectal cancer development and therapy
Chi Chun Wong, Jun Yu
Nature Reviews Clinical Oncology.2023; 20(7): 429. CrossRef
Phytochemicals targeting glycolysis in colorectal cancer therapy: effects and mechanisms of action
Lu Zhan, Fangting Su, Qiang Li, Yueqiang Wen, Feng Wei, Zhelin He, Xiaoyan Chen, Xiang Yin, Jian Wang, Yilin Cai, Yuxia Gong, Yu Chen, Xiao Ma, Jinhao Zeng
Frontiers in Pharmacology.2023;[Epub] CrossRef
Crosstalk between gut microbiota and RNA N6-methyladenosine modification in cancer
Hao Su, Henley Cheung, Harry Cheuk-Hay Lau, Hongyan Chen, Xiaoting Zhang, Na Qin, Yifei Wang, Matthew Tak Vai Chan, William Ka Kei Wu, Huarong Chen
FEMS Microbiology Reviews.2023;[Epub] CrossRef

Crystal structure of the phage-encoded N-acetyltransferase in complex with acetyl-CoA, revealing a novel dimeric arrangement: Nayeon Ki , Inseong Jo , Yongseong Hyun , Jinwook Lee , Nam-Chul Ha , Hyun-Myung Oh; J. Microbiol. 2022;60(7):746-755. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-2030-2

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Abstract

Bacteriophages employ diverse mechanisms to facilitate the proliferation of bacteriophages. The Salmonella-infecting phage SPN3US contains a putative N-acetyltransferase, which is widely found in bacteriophages. However, due to low sequence similarity to the N-acetyltransferases from bacteria and eukaryotic cells, the structure and function of phage-encoded acetyltransferases are mainly unknown. This study determines the crystal structure of the putative N-acetyltransferase of SPN3US in complex with acetyl-CoA. The crystal structure showed a novel homodimeric arrangement stabilized by exchanging the C-terminal α-helix within the dimer. The following biochemical analyses suggested that the phageencoded acetyltransferase might have a very narrow substrate specificity. Further studies are required to reveal the biochemical activity, which would help elucidate the interaction between the phage and host bacteria in controlling pathogenic bacteria.

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Posttranslational modifications in bacteria during phage infection
Hannelore Longin, Nand Broeckaert, Vera van Noort, Rob Lavigne, Hanne Hendrix
Current Opinion in Microbiology.2024; 77: 102425. CrossRef

Predicting quorum sensing peptides using stacked generalization ensemble with gradient boosting based feature selection: Muthusaravanan Sivaramakrishnan , Rahul Suresh , Kannapiran Ponraj; J. Microbiol. 2022;60(7):756-765. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2044-9

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Abstract

Bacteria exist in natural environments for most of their life as complex, heterogeneous, and multicellular aggregates. Under these circumstances, critical cell functions are controlled by several signaling molecules known as quorum sensing (QS) molecules. In Gram-positive bacteria, peptides are deployed as QS molecules. The development of antibodies against such QS molecules has been identified as a promising therapeutic intervention for bacterial control. Hence, the identification of QS peptides has received considerable attention. Availability of a fast and reliable predictive model to effectively identify QS peptides can help the existing high throughput experiments. In this study, a stacked generalization ensemble model with Gradient Boosting Machine (GBM)-based feature selection, namely EnsembleQS was developed to predict QS peptides with high accuracy. On selected GBM features (791D), the EnsembleQS outperformed finely tuned baseline classifiers and demonstrated robust performance, indicating the superiority of the model. The accuracy of EnsembleQS is 4% higher than those resulting from ensemble model on hybrid dataset. When evaluating an independent data set of 40 QS peptides, the EnsembleQS model showed an accuracy of 93.4% with Matthew’s Correlation Coefficient (MCC) and area under the ROC curve (AUC) values 􀁇􀁇of 0.91 and 0.951, respectively. These
results
suggest that EnsembleQS will be a useful computational framework for predicting QS peptides and will efficiently support proteomics research. The source code and all datasets used in this study are publicly available at https:// github.com/proteinexplorers/EnsembleQS.

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Revolutionizing physics: a comprehensive survey of machine learning applications
Rahul Suresh, Hardik Bishnoi, Artem V. Kuklin, Atharva Parikh, Maxim Molokeev, R. Harinarayanan, Sarvesh Gharat, P. Hiba
Frontiers in Physics.2024;[Epub] CrossRef
DeepQSP: Identification of Quorum Sensing Peptides Through Neural Network Model
Md. Ashikur Rahman, Md. Mamun Ali, Kawsar Ahmed, Imran Mahmud, Francis M. Bui, Li Chen, Santosh Kumar, Mohammad Ali Moni
Results in Engineering.2024; 24: 102878. CrossRef
Computational tools for exploring peptide-membrane interactions in gram-positive bacteria
Shreya Kumar, Rex Devasahayam Arokia Balaya, Saptami Kanekar, Rajesh Raju, Thottethodi Subrahmanya Keshava Prasad, Richard K. Kandasamy
Computational and Structural Biotechnology Journal.2023; 21: 1995. CrossRef
DeepTPpred: A Deep Learning Approach With Matrix Factorization for Predicting Therapeutic Peptides by Integrating Length Information
Zhen Cui, Si-Guo Wang, Ying He, Zhan-Heng Chen, Qin-Hu Zhang
IEEE Journal of Biomedical and Health Informatics.2023; 27(9): 4611. CrossRef
PSRQSP: An effective approach for the interpretable prediction of quorum sensing peptide using propensity score representation learning
Phasit Charoenkwan, Pramote Chumnanpuen, Nalini Schaduangrat, Changmin Oh, Balachandran Manavalan, Watshara Shoombuatong
Computers in Biology and Medicine.2023; 158: 106784. CrossRef

Published Erratum

[Erratum] A split face study on the effect of an anti-acne product containing fermentation products of Enterococcus faecalis CBT SL-5 on skin microbiome modification and acne improvement: Hye Sung Han , Sun Hye Shin , Bo-Yun Choi , Nayeon Koo , Sanghyun Lim , Dooheon Son , Myung Jun Chung , Kui Young Park , Woo Jun Sul; J. Microbiol. 2022;60(7):766-766.; DOI: https://doi.org/10.1007/s12275-022-1682-2

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Skin Microbiome and Acne: Microbial Imbalances and Impact – Interview with Three Key Opinion Leaders
Brigitte Scott
EMJ Dermatology.2024; : 83. CrossRef

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