Journal of Microbiology

Research Article

Synbiotic combination of fructooligosaccharides and probiotics ameliorates the metabolic dysfunction-associated steatotic liver disease: Sang Yoon Lee, Su-Been Lee, Goo-Hyun Kwon, Seol Hee Song, Jeong Ha Park, Min Ju Kim, Jung A Eom, Kyeong Jin Lee, Sang Jun Yoon, Hyunjoon Park, Sung-Min Won, Jin-Ju Jeong, Ki-Kwang Oh, Young Lim Ham, Gwang Ho Baik, Dong Joon Kim, Satya Priya Sharma, Ki Tae Suk; J. Microbiol. 2025;63(2):e2411002. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411002

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Abstract PDF: Synbiotics have become a new-age treatment tool for limiting the progression of metabolic dysfunction-associated steatotic liver disease; however, inclusive comparisons of various synbiotic treatments are still lacking. Here, we have explored and evaluated multiple synbiotic combinations incorporating three distinctive prebiotics, lactitol, lactulose and fructooligosaccharides. Of the synbiotic treatments evaluated, a combination of fructooligosaccharides and probiotics (FOS+Pro) exhibited superior protection against western diet-induced liver degeneration. This synbiotic (FOS+Pro) combination resulted in the lowest body weight gains, liver weights and liver/body weight ratios. The FOS+Pro synbiotic combination substantially alleviated liver histopathological markers and reduced serum AST and cholesterol levels. FOS+Pro ameliorated hepatic inflammation by lowering expression of proinflammatory markers including TNF-α, IL-1β, IL-6, and CCL2. FOS+Pro significantly improved steatosis by restricting the expression of lipid metabolic regulators (ACC1, FAS) and lipid transporters (CD36) in the liver. These findings are critical in suggesting that synbiotic treatments are capable of restraining western diet-induced metabolic dysfunction in the liver. Additionally, this study demonstrated that adding probiotic strains amplified the effectiveness of fructooligosaccharides but not all prebiotics.

Journal Articles

Genetic and Functional Characterization of a Salicylate 1‑monooxygenase Located on an Integrative and Conjugative Element (ICE) in Pseudomonas stutzeri AJR13: Igor Ivanovski , Gerben J. Zylstra; J. Microbiol. 2023;61(12):1025-1032. Published online December 15, 2023; DOI: https://doi.org/10.1007/s12275-023-00093-x

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Abstract: Pseudomonas stutzeri strain AJR13 was isolated for growth on the related compounds biphenyl (BPH) and diphenylmethane (DPM). The BPH and DPM degradative pathway genes are present on an integrative and conjugative element (ICE) in the chromosome. Examination of the genome sequence of AJR13 revealed a gene encoding a salicylate 1-monooxygenase (salA) associated with the ICE even though AJR13 did not grow on salicylate. Transfer of the ICE to the well-studied Pseudomonas putida KT2440 resulted in a KT2440 strain that could grow on salicylate. Knockout mutagenesis of the salA gene on the ICE in KT2440 eliminated the ability to grow on salicylate. Complementation of the knockout with the cloned salA gene restored growth on salicylate. Transfer of the cloned salA gene under control of the lac promoter to KT2440 resulted in a strain that could grow on salicylate. Heterologous expression of the salA gene in E. coli BL21 DE3 resulted in the production of catechol from salicylate, confirming that it is indeed a salicylate 1-monooxygenase. Interestingly, transfer of the cloned salA gene under control of the lac promoter to AJR13 resulted in a strain that could now grow on salicylate, suggesting that gene expression for the downstream catechol pathway is intact.

Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids: Dongjin Choi , Yoonsoo Hahn; J. Microbiol. 2023;61(10):917-927. Published online October 16, 2023; DOI: https://doi.org/10.1007/s12275-023-00083-z

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Abstract

Potyvirids, members of the family Potyviridae, produce the P3N-PIPO protein, which is crucial for the cell-to-cell transport of viral genomic RNAs. The production of P3N-PIPO requires an adenine (A) insertion caused by RNA polymerase slippage at a conserved GAA AAA A ( GA6) sequence preceding the PIPO open reading frame. Presently, the slippage rate of RNA polymerase has been estimated in only a few potyvirids, ranging from 0.8 to 2.1%. In this study, we analyzed publicly available plant RNA-seq data and identified 19 genome contigs from 13 distinct potyvirids. We further investigated the RNA polymerase slippage rates at the GA6 motif. Our analysis revealed that the frequency of the A insertion variant ranges from 0.53 to 4.07% in 11 potyviruses (genus Potyvirus). For the two macluraviruses (genus Macluravirus), the frequency of the A insertion variant was found to be 0.72% and 10.96% respectively. Notably, the estimated RNA polymerase slippage rates for 12 out of the 13 investigated potyvirids were reported for the first time in this study. Our findings underscore the value of plant RNA-seq data for quantitative analysis of potyvirid genome variants, specifically at the GA6 slippage site, and contribute to a more comprehensive understanding of the RNA polymerase slippage phenomenon in potyvirids.

