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Characteristic alterations of gut microbiota in uncontrolled gout
Asad ul-Haq , Kyung-Ann Lee , Hoonhee Seo , Sukyung Kim , Sujin Jo , Kyung Min Ko , Su-Jin Moon , Yun Sung Kim , Jung Ran Choi , Ho-Yeon Song , Hyun-Sook Kim
J. Microbiol. 2022;60(12):1178-1190.   Published online November 24, 2022
DOI: https://doi.org/10.1007/s12275-022-2416-1
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  • 10 Web of Science
  • 11 Crossref
AbstractAbstract
Microbiome research has been on the rise recently for a more in-depth understanding of gout. Meanwhile, there is a need to understand the gut microbiome related to uric acid-lowering drug resistance. In this study, 16S rRNA gene-based microbiota analysis was performed for a total of 65 stool samples from 17 healthy controls and 48 febuxostat-treated gout patients (including 28 controlled subjects with decreased uric acid levels and 20 uncontrolled subjects with non-reduced uric acid levels). Alpha diversity of bacterial community decreased in the healthy control, controlled, and uncontrolled groups. In the case of beta diversity, the bacterial community was significantly different among groups (healthy control, controlled, and uncontrolled groups). Taxonomic biomarker analysis revealed the increased population of g-Bifidobacterium in healthy controls and g-Prevotella in uncontrolled patients. PCR further confirmed this result at the species level. Additionally, functional metagenomics predictions led to the exploration of various functional biomarkers, including purine metabolism. The results of this study can serve as a basis for developing potential new strategies for diagnosing and treating gout from microbiome prospects.

Citations

Citations to this article as recorded by  
  • Different Prostatic Tissue Microbiomes between High- and Low-Grade Prostate Cancer Pathogenesis
    Jae Heon Kim, Hoonhee Seo, Sukyung Kim, Md Abdur Rahim, Sujin Jo, Indrajeet Barman, Hanieh Tajdozian, Faezeh Sarafraz, Ho-Yeon Song, Yun Seob Song
    International Journal of Molecular Sciences.2024; 25(16): 8943.     CrossRef
  • Reassessing Gout Management through the Lens of Gut Microbiota
    Jean Demarquoy, Oumaima Dehmej
    Applied Microbiology.2024; 4(2): 824.     CrossRef
  • Changes in gut microbiota structure and function in gout patients
    Feiyan Zhao, Zhixin Zhao, Dafu Man, Zhihong Sun, Ning Tie, Hongbin Li, Heping Zhang
    Food Bioscience.2023; 54: 102912.     CrossRef
  • Effect of a Novel Handheld Photobiomodulation Therapy Device in the Management of Chemoradiation Therapy-Induced Oral Mucositis in Head and Neck Cancer Patients: A Case Series Study
    In-Young Jo, Hyung-Kwon Byeon, Myung-Jin Ban, Jae-Hong Park, Sang-Cheol Lee, Yong Kyun Won, Yun-Su Eun, Jae-Yun Kim, Na-Gyeong Yang, Sul-Hee Lee, Pyeongan Lee, Nam-Hun Heo, Sujin Jo, Hoonhee Seo, Sukyung Kim, Ho-Yeon Song, Jung-Eun Kim
    Photonics.2023; 10(3): 241.     CrossRef
  • New drug targets for the treatment of gout arthritis: what’s new?
    Tiago H. Zaninelli, Geovana Martelossi-Cebinelli, Telma Saraiva-Santos, Sergio M. Borghi, Victor Fattori, Rubia Casagrande, Waldiceu A. Verri
    Expert Opinion on Therapeutic Targets.2023; 27(8): 679.     CrossRef
  • A dynamics association study of gut barrier and microbiota in hyperuricemia
    Qiulan Lv, Jun Zhou, Changyao Wang, Xiaomin Yang, Yafei Han, Quan Zhou, Ruyong Yao, Aihua Sui
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Biochemical Recurrence in Prostate Cancer Is Associated with the Composition of Lactobacillus: Microbiome Analysis of Prostatic Tissue
    Jae Heon Kim, Hoonhee Seo, Sukyung Kim, Asad Ul-Haq, Md Abdur Rahim, Sujin Jo, Ho-Yeon Song, Yun Seob Song
    International Journal of Molecular Sciences.2023; 24(13): 10423.     CrossRef
  • Remote effects of kidney drug transporter OAT1 on gut microbiome composition and urate homeostasis
    Vladimir S. Ermakov, Jeffry C. Granados, Sanjay K. Nigam
    JCI Insight.2023;[Epub]     CrossRef
  • Causal Relationship between Gut Microbiota and Gout: A Two-Sample Mendelian Randomization Study
    Mengna Wang, Jiayao Fan, Zhaohui Huang, Dan Zhou, Xue Wang
    Nutrients.2023; 15(19): 4260.     CrossRef
  • Emerging Urate-Lowering Drugs and Pharmacologic Treatment Strategies for Gout: A Narrative Review
    Robert Terkeltaub
    Drugs.2023; 83(16): 1501.     CrossRef
  • Characterization of Fecal Microbiomes of Osteoporotic Patients in Korea
    Asad Ul-Haq, Hoonhee Seo, Sujin Jo, Hyuna Park, Sukyung Kim, Youngkyoung Lee, Saebim Lee, Je Hoon Jeong, Ho‑Yeon Song
    Polish Journal of Microbiology.2022; 71(4): 601.     CrossRef
Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
Jihoon Jo , Jooseong Oh , Chungoo Park
J. Microbiol. 2020;58(3):176-192.   Published online February 27, 2020
DOI: https://doi.org/10.1007/s12275-020-9525-5
  • 46 View
  • 0 Download
  • 43 Web of Science
  • 41 Crossref
AbstractAbstract
Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted (“shotgun”) sequencing of all (“meta”) microbial genomes (“genomic”) present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.

