Journal of Microbiology

Journal Article

Effects of digested Cheonggukjang on human microbiota assessed by in vitro fecal fermentation: Vineet Singh , Nakwon Hwang , Gwangpyo Ko , Unno Tatsuya; J. Microbiol. 2021;59(2):217-227. Published online February 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0525-x

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In vitro fecal fermentation is an assay that uses fecal microbes to ferment foods, the results of which can be used to evaluate the potential of prebiotic candidates. To date, there have been various protocols used for in vitro fecal fermentation- based assessments of food substances. In this study, we investigated how personal gut microbiota differences and external factors affect the results of in vitro fecal fermentation assays. We used Cheonggukjang (CGJ), a Korean traditional fermented soybean soup that is acknowledged as healthy functional diet. CGJ was digested in vitro using acids and enzymes, and then fermented with human feces anaerobically. After fecal fermentation, the microbiota was analyzed using MiSeq, and the amount of short chain fatty acids (SCFAs) were measured using GC-MS. Our results suggest that CGJ was effectively metabolized by fecal bacteria to produce SCFAs, and this process resulted in an increase in the abundance of Coprococcus, Ruminococcus, and Bifidobacterium and a reduction in the growth of Sutterella, an opportunistic pathogen. The metabolic activities predicted from the microbiota shifts indicated enhanced metabolism linked to methionine biosynthesis and depleted chondroitin sulfate degradation. Moreover, the amount of SCFAs and microbiota shifts varied depending on personal microbiota differences. Our findings also suggest that in vitro fecal fermentation of CGJ for longer durations may partially affect certain fecal microbes. Overall, the study discusses the usability of in vitro gastrointestinal digestion and fecal fermentation (GIDFF) to imitate the effects of diet-induced microbiome modulation and its impact on the host.

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Significance of Soy-Based Fermented Food and Their Bioactive Compounds Against Obesity, Diabetes, and Cardiovascular Diseases
Sushmita Dwivedi, Vineet Singh, Kritika Sharma, Amani Sliti, Mamta Baunthiyal, Jae-Ho Shin
Plant Foods for Human Nutrition.2024; 79(1): 1. CrossRef
Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health
Ramya Balasubramanian, Elizabeth Schneider, Eoin Gunnigle, Paul D. Cotter, John F. Cryan
Neuroscience & Biobehavioral Reviews.2024; 158: 105562. CrossRef
The nutrition and therapeutic potential of millets: an updated narrative review
Jinu Jacob, Veda Krishnan, Chris Antony, Masimukka Bhavyasri, C. Aruna, Kiran Mishra, Thirunavukkarasu Nepolean, Chellapilla Tara Satyavathi, Kurella B. R. S. Visarada
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Effects of OsomeFood Clean Label plant-based meals on the gut microbiome
Dwiyanto Jacky, Chia Bibi, Look Melvin Chee Meng, Fong Jason, Tan Gwendoline, Lim Jeremy, Chong Chun Wie
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Fermented soybean foods and diabetes
Yoshitaka Hashimoto, Masahide Hamaguchi, Michiaki Fukui
Journal of Diabetes Investigation.2023; 14(12): 1329. CrossRef
Early response of the gut microbiome and serum metabolites to Cheonggukjang intake in healthy Korean subjects
Eun-Ji Song, Min Jung Kim, Chang Hwa Jung, Won-Hyong Chung, Young-Do Nam, Mi Young Lim
Journal of Functional Foods.2023; 101: 105420. CrossRef
Role, relevance, and possibilities of in vitro fermentation models in human dietary, and gut‐microbial studies
Vineet Singh, HyunWoo Son, GyuDae Lee, Sunwoo Lee, Tatsuya Unno, Jae‐Ho Shin
Biotechnology and Bioengineering.2022; 119(11): 3044. CrossRef
Evaluation of Prebiotics through an In Vitro Gastrointestinal Digestion and Fecal Fermentation Experiment: Further Idea on the Implementation of Machine Learning Technique
Hokyung Song, Dabin Jeon, Tatsuya Unno
Foods.2022; 11(16): 2490. CrossRef
Anti-diabetic prospects of dietary bio-actives of millets and the significance of the gut microbiota: A case of finger millet
Vineet Singh, GyuDae Lee, HyunWoo Son, Sliti Amani, Mamta Baunthiyal, Jae-Ho Shin
Frontiers in Nutrition.2022;[Epub] CrossRef
Current Perspectives on the Physiological Activities of Fermented Soybean-Derived Cheonggukjang
Il-Sup Kim, Cher-Won Hwang, Woong-Suk Yang, Cheorl-Ho Kim
International Journal of Molecular Sciences.2021; 22(11): 5746. CrossRef
Alleviation of Neuronal Cell Death and Memory Deficit with Chungkookjang Made with Bacillus amyloliquefaciens and Bacillus subtilis Potentially through Promoting Gut–Brain Axis in Artery-Occluded Gerbils
Ting Zhang, Myeong-Seon Ryu, Xuangao Wu, Hee-Jong Yang, Su Ji Jeong, Ji-Won Seo, Do-Yeon Jeong, Sunmin Park
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The final fate of food: On the establishment of in vitro colon models
Saartje Hernalsteens, Song Huang, Hai Hua Cong, Xiao Dong Chen
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In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools
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Reviews