Citations

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Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data
Dongjin Choi, Hyerin Park, Seungwoo Baek, Myeung Seok Choi, Sylvain Legay, Gea Guerriero, Jean-François Hausman, Yoonsoo Hahn
Acta Virologica.2025;[Epub] CrossRef
Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins
Veronika Hýsková, Kateřina Bělonožníková, Josef Chmelík, Hana Hoffmeisterová, Noemi Čeřovská, Tomáš Moravec, Helena Ryšlavá
Plants.2024; 13(9): 1236. CrossRef
Reconceptualizing transcriptional slippage in plant RNA viruses
Adrian A. Valli, María Luisa Domingo-Calap, Alfonso González de Prádena, Juan Antonio García, Hongguang Cui, Cécile Desbiez, Juan José López-Moya, Shou-Wei Ding, Andrew Firth
mBio.2024;[Epub] CrossRef

Synthesis of pinene in the industrial strain Candida glycerinogenes by modification of its mevalonate pathway: Tengfei Ma , Hong Zong , Xinyao Lu , Bin Zhuge; J. Microbiol. 2022;60(12):1191-1200. Published online October 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2344-0

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Abstract

Terpenes have many applications and are widely found in nature, but recent progress in synthetic biology has enabled the use of microorganisms as chassis cells for the synthesis of these compounds. Candida glycerinogenes (C. glycerinogenes) is an industrial strain that may be developed as a chassis for the synthesis of terpenes since it has a tolerance to hyperosmolality and high sugar, and has a complete mevalonate (MVA) pathway. However, monoterpenes such as pinene are highly toxic, and the tolerance of C. glycerinogenes to pinene was investigated. We also measured the content of mevalonate and squalene to evaluate the strength of the MVA pathway. To determine terpene synthesis capacity, a pathway for the synthesis of pinene was constructed in C. glycerinogenes. Pinene production was improved by overexpression, gene knockdown and antisense RNA inhibition. Pinene production was mainly enhanced by strengthening the upstream MVA pathway and inhibiting the production of by-products from the downstream pathway. With these strategies, yield could be increased by almost 16 times, to 6.0 mg/L. Overall, we successfully constructed a pinene synthesis pathway in C. glycerinogenes and enhanced pinene production through metabolic modification.

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Recent advances in genome mining and synthetic biology for discovery and biosynthesis of natural products
Mingpeng Wang, Lei Chen, Zhaojie Zhang, Qinhong Wang
Critical Reviews in Biotechnology.2025; 45(1): 236. CrossRef
Two-Phase Fermentation Systems for Microbial Production of Plant-Derived Terpenes
Tuo Li, Ximeng Liu, Haoyu Xiang, Hehua Zhu, Xuan Lu, Baomin Feng
Molecules.2024; 29(5): 1127. CrossRef
Acetic acid stress and utilization synergistically enhance squalene biosynthesis in Candida glycerinogenes
Zhenzhen You, Xueqing Du, Hong Zong, Xinyao Lu, Bin Zhuge
Biochemical Engineering Journal.2024; 210: 109413. CrossRef
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Roman M. Dickey, Madan R. Gopal, Priyanka Nain, Aditya M. Kunjapur
Journal of Biotechnology.2024; 389: 43. CrossRef
Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica
Dong-Xun Li, Qi Guo, Yu-Xin Yang, Shun-Jie Jiang, Xiao-Jun Ji, Chao Ye, Yue-Tong Wang, Tian-Qiong Shi
ACS Synthetic Biology.2024; 13(6): 1647. CrossRef
Gene Editing of Candida glycerinogenes by Designed Toxin–Antitoxin Cassette
Wen Lv, Xinyao Lu, Bin Zhuge, Hong Zong
ACS Synthetic Biology.2024; 13(3): 816. CrossRef
Candida glycerinogenes-Promoted α-Pinene and Squalene Co-production Strategy Based on α-Pinene Stress
Tengfei Ma, Hong Zong, Xinyao Lu, Bin Zhuge
Journal of Agricultural and Food Chemistry.2023; 71(13): 5250. CrossRef

Deletion of lacD gene affected stress tolerance and virulence of Streptococcus suis serotype 2: Xiaowu Jiang , Lexin Zhu , Dongbo Zhan; J. Microbiol. 2022;60(9):948-959. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2146-4

