Journal of Microbiology

Journal Articles

Probiotic supplements alleviate gestational diabetes mellitus by restoring the diversity of gut microbiota: a study based on 16S rRNA sequencing: Qing-Xiang Zheng , Xiu-Min Jiang , Hai-Wei Wang , Li Ge , Yu-Ting Lai , Xin-Yong Jiang , Fan Chen , Ping-Ping Huang; J. Microbiol. 2021;59(9):827-839. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1094-8

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Probiotics effectively prevent and improve metabolic diseases such as diabetes by regulating the intestinal microenvironment and gut microbiota. However, the effects of probiotics in gestational diabetes mellitus are not clear. Here, we showed that probiotic supplements significantly improved fasting blood glucose in a gestational diabetes mellitus rat model. To further understand the mechanisms of probiotics in gestational diabetes mellitus, the gut microbiota were analyzed via 16S rRNA sequencing. We found that compared with the normal pregnant group, the gestational diabetes mellitus rats had decreased diversity of gut microbiota. Moreover, probiotic supplementation restored the diversity of the gut microbiota in gestational diabetes mellitus rats, and the gut microbiota structure tended to be similar to that of normal pregnant rats. In particular, compared with gestational diabetes mellitus rats, the abundance of Firmicutes and Actinobacteria was higher after probiotic supplementation. Furthermore, activating carbohydrate metabolism and membrane transport pathways may be involved in the potential mechanisms by which probiotic supplements alleviate gestational diabetes mellitus. Overall, our results suggested that probiotic supplementation might be a novel approach to restore the gut microbiota of gestational diabetes mellitus rats and provided an experimental evidence for the use of probiotic supplements to treat gestational diabetes melitus.