[MINIREVIEW]Regulation of gene expression by protein lysine acetylation in Salmonella: Hyojeong Koo , Shinae Park , Min-Kyu Kwak , Jung-Shin Lee; J. Microbiol. 2020;58(12):979-987. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-020-0483-8

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Abstract

Protein lysine acetylation influences many physiological functions, such as gene regulation, metabolism, and disease in eukaryotes. Although little is known about the role of lysine acetylation in bacteria, several reports have proposed its importance in various cellular processes. Here, we discussed the function of the protein lysine acetylation and the post-translational modifications (PTMs) of histone-like proteins in bacteria focusing on Salmonella pathogenicity. The protein lysine residue in Salmonella is acetylated by the Pat-mediated enzymatic pathway or by the acetyl phosphate-mediated non-enzymatic pathway. In Salmonella, the acetylation of lysine 102 and lysine 201 on PhoP inhibits its protein activity and DNAbinding, respectively. Lysine acetylation of the transcriptional regulator, HilD, also inhibits pathogenic gene expression. Moreover, it has been reported that the protein acetylation patterns significantly differ in the drug-resistant and -sensitive Salmonella strains. In addition, nucleoid-associated proteins such as histone-like nucleoid structuring protein (H-NS) are critical for the gene silencing in bacteria, and PTMs in H-NS also affect the gene expression. In this review, we suggest that protein lysine acetylation and the post-translational modifications of H-NS are important factors in understanding the regulation of gene expression responsible for pathogenicity in Salmonella.