Citations

Citations to this article as recorded by  
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    Soumik Das, V Devi Rajeswari, Ganesh Venkatraman, Ramprasad Elumalai, Sivaraman Dhanasekaran, Gnanasambandan Ramanathan
    Translational Research.2024; 265: 71.     CrossRef
  • The Role of Soil Microbiome in Driving Plant Performance: An Overview Based on Ecological and Ecosystem Advantages to the Plant Community
    Grace Gachara, Jihane Kenfaoui, Rashid Suleiman, Beatrice Kilima, Mohammed Taoussi, Kamal Aberkani, Zineb Belabess, Abdelilah Meddich, Nadia Handaq, Salah-Eddine Laasli, Essaid Ait Barka, Rachid Lahlali
    Journal of Crop Health.2024; 76(1): 3.     CrossRef
  • Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves
    Rok Tomazin, Tjaša Cerar Kišek, Tea Janko, Tina Triglav, Katja Strašek Smrdel, Vesna Cvitković Špik, Andreja Kukec, Janez Mulec, Tadeja Matos
    Microorganisms.2024; 12(7): 1427.     CrossRef
  • The infants’ gut microbiome: setting the stage for the early onset of obesity
    Yvonne Vallès, Muhammad Arshad, Mamoun Abdalbaqi, Claire K. Inman, Amar Ahmad, Nizar Drou, Kristin C. Gunsalus, Raghib Ali, Muna Tahlak, Abdishakur Abdulle
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Metabarcoding of zooplankton communities of Dianchi Lake based on the mitochondrial cytochrome oxidase subunit 1 gene
    Fu Cen, Shan Xu, Genshen Yin, Minghua Dong
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform
    Yu Liu, Boyuan Xue, Hao Liu, Shaojie Wang, Haijia Su
    Biotechnology Advances.2024; 72: 108348.     CrossRef
  • Genome mining of Mycobacterium tuberculosis: targeting SufD as a novel drug candidate through in silico characterization and inhibitor screening
    Neelima Gorityala, Anthony Samit Baidya, Someswar R. Sagurthi
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Human oral microbiome as forensic biomarkers for individual identification: A systematic review
    Vezhavendhan Nagaraj, Vidhya Arumugam, Sivaramakrishnan Muthanandam, Santhadevy Arumugam, Dhamodharan Ramasamy
    Indian Journal of Microbiology Research.2024; 11(4): 230.     CrossRef
  • Whole-genome resequencing highlights the phycosphere microbial network in global populations of the edible kelp Undaria pinnatifida
    Jihoon Jo, Hyun Hee Hong, Louis Graf, Che Ok Jeon, Hwan Su Yoon
    Algal Research.2024; 82: 103656.     CrossRef
  • Overlooked drivers of the greenhouse effect: The nutrient-methane nexus mediated by submerged macrophytes
    Jichun Mu, Zhenhan Li, Quanlin Lu, Hongwei Yu, Chengzhi Hu, Yujing Mu, Jiuhui Qu
    Water Research.2024; 266: 122316.     CrossRef
  • The diversity of endophytic fungi in Tartary buckwheat (Fagopyrum tataricum) and its correlation with flavonoids and phenotypic traits
    Meiqi Chen, Ziqi Ding, Min Zhou, Yukun Shang, Chenglei Li, Qingfeng Li, Tongliang Bu, Zizhong Tang, Hui Chen
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal
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    Scientific Reports.2024;[Epub]     CrossRef
  • Community Diversity of Fungi Carried by Four Common Woodpeckers in Heilongjiang Province, China
    Wenhui Shi, Iram Maqsood, Keying Liu, Meichen Yu, Yuhui Si, Ke Rong
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    O.S. Lavrukova, N.A. Sidorova
    Forensic Medical Expertise.2024; 67(5): 55.     CrossRef
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    Aquaculture.2023; 575: 739818.     CrossRef
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    PLOS Computational Biology.2023; 19(5): e1011001.     CrossRef
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    Environmental Research.2023; 231: 116185.     CrossRef
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  • Omics-based microbiome analysis in microbial ecology: from sequences to information
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    Journal of Microbiology.2021; 59(3): 229.     CrossRef
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    IOP Conference Series: Earth and Environmental Science.2021; 651(4): 042023.     CrossRef
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