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Dietary Polyphenols Support Akkermansia muciniphila Growth via Mediation of the Gastrointestinal Redox Environment
Charlene B. Van Buiten, Valerie A. Seitz, Jessica L. Metcalf, Ilya Raskin
Antioxidants.2024; 13(3): 304. CrossRef
The Intervention of Probiotics on Type 2 Diabetes Mellitus in Animal Models
Qianyu Qu, Penggang He, Yuqi Zhang, Shujuan Yang, Peibin Zeng
Molecular Nutrition & Food Research.2024;[Epub] CrossRef
Lactobacillus gasseri BNR17 and Limosilactobacillus fermentum ABF21069 Ameliorate High Sucrose-Induced Obesity and Fatty Liver via Exopolysaccharide Production and β-oxidation
Yu Mi Jo, Yoon Ji Son, Seul-Ah Kim, Gyu Min Lee, Chang Won Ahn, Han-Oh Park, Ji-Hyun Yun
Journal of Microbiology.2024; 62(10): 907. CrossRef
Probiotic therapy as a promising strategy for gestational diabetes mellitus management
Deborah Emanuelle de Albuquerque Lemos, José Luiz de Brito Alves, Evandro Leite de Souza
Expert Opinion on Biological Therapy.2024; 24(11): 1207. CrossRef
Influence of Symbiotic Fermentation Broth on Regulating Metabolism with Gut Microbiota and Metabolite Profiles Is Estimated Using a Third-Generation Sequencing Platform
Chih-Yin Wu, Chun-Kai Huang, Wei-Sheng Hong, Yin-Hsiu Liu, Ming-Chi Shih, Jung-Chun Lin
Metabolites.2023; 13(9): 999. CrossRef
Neuroprotective Effect of Ponicidin Alleviating the Diabetic Cognitive Impairment: Regulation of Gut Microbiota
Xiaojuan Zhang, Feng Guo, Dujuan Cao, Yinan Yan, Ning Zhang, Kaili Zhang, Xinyi Li, Prashant Kumar, Xiaojuan Zhang
Applied Biochemistry and Biotechnology.2023; 195(2): 735. CrossRef
Antidiabetogenic mechanisms of probiotic action in food matrices: A review
Vanessa Moraes Ramalho Castro, Rosa Helena Luchese
PharmaNutrition.2022; 21: 100302. CrossRef
Prepregnancy body mass index and gestational weight gain are associated with maternal and infant adverse outcomes in Chinese women with gestational diabetes
Qing-Xiang Zheng, Hai-Wei Wang, Xiu-Min Jiang, Yan Lin, Gui-Hua Liu, Mian Pan, Li Ge, Xiao-Qian Chen, Jing-Ling Wu, Xiao-Yun Zhang, Yu-Qing Pan, Hong-Gu He
Scientific Reports.2022;[Epub] CrossRef
Probiotic Intervention in the Treatment of Diabetes Mellitus: A Review
Navya Sreepathi, M.K. Jayanthi, S. Jagadeep Chandra, Shrisha Naik Bajpe, Ramith Ramu
Journal of Pure and Applied Microbiology.2022; 16(3): 1519. CrossRef
Ameliorative Effects of Bifidobacterium animalis subsp. lactis J-12 on Hyperglycemia in Pregnancy and Pregnancy Outcomes in a High-Fat-Diet/Streptozotocin-Induced Rat Model
Jianjun Yang, Yumeng Ma, Tong Li, Yuanxiang Pang, Hongxing Zhang, Yuanhong Xie, Hui Liu, Yanfang Sun, Jianhua Ren, Junhua Jin
Nutrients.2022; 15(1): 170. CrossRef
Probiotic Mechanisms Affecting Glucose Homeostasis: A Scoping Review
Maša Pintarič, Tomaž Langerholc
Life.2022; 12(8): 1187. CrossRef
The Roles of Probiotics in the Gut Microbiota Composition and Metabolic Outcomes in Asymptomatic Post-Gestational Diabetes Women: A Randomized Controlled Trial
Zubaidah Hasain, Raja Affendi Raja Ali, Hajar Fauzan Ahmad, Ummul Fahri Abdul Rauf, Seok Fang Oon, Norfilza Mohd Mokhtar
Nutrients.2022; 14(18): 3878. CrossRef
Changes in the Gut Metabolic Profile of Gestational Diabetes Mellitus Rats Following Probiotic Supplementation
Qing-Xiang Zheng, Hai-Wei Wang, Xiu-Min Jiang, Li Ge, Yu-Ting Lai, Xin-Yong Jiang, Ping-Ping Huang, Fan Chen, Xiao-Qian Chen
Frontiers in Microbiology.2022;[Epub] CrossRef
Microorganisms in the reproductive system and probiotic's regulatory effects on reproductive health
Tao Feng, Yan Liu
Computational and Structural Biotechnology Journal.2022; 20: 1541. CrossRef
Several Shaping Characteristics of OneCurve Continuously Rotating System versus Three Different Kinematic Systems: ProTaper Universal, Twisted File Adaptive and WaveOne Gold
Ali Türkyılmaz, Volkan Arıkan
Meandros Medical and Dental Journal.2022; 23(1): 67. CrossRef

The putative C2H2 transcription factor RocA is a novel regulator of development and secondary metabolism in Aspergillus nidulans: Dong Chan Won , Yong Jin Kim , Da Hye Kim , Hee-Moon Park , Pil Jae Maeng; J. Microbiol. 2020;58(7):574-587. Published online April 22, 2020; DOI: https://doi.org/10.1007/s12275-020-0083-7