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Bacterial protein acetylation: mechanisms, functions, and methods for study
Jocelin Rizo, Sergio Encarnación-Guevara
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Acetyl-proteome profiling revealed the role of lysine acetylation in erythromycin resistance of Staphylococcus aureus
Miao Feng, Xiaoyu Yi, Yanling Feng, Feng He, Zonghui Xiao, Hailan Yao
Heliyon.2024; 10(15): e35326. CrossRef
Short-chain fatty acids in breast milk and their relationship with the infant gut microbiota
Menglu Xi, Yalu Yan, Sufang Duan, Ting Li, Ignatius Man-Yau Szeto, Ai Zhao
Frontiers in Microbiology.2024;[Epub] CrossRef
Global Insights into the Lysine Acetylome Reveal the Role of Lysine Acetylation in the Adaptation of Bacillus altitudinis to Salt Stress
Xujian Li, Shanshan Dai, Shanshan Sun, Dongying Zhao, Hui Li, Junyi Zhang, Jie Ma, Binghai Du, Yanqin Ding
Journal of Proteome Research.2024;[Epub] CrossRef
Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa
Nand Broeckaert, Hannelore Longin, Hanne Hendrix, Jeroen De Smet, Mirita Franz-Wachtel, Boris Maček, Vera van Noort, Rob Lavigne
microLife.2024;[Epub] CrossRef
Lysine acetylation regulates the AT-rich DNA possession ability of H-NS
Yabo Liu, Mengqing Zhou, Yifan Bu, Liang Qin, Yuanxing Zhang, Shuai Shao, Qiyao Wang
Nucleic Acids Research.2024; 52(4): 1645. CrossRef
Acetylation of K188 and K192 inhibits the DNA-binding ability of NarL to regulate Salmonella virulence
Liu-Qing Zhang, Yi-Lin Shen, Bang-Ce Ye, Ying Zhou, Christopher A. Elkins
Applied and Environmental Microbiology.2023;[Epub] CrossRef
Acetylome and Succinylome Profiling of Edwardsiella tarda Reveals Key Roles of Both Lysine Acylations in Bacterial Antibiotic Resistance
Yuying Fu, Lishan Zhang, Huanhuan Song, Junyan Liao, Li Lin, Wenjia Jiang, Xiaoyun Wu, Guibin Wang
Antibiotics.2022; 11(7): 841. CrossRef
Pat- and Pta-mediated protein acetylation is required for horizontally-acquired virulence gene expression in Salmonella Typhimurium
Hyojeong Koo, Eunna Choi, Shinae Park, Eun-Jin Lee, Jung-Shin Lee
Journal of Microbiology.2022; 60(8): 823. CrossRef
Acetylation of CspC Controls the Las Quorum-Sensing System through Translational Regulation of rsaL in Pseudomonas aeruginosa
Shouyi Li, Xuetao Gong, Liwen Yin, Xiaolei Pan, Yongxin Jin, Fang Bai, Zhihui Cheng, Un-Hwan Ha, Weihui Wu, Pierre Cornelis, Gerald B. Pier
mBio.2022;[Epub] CrossRef
Trans-acting regulators of ribonuclease activity
Jaejin Lee, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(4): 341. CrossRef
Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation ofexsAinPseudomonas aeruginosa
Shouyi Li, Yuding Weng, Xiaoxiao Li, Zhuo Yue, Zhouyi Chai, Xinxin Zhang, Xuetao Gong, Xiaolei Pan, Yongxin Jin, Fang Bai, Zhihui Cheng, Weihui Wu
Nucleic Acids Research.2021; 49(12): 6756. CrossRef
Transcriptional Regulation of the Multiple Resistance Mechanisms in Salmonella—A Review
Michał Wójcicki, Olga Świder, Kamila J. Daniluk, Paulina Średnicka, Monika Akimowicz, Marek Ł. Roszko, Barbara Sokołowska, Edyta Juszczuk-Kubiak
Pathogens.2021; 10(7): 801. CrossRef

Functional interplay between the oxidative stress response and DNA damage checkpoint signaling for genome maintenance in aerobic organisms: Ji Eun Choi , Woo-Hyun Chung; J. Microbiol. 2020;58(2):81-91. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9520-x

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Abstract

The DNA damage checkpoint signaling pathway is a highly conserved surveillance mechanism that ensures genome integrity by sequential activation of protein kinase cascades. In mammals, the main pathway is orchestrated by two central sensor kinases, ATM and ATR, that are activated in response to DNA damage and DNA replication stress. Patients lacking functional ATM or ATR suffer from ataxia-telangiectasia (A-T) or Seckel syndrome, respectively, with pleiotropic degenerative phenotypes. In addition to DNA strand breaks, ATM and ATR also respond to oxidative DNA damage and reactive oxygen species (ROS), suggesting an unconventional function as regulators of intracellular redox status. Here, we summarize the multiple roles of ATM and ATR, and of their orthologs in Saccharomyces cerevisiae, Tel1 and Mec1, in DNA damage checkpoint signaling and the oxidative stress response, and discuss emerging ideas regarding the possible mechanisms underlying the elaborate crosstalk between those pathways. This review may provide new insights into the integrated cellular strategies responsible for maintaining genome stability in eukaryotes with a focus on the yeast model organism.

