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- 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
- 59 View
- 0 Download
- 13 Web of Science
- 14 Crossref
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Abstract
- 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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Citations
Citations to this article as recorded by
- Seeds for Gut Health: Prebiotic potential of seed mucilages from Chia, Fenugreek, Basil, Mustard, and Flaxseed and their impact on adult and toddler's gut microbiome
Kanika Mahra, Vineet Singh, Justina Klingate, Jae-Ho Shin
Future Foods.2025; : 100628. CrossRef - 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
Frontiers in Nutrition.2024;[Epub] CrossRef - 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
BMC Microbiology.2023;[Epub] CrossRef - 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
Foods.2021; 10(11): 2697. CrossRef - The final fate of food: On the establishment of in vitro colon models
Saartje Hernalsteens, Song Huang, Hai Hua Cong, Xiao Dong Chen
Food Research International.2021; 150: 110743. CrossRef - In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools
Elena Veintimilla-Gozalbo, Andrea Asensio-Grau, Joaquim Calvo-Lerma, Ana Heredia, Ana Andrés
Applied Sciences.2021; 11(17): 8135. CrossRef
- Seeds for Gut Health: Prebiotic potential of seed mucilages from Chia, Fenugreek, Basil, Mustard, and Flaxseed and their impact on adult and toddler's gut microbiome
Reviews
- 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
- 51 View
- 0 Download
- 10 Web of Science
- 9 Crossref
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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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Citations
Citations to this article as recorded by- DSB-induced oxidative stress: Uncovering crosstalk between DNA damage response and cellular metabolism
Xinyu Li, Caini Yang, Hengyu Wu, Hongran Chen, Xing Gao, Sa Zhou, Tong-Cun Zhang, Wenjian Ma
DNA Repair.2024; 141: 103730. CrossRef - Effects of Stress on Biological Characteristics and Metabolism of Periodontal Ligament Stem Cells of Deciduous Teeth
Zhengyang Li, Jinyi Li, Shanshan Dai, Xuelong Su, Meiyue Ren, Shuyang He, Qingyu Guo, Fei Liu
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
Antioxidants.2022; 11(4): 653. CrossRef - The Rad9–Rad1–Hus1 DNA Repair Clamp is Found in Microsporidia
Anne Caroline Mascarenhas dos Santos, Alexander Thomas Julian, Jean-François Pombert, Emmanuelle Lerat
Genome Biology and Evolution.2022;[Epub] CrossRef - Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)
Elias A. Tannous, Peter M. Burgers
Critical Reviews in Biochemistry and Molecular Biology.2021; 56(5): 441. CrossRef - DNA damage checkpoint and repair: From the budding yeast Saccharomyces cerevisiae to the pathogenic fungus Candida albicans
Shuangyan Yao, Yuting Feng, Yan Zhang, Jinrong Feng
Computational and Structural Biotechnology Journal.2021; 19: 6343. CrossRef - Acute Toxicity and DNA Instability Induced by Exposure to Low Doses of Triclosan and Phthalate DEHP, and Their Combinations, in vitro
Nathalia de Assis Aguilar Duarte, Lindiane Eloisa de Lima, Flora Troina Maraslis, Michael Kundi, Emilene Arusievicz Nunes, Gustavo Rafael Mazzaron Barcelos
Frontiers in Genetics.2021;[Epub] CrossRef - The mechanism and prevention of mitochondrial injury after exercise
Mingzhe Li, Baoan Ning, Tianhui Wang
Journal of Physiology and Biochemistry.2021; 77(2): 215. CrossRef
- DSB-induced oxidative stress: Uncovering crosstalk between DNA damage response and cellular metabolism
- MINIREVIEW] Synthetic lethal interaction between oxidative stress response and DNA damage repair in the budding yeast and its application to targeted anticancer therapy
- Ji Eun Choi , Woo-Hyun Chung
- J. Microbiol. 2019;57(1):9-17. Published online December 29, 2018
- DOI: https://doi.org/10.1007/s12275-019-8475-2
- 62 View
- 0 Download
- 7 Web of Science
- 6 Crossref
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Abstract
- Synthetic lethality is an extreme form of negative genetic epistasis that arises when a combination of functional deficiency in two or more genes results in cell death, whereas none of the single genetic perturbations are lethal by themselves. This unconventional genetic interaction is a modification of the concept of essentiality that can be exploited for the purpose of targeted cancer therapy. The yeast Saccharomyces cerevisiae has been pivotally used for early large-scale synthetic lethal screens due to its experimental advantages, but recent advances in gene silencing technology have now made direct high-throughput analysis possible in higher organisms. Identification of tumor-specific alterations and characterization of the mechanistic principles underlying synthetic lethal interaction are the key to applying synthetic lethality to clinical cancer treatment by enabling genome-driven oncological research. Here, we provide emerging ideas on the synthetic lethal interactions in budding yeast, particularly between cellular processes responsible for oxidative stress response and DNA damage repair, and discuss how they can be appropriately utilized for context-dependent cancer therapeutics.