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Abstract

Multiple transcriptional regulators play important roles in the coordination of developmental processes, including asexual and sexual development, and secondary metabolism in the filamentous fungus Aspergillus nidulans. In the present study, we characterized a novel putative C2H2-type transcription factor (TF), RocA, in relation to development and secondary metabolism. Deletion of rocA increased conidiation and caused defective sexual development. In contrast, the overexpression of rocA exerted opposite effects on both phenotypes. Additionally, nullifying rocA resulted in enhanced brlA expression and reduced nsdC expression, whereas its overexpression exerted the opposite effects. These results suggest that RocA functions as a negative regulator of asexual development by repressing the expression of brlA encoding a key asexual development activator, but as a positive regulator of sexual development by enhancing the expression of nsdC encoding a pivotal sexual development activator. Deletion of rocA increased the production of sterigmatocystin (ST), as well as the expression of its biosynthetic genes, aflR and stcU. Additionally, the expression of the biosynthetic genes for penicillin (PN), ipnA and acvA, and for terrequinone (TQ), tdiB and tdiE, was increased by rocA deletion. Thus, it appears that RocA functions as a negative transcriptional modulator of the secondary metabolic genes involved in ST, PN, and TQ biosynthesis. Taken together, we propose that RocA is a novel transcriptional regulator that may act either positively or negatively at multiple target genes necessary for asexual and sexual development and secondary metabolism.

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srdA mutations suppress the rseA/cpsA deletion mutant conidiation defect in Aspergillus nidulans
Masahiro Ogawa, Ryouichi Fukuda, Ryo Iwama, Yasuji Koyama, Hiroyuki Horiuchi
Scientific Reports.2023;[Epub] CrossRef
Identification of a Novel Pleiotropic Transcriptional Regulator Involved in Sporulation and Secondary Metabolism Production in Chaetomium globosum
Shanshan Zhao, Kai Zhang, Congyu Lin, Ming Cheng, Jinzhu Song, Xin Ru, Zhengran Wang, Wan Wang, Qian Yang
International Journal of Molecular Sciences.2022; 23(23): 14849. CrossRef

Editorial

User guides for biologists to learn computational methods: Dokyun Na; J. Microbiol. 2020;58(3):173-175. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9723-1

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Abstract

System-wide studies of a given molecular type are referred to as “omics.” These include genomics, proteomics, and metabolomics, among others. Recent biotechnological advances allow for high-throughput measurement of cellular components, and thus it becomes possible to take a snapshot of all molecules inside cells, a form of omics study. Advances in computational modeling methods also make it possible to predict cellular mechanisms from the snapshots. These technologies have opened an era of computation-based biology. Component snapshots allow the discovery of gene-phenotype relationships in diseases, microorganisms in the human body, etc. Computational models allow us to predict new outcomes, which are useful in strain design in metabolic engineering and drug discovery from protein-ligand interactions. However, as the quantity of data increases or the model becomes complicated, the process becomes less accessible to biologists. In this special issue, six protocol articles are presented as user guides in the field of computational biology.

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Self-controlled in silico gene knockdown strategies to enhance the sustainable production of heterologous terpenoid by Saccharomyces cerevisiae
Na Zhang, Xiaohan Li, Qiang Zhou, Ying Zhang, Bo Lv, Bing Hu, Chun Li
Metabolic Engineering.2024; 83: 172. CrossRef
Comparative Transcriptomic Analysis of Flagellar-Associated Genes in Salmonella Typhimurium and Its rnc Mutant
Seungmok Han, Ji-Won Byun, Minho Lee
Journal of Microbiology.2024; 62(1): 33. CrossRef
Automation of Drug Discovery through Cutting-edge In-silico Research in Pharmaceuticals: Challenges and Future Scope
Smita Singh, Pranjal Kumar Singh, Kapil Sachan, Mukesh Kumar, Poonam Bhardwaj
Current Computer-Aided Drug Design.2024; 20(6): 723. CrossRef
A review of Ribosome profiling and tools used in Ribo-seq data analysis
Mingso Sherma Limbu, Tianze Xiong, Sufang Wang
Computational and Structural Biotechnology Journal.2024; 23: 1912. CrossRef
Curcumin-Incorporated Biomaterials: In silico and in vitro evaluation of biological potentials
Nasim Azari Torbat, Iman Akbarzadeh, Niloufar Rezaei, Zahra Salehi Moghaddam, Saba Bazzazan, Ebrahim Mostafavi
Coordination Chemistry Reviews.2023; 492: 215233. CrossRef
Regulator of RNase E activity modulates the pathogenicity of Salmonella Typhimurium
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
Microbial Pathogenesis.2022; 165: 105460. CrossRef
Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6
Younkyung Choi, Minju Joo, Wooseok Song, Minho Lee, Hana Hyeon, Hyun-Lee Kim, Ji-Hyun Yeom, Kangseok Lee, Eunkyoung Shin
Journal of Microbiology.2022; 60(12): 1162. CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef
Trans-acting regulators of ribonuclease activity
Jaejin Lee, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(4): 341. CrossRef
Regulator of ribonuclease activity modulates the pathogenicity of Vibrio vulnificus
Jaejin Lee, Eunkyoung Shin, Jaeyeong Park, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(12): 1133. CrossRef