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DNA Repair.2024; 141: 103730. CrossRef
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International Dental Journal.2024;[Epub] CrossRef
Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics
Woo-Hyun Chung
Journal of Microbiology.2023; 61(12): 1013. CrossRef
Metabolic Stress and Mitochondrial Dysfunction in Ataxia-Telangiectasia
Goutham Narayanan Subramanian, Abrey Jie Yeo, Magtouf Hnaidi Gatei, David John Coman, Martin Francis Lavin
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The Rad9–Rad1–Hus1 DNA Repair Clamp is Found in Microsporidia
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Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)
Elias A. Tannous, Peter M. Burgers
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DNA damage checkpoint and repair: From the budding yeast Saccharomyces cerevisiae to the pathogenic fungus Candida albicans
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[Minireview] Unraveling new functions of superoxide dismutase using yeast model system: Beyond its conventional role in superoxide radical scavenging: Woo-Hyun Chung ,; J. Microbiol. 2017;55(6):409-416. Published online March 9, 2017; DOI: https://doi.org/10.1007/s12275-017-6647-5

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Abstract

To deal with chemically reactive oxygen molecules constantly threatening aerobic life, cells are readily equipped with elabo-rate biological antioxidant systems. Superoxide dismutase is a metalloenzyme catalytically eliminating superoxide radi-cal as a first-line defense mechanism against oxidative stress. Multiple different SOD isoforms have been developed through-out evolution to play distinct roles in separate subcellular com-partments. SOD is not essential for viability of most aerobic organisms and intriguingly found even in strictly anaerobic bacteria. Sod1 has recently been known to play important roles as a nuclear transcription factor, an RNA binding pro-tein, a synthetic lethal interactor, and a signal modulator in glucose metabolism, most of which are independent of its canonical function as an antioxidant enzyme. In this review, recent advances in understanding the unconventional role of Sod1 are highlighted and discussed with an emphasis on its genetic crosstalk with DNA damage repair/checkpoint path-ways. The budding yeast Saccharomyces cerevisiae has been successfully used as an efficient tool and a model organism to investigate a number of novel functions of Sod1.

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MINIREVIEW] To Peep into Pif1 Helicase: Multifaceted All the Way from Genome Stability to Repair-Associated DNA Synthesis: Woo-Hyun Chung; J. Microbiol. 2014;52(2):89-98. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3524-3

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Abstract

Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.