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Citations
Citations to this article as recorded by- CSSLdb: Discovery of cancer-specific synthetic lethal interactions based on machine learning and statistic inference
Yuyang Dou, Yujie Ren, Xinmiao Zhao, Jiaming Jin, Shizheng Xiong, Lulu Luo, Xinru Xu, Xueni Yang, Jiafeng Yu, Li Guo, Tingming Liang
Computers in Biology and Medicine.2024; 170: 108066. CrossRef - ML216-Induced BLM Helicase Inhibition Sensitizes PCa Cells to the DNA-Crosslinking Agent Cisplatin
Xiao-Yan Ma, Jia-Fu Zhao, Yong Ruan, Wang-Ming Zhang, Lun-Qing Zhang, Zheng-Dong Cai, Hou-Qiang Xu
Molecules.2022; 27(24): 8790. CrossRef - Clinical significance of chromosomal integrity in gastric cancers
Rukui Zhang, Zhaorui Liu, Xusheng Chang, Yuan Gao, Huan Han, Xiaona Liu, Hui Cai, Qiqing Fu, Lei Liu, Kai Yin
The International Journal of Biological Markers.2022; 37(3): 296. 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
Journal of Microbiology.2020; 58(2): 81. CrossRef - Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants
Jenna E. Gallegos, Neil R. Adames, Mark F. Rogers, Pavel Kraikivski, Aubrey Ibele, Kevin Nurzynski-Loth, Eric Kudlow, T. M. Murali, John J. Tyson, Jean Peccoud
npj Systems Biology and Applications.2020;[Epub] CrossRef - DNA damage induces Yap5-dependent transcription of ECO1/CTF7 in Saccharomyces cerevisiae
Michael G. Mfarej, Robert V. Skibbens, Marco Muzi-Falconi
PLOS ONE.2020; 15(12): e0242968. CrossRef
- CSSLdb: Discovery of cancer-specific synthetic lethal interactions based on machine learning and statistic inference
Research Support, Non-U.S. Gov't
- The Mutation of a Novel Saccharomyces cerevisiae SRL4 Gene Rescues the Lethality of rad53 and lcd1 Mutations by Modulating dNTP Levels
- Do-Hee Choi , Young-Mi Oh , Sung-Hun Kwon , Sung-Ho Bae
- J. Microbiol. 2008;46(1):75-80.
- DOI: https://doi.org/10.1007/s12275-008-0013-6
- 42 View
- 0 Download
- 5 Scopus
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Abstract
- The SRL4 (YPL033C) gene was initially identified by the screening of Saccharomyces cerevisiae genes that play a role in DNA metabolism and/or genome stability using the SOS system of Escherichia coli. In this study, we found that the srl4Δ; mutant cells were resistant to the chemicals that inhibit nucleotide metabolism and evidenced higher dNTP levels than were observed in the wild-type cells in the presence of hydroxyurea. The mutant cells also showed a significantly faster growth rate and higher dNTP levels at low temperature (16 oC) than were observed in the wild-type cells, whereas we detected no differences in the growth rate at 30oC. Furthermore, srl4Δ was shown to suppress the lethality of mutations of the essential S phase checkpoint genes, RAD53 and LCD1. These results indicate that SRL4 may be involved in the regulation of dNTP production by its function as a negative regulator of ribonucleotide reductase.
- Characterization of a Putative F-box Motif in Ibd1p/Bfa1p, a Spindle Checkpoint Regulator of Budding Yeast Saccharomyces cerevisiae
- Kyum-Jung Lee , Hyung-Seo Hwang , Kiwon Song
- J. Microbiol. 2001;39(4):286-292.
- 41 View
- 0 Download
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Abstract
- During mitosis, the proper segregation of duplicated chromosomes is coordinated by a spindle checkpoint. The bifurcated spindle checkpoint blocks cell cycle progression at metaphase by monitoring unattached kinetochores and inhibits mitotic exit in response to the misorientation of the mitotic spindle. Ibd1p/Bfa1p is a spindle checkpoint regulator of budding yeast in the Bub2p checkpoint pathway for mitotic exit and its disruption abolishes mitotic arrest when proper organization of the mitotic spindle is inhibited. Ibd1p/Bfa1p localizes to the spindle pole body, a microtubule-organizing center in yeast, and its overexpression arrests the cell cycle in 80% of cells with an enlarged bud at mitosis and in 20% of cells with multiple buds. In this study, we found that the C-terminus of Ibd1p/Bfa1p physically interacts with Skp1p, a key component of SCF (Skp1/cullin/F-box) complex for ubiquitin-mediated proteolysis of cell cycle regulators as well as an evolutionally conserved kinetochore protein for cell cycle progression. A putative F-box motif was found in the C-terminus of Ibd1p/Bfa1p and its function was investigated by making mutants of conserved residues in the motif. These Ibd1p/Bfa1p mutants of a putative F-box interacted with Skp1p in vitro by two-hybrid assays as wild type Ibd1p/Bfa1p. Also, these Ibd1p/Bfa1p mutants displayed the overexpression phenotypes of wild type Ibd1p, when over-expressed under inducible promoters. These results suggest that a putative F-box motif of Ibd1p/Bfa1p is not essential for the interaction with Skp1p and its function in mitotic exit and cytokinesis.
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