Journal Article

STATR: A simple analysis pipeline of Ribo-Seq in bacteria: Donghui Choe , Bernhard Palsson , Byung-Kwan Cho; J. Microbiol. 2020;58(3):217-226. Published online January 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9536-2

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Abstract

Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances in next-generation sequencing (NGS), the abundance of cellular mRNA has been elucidated via transcriptome sequencing. However, several studies have found a discrepancy between mRNA abundance and protein levels induced by translational regulation, including different rates of ribosome entry and translational pausing. As such, the levels of mRNA are not necessarily a direct representation of the protein levels found in a cell. To determine a more precise way to measure protein expression in cells, the analysis of the levels of mRNA associated with ribosomes is being adopted. With an aid of NGS techniques, a single nucleotide resolution footprint of the ribosome was determined using a method known as Ribo- Seq or ribosome profiling. This method allows for the highthroughput measurement of translation in vivo, which was further analyzed to determine the protein synthesis rate, translational pausing, and cellular responses toward a variety of environmental changes. Here, we describe a simple analysis pipeline for Ribo-Seq in bacteria, so-called simple translatome analysis tool for Ribo-Seq (STATR). STATR can be used to carry out the primary processing of Ribo-Seq data, subsequently allowing for multiple levels of translatome study, from experimental validation to in-depth analyses. A command- by-command explanation is provided here to allow a broad spectrum of biologists to easily reproduce the analysis.

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Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation
Olga Iwańska, Przemysław Latoch, Natalia Kopik, Mariia Kovalenko, Małgorzata Lichocka, Remigiusz Serwa, Agata L. Starosta
Nature Communications.2024;[Epub] CrossRef
Comparative Transcriptome Analysis of Zerumbone-Treated Helicobacter pylori
Hyun Jun Woo, Ji Yeong Yang, Sa-Hyun Kim
Microbiology and Biotechnology Letters.2022; 50(2): 301. CrossRef
Synthetic 3′-UTR valves for optimal metabolic flux control in Escherichia coli
Donghui Choe, Kangsan Kim, Minjeong Kang, Seung-Goo Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Nucleic Acids Research.2022; 50(7): 4171. CrossRef
Comparative Transcriptome Analysis of Caryophyllene- Treated Helicobacter pylori
Hyun Jun Woo, Ji Yeong Yang, Hye Jin Kwon, Hyun Woo Kim, Sa-Hyun Kim, Jong-Bae Kim
Microbiology and Biotechnology Letters.2021;[Epub] CrossRef
RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
Donghui Choe, Richard Szubin, Saugat Poudel, Anand Sastry, Yoseb Song, Yongjae Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho, Lefu Lan
PLOS Genetics.2021; 17(9): e1009821. CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef
HRIBO: high-throughput analysis of bacterial ribosome profiling data
Rick Gelhausen, Sarah L Svensson, Kathrin Froschauer, Florian Heyl, Lydia Hadjeras, Cynthia M Sharma, Florian Eggenhofer, Rolf Backofen, Valencia Alfonso
Bioinformatics.2021; 37(14): 2061. CrossRef
User guides for biologists to learn computational methods
Dokyun Na
Journal of Microbiology.2020; 58(3): 173. CrossRef

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