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Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics
Woo-Hyun Chung
Journal of Microbiology.2023; 61(12): 1013. CrossRef
The Pif1 helicase is actively inhibited during meiotic recombination which restrains gene conversion tract length
Dipti Vinayak Vernekar, Giordano Reginato, Céline Adam, Lepakshi Ranjha, Florent Dingli, Marie-Claude Marsolier, Damarys Loew, Raphaël Guérois, Bertrand Llorente, Petr Cejka, Valérie Borde
Nucleic Acids Research.2021; 49(8): 4522. CrossRef
Approaching Protein Barriers: Emerging Mechanisms of Replication Pausing in Eukaryotes
Maksym Shyian, David Shore
Frontiers in Cell and Developmental Biology.2021;[Epub] CrossRef
Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition
Yang-Xue Dai, Wei-Fei Chen, Na-Nv Liu, Fang-Yuan Teng, Hai-Lei Guo, Xi-Miao Hou, Shuo-Xing Dou, Stephane Rety, Xu-Guang Xi
Nucleic Acids Research.2021; 49(7): 4129. CrossRef
When the Ends Justify the Means: Regulation of Telomere Addition at Double-Strand Breaks in Yeast
Remington E. Hoerr, Katrina Ngo, Katherine L. Friedman
Frontiers in Cell and Developmental Biology.2021;[Epub] CrossRef
Lysine acetylation regulates the activity of nuclear Pif1
Onyekachi E. Ononye, Christopher W. Sausen, Lata Balakrishnan, Matthew L. Bochman
Journal of Biological Chemistry.2020; 295(46): 15482. CrossRef
Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family
Julius Muellner, Kristina H. Schmidt
Genes.2020; 11(2): 224. CrossRef
Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation in Saccharomyces cerevisiae
Chi-Fu Chen, Thomas J Pohl, Sebastian Pott, Virginia A Zakian
Genetics.2019; 211(1): 105. CrossRef
Ku complex suppresses recombination in the absence of MRX activity during budding yeast meiosis
Hyeseon Yun, Keunpil Kim
BMB Reports.2019; 52(10): 607. CrossRef
Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases
Nannan Su, Alicia K. Byrd, Sakshibeedu R. Bharath, Olivia Yang, Yu Jia, Xuhua Tang, Taekjip Ha, Kevin D. Raney, Haiwei Song
Nature Communications.2019;[Epub] CrossRef
The nature of meiotic chromosome dynamics and recombination in budding yeast
Soogil Hong, Jeong Hwan Joo, Hyeseon Yun, Keunpil Kim
Journal of Microbiology.2019; 57(4): 221. CrossRef
The Drosophila melanogaster PIF1 Helicase Promotes Survival During Replication Stress and Processive DNA Synthesis During Double-Strand Gap Repair
Ece Kocak, Sarah Dykstra, Alexandra Nemeth, Catherine G Coughlin, Kasey Rodgers, Mitch McVey
Genetics.2019; 213(3): 835. CrossRef
The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity
Carly L Geronimo, Saurabh P Singh, Roberto Galletto, Virginia A Zakian
Nucleic Acids Research.2018; 46(16): 8357. CrossRef
DNA-unwinding activity of Saccharomyces cerevisiae Pif1 is modulated by thermal stability, folding conformation, and loop lengths of G-quadruplex DNA
Lei Wang, Qing-Man Wang, Yi-Ran Wang, Xu-Guang Xi, Xi-Miao Hou
Journal of Biological Chemistry.2018; 293(48): 18504. CrossRef
Role of the Pif1-PCNA Complex in Pol δ-Dependent Strand Displacement DNA Synthesis and Break-Induced Replication
Olga Buzovetsky, Youngho Kwon, Nhung Tuyet Pham, Claire Kim, Grzegorz Ira, Patrick Sung, Yong Xiong
Cell Reports.2017; 21(7): 1707. CrossRef
Structure and function of Pif1 helicase
Alicia K. Byrd, Kevin D. Raney
Biochemical Society Transactions.2017; 45(5): 1159. CrossRef
Mechanistic and biological considerations of oxidatively damaged DNA for helicase-dependent pathways of nucleic acid metabolism
Jack D. Crouch, Robert M. Brosh
Free Radical Biology and Medicine.2017; 107: 245. CrossRef
PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes
Phong Lan Thao Tran, Thomas J. Pohl, Chi-Fu Chen, Angela Chan, Sebastian Pott, Virginia A. Zakian
Nature Communications.2017;[Epub] CrossRef
Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes
Shubeena Chib, Alicia K. Byrd, Kevin D. Raney
Journal of Biological Chemistry.2016; 291(11): 5889. CrossRef
Getting it done at the ends: Pif1 family DNA helicases and telomeres
Carly L. Geronimo, Virginia A. Zakian
DNA Repair.2016; 44: 151. CrossRef
Genetic instability in budding and fission yeast—sources and mechanisms
Adrianna Skoneczna, Aneta Kaniak, Marek Skoneczny, Antoine Danchin
FEMS Microbiology Reviews.2015; 39(6): 917. CrossRef
TheBacteroides sp. 3_1_23Pif1 protein is a multifunctional helicase
Na-Nv Liu, Xiao-Lei Duan, Xia Ai, Yan-Tao Yang, Ming Li, Shuo-Xing Dou, Stephane Rety, Eric Deprez, Xu-Guang Xi
Nucleic Acids Research.2015; 43(18): 8942. CrossRef
Yeast Pif1 Accelerates Annealing of Complementary DNA Strands
Ramanagouda Ramanagoudr-Bhojappa, Alicia K. Byrd, Christopher Dahl, Kevin D. Raney
Biochemistry.2014; 53(48): 7659. CrossRef

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