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Abstract

Streptococcus suis type 2 (S. suis type 2, SS2), an infectious pathogen which is zoonotic and can induce severely public health concern. Our previous research identified a newly differential secreted effector of tagatose-bisphosphate aldolase (LacD) mediated by VirD4 factor within the putative type IV secretion system of SS2, whereas the functional basis and roles in virulence of LacD remain elusive. Here in this study, the LacD was found enzymatic and can be activated to express under oxidative stress. Gene mutant and its complemental strain (ΔlacD and cΔlacD) were constructed to analyze the phenotypes, virulence and transcriptomic profiles as compared with the parental strain. The lacD gene deletion showed no effect on growth capability and cells morphology of SS2. However, reduced tolerance to oxidative and heat stress conditions, increased antimicrobial susceptibility to ciprofloxacin and kanamycin were found in ΔlacD strain. Further, the LacD deficiency led to weakened invasion and attenuated virulence since an easier phagocytosed and more prone to be cleared of SS2 in macrophages were shown in ΔlacD mutant. Distinctive transcriptional profiling in ΔlacD strain and typical downregulated genes with significant mRNA changes including alcohol dehydrogenase, GTPase, integrative and conjugative elements, and iron ABC transporters which were mainly involved in cell division, stress response, antimicrobial susceptibility and virulence regulation, were examined and confirmed by RNA sequencing and real time qPCR. In summary, the
results
demonstrated for the first time that LacD was a pluripotent protein mediated the metabolic, stress and virulent effect of SS2.

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Investigation of choline-binding protein of CbpD in the pathogenesis of Streptococcus suis type 2
Lexin Zhu, Mengqing Li, Guijun Yu, Dongbo Zhan, Wenzhen Zeng, Nanyan Fu, Xiaowu Jiang
Frontiers in Veterinary Science.2024;[Epub] CrossRef

Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola: Yurim Bae , Sujin Lee , Kitae Kim , Hyun-Kwon Lee , Soon-Kyeong Kwon , Jihyun F. Kim; J. Microbiol. 2021;59(11):1010-1018. Published online November 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1452-6

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Abstract

The actinobacterial group is regarded as a reservoir of biologically active natural products and hydrolytic enzymes with the potential for biomedical and industrial applications. Here, we present the complete genome sequence of Isoptericola dokdonensis DS-3 isolated from soil in Dokdo, small islets in the East Sea of Korea. This actinomycete harbors a large number of genes encoding carbohydrate-degrading enzymes, and its activity to degrade carboxymethyl cellulose into glucose was experimentally evaluated. Since the genus Isoptericola was proposed after reclassification based on phylogenetic analysis, strains of Isoptericola have been continuously isolated from diverse environments and the importance of this genus in the ecosystem has been suggested by recent culturomic or metagenomic studies. The phylogenic relationships of the genus tended to be closer among strains that had been isolated from similar habitats. By analyzing the properties of published genome sequences of seven defined species in the genus, a large number of genes for carbohydrate hydrolysis and utilization, as well as several biosynthetic gene clusters for secondary metabolites, were identified. Genomic information of I. dokdonensis DS-3 together with comparative analysis of the genomes of Isoptericola provides insights into understanding this actinobacterial group with a potential for industrial applications.

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From lignocellulosic biomass to single cell oil for sustainable biomanufacturing: Current advances and prospects
Yu Duan, Limei Chen, Longxue Ma, Farrukh Raza Amin, Yida Zhai, Guofu Chen, Demao Li
Biotechnology Advances.2024; 77: 108460. CrossRef
A comprehensive review on strategic study of cellulase producing marine actinobacteria for biofuel applications
Ashwini John J, Melvin S. Samuel, Muthusamy Govarthanan, Ethiraj Selvarajan
Environmental Research.2022; 214: 114018. CrossRef

Extracellular products-mediated interspecific interaction between Pseudomonas aeruginosa and Escherichia coli: Yang Yuan , Jing Li , Jiafu Lin , Wenjuan Pan , Yiwen Chu , Balakrishnan Prithiviraj , Yidong Guo , Xinrong Wang , Kelei Zhao; J. Microbiol. 2021;59(1):29-40. Published online December 23, 2020; DOI: https://doi.org/10.1007/s12275-021-0478-0

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Abstract

The Gram-negative pathogen Pseudomonas aeruginosa adopts several elaborate strategies to colonize a wide range of natural or clinical niches and to overcome the neighboring bacterial competitors in polymicrobial communities. However, the relationship and interaction mechanism of P. aeruginosa with other bacterial pathogens remains largely unexplored. Here we explore the interaction dynamics of P. aeruginosa and Escherichia coli, which frequently coinfect the lungs of immunocompromised hosts, by using a series of on-plate proximity assays and RNA-sequencing. We show that the extracellular products of P. aeruginosa can inhibit the growth of neighboring E. coli and induce a large-scale of transcriptional reprogramming of E. coli, especially in terms of cellular respiration- related primary metabolisms and membrane components. In contrast, the presence of E. coli has no significant effect on the growth of P. aeruginosa in short-term culture, but causes a dysregulated expression of genes positively controlled by the quorum-sensing (QS) system of P. aeruginosa during subsequent pairwise culture. We further demonstrate that the divergent QS-regulation of P. aeruginosa may be related to the function of the transcriptional regulator PqsR, which can be enhanced by E. coli culture supernatant to increase the pyocyanin production by P. aeruginosa in the absence of the central las-QS system. Moreover, the extracellular products of E. coli promote the proliferation and lethality of P. aeruginosa in infecting the Caenorhabditis elegans model. The current study provides a general characterization of the extracellular products-mediated interactions between P. aeruginosa and E. coli, and may facilitate the understanding of polymicrobial infections.

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Pigments from pathogenic bacteria: a comprehensive update on recent advances
Kusumita Acharya, Swarna Shaw, Sudipta Paul Bhattacharya, Shatarupa Biswas, Suman Bhandary, Arijit Bhattacharya
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Selective detection of two bacterial species in a single collision system targeting metabolic products
Jun Lin, Qingwen Wang, Huike Tian, Qing Xin, Dong Zhang
Microchemical Journal.2024; 206: 111572. CrossRef
Effect of the Type VI Secretion System Secreted Protein Hcp on the Virulence of Aeromonas salmonicida
Hongyan Cai, Jiaying Yu, Ying Qiao, Ying Ma, Jiang Zheng, Mao Lin, Qingpi Yan, Lixing Huang
Microorganisms.2022; 10(12): 2307. CrossRef

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; J. Microbiol. 2020;58(5):350-356. Published online April 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9471-2

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Abstract

A nitrate-reducing Fe(II)-oxidizing bacterial strain, F8825T, was isolated from the Fe(II)-rich sediment of an urban creek in Pearl River Delta, China. The strain was Gram-negative, facultative chemolithotrophic, facultative anaerobic, nonspore- forming, and rod-shaped with a single flagellum. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that it belongs to the genus Ciceribacter and is most closely related to C. lividus MSSRFBL1T (99.4%), followed by C. thiooxidans F43bT (98.8%) and C. azotifigens A.slu09T (98.0%). Fatty acid, polar lipid, respiratory quinone, and DNA G + C content analyses supported its classification in the genus Ciceribacter. Multilocus sequence analysis of concatenated 16S rRNA, atpD, glnII, gyrB, recA, and thrC suggested that the isolate was a novel species. DNA–DNA hybridization and genome sequence comparisons (90.88 and 89.86%, for values of ANIm and ANIb between strains F8825T with MSSRFBL1T, respectively) confirmed that strain F8825T was a novel species, different from C. lividus MSSRFBL1T, C. thiooxidans F43bT, and C. azotifigens A.slu09T. The physiological and biochemical properties of the strain, such as carbon source utilization, nitrate reduction, and ferrous ion oxidation, further supported that this is a novel species. Based on the polyphasic taxonomic results, strain F8825T was identified as a novel species in the genus Ciceribacter, for which the name Ciceribacter ferrooxidans sp. nov. is proposed. The type strain is F8825T (= CCTCC AB 2018196T = KCTC 62948T).

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Review

[MINIREVIEW] Probiotics in human health and disease: from nutribiotics to pharmabiotics: Eun-Sook Lee , Eun-Ji Song , Young-Do Nam , So-Young Lee; J. Microbiol. 2018;56(11):773-782. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8293-y

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Abstract

Probiotics are the most useful tools for balancing the gut microbiota and thereby influencing human health and disease. Probiotics have a range of effects, from those on nutritional status to medical conditions throughout the body from the gut to non-intestinal body sites such as the brain and skin. Research interest in probiotics with nutritive claims (categorized as nutribiotics) has evolved into interest in therapeutic and pharmacological probiotics with health claims (pharmabiotics). The concept of pharmabiotics emerged only two decades ago, and the new categorization of probiotics to nutribiotics and pharmabiotics was recently suggested, which are under the different regulation depending on that they are food or drug. Information of the gut microbiome has been continuously accumulating, which will make possible the gut microbiome-based healthcare in the future, when nutribiotics show potential for maintaining health while pharmabiotics are effective therapeutic tools for human diseases. This review describes the current understanding in the conceptualization and classification of probiotics. Here, we reviewed probiotics as nutribiotics with nutritional functions and pharmabiotics with pharmaceutic functions in different diseases.

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Published Erratum

Erratum to: Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyeong Park , Shinnam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(6):653-653.; DOI: https://doi.org/10.1007/s12275-023-00060-6

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Abstract: Correction to: Journal of Microbiology (2023) 61:189–197 https://doi.org/10.1007/s12275-023-00017-9 In this article two author names are given erroneaously: Written incorrectly: Ki Hyung Park · Shin Nam Yoo It should be read: Ki Hyeong Park · Shinnam Yoo

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