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Meta-Analysis
Exploring COVID-19 Pandemic Disparities with Transcriptomic Meta-analysis from the Perspective of Personalized Medicine
Medi Kori, Ceyda Kasavi, Kazim Yalcin Arga
J. Microbiol. 2024;62(9):785-798.   Published online July 9, 2024
DOI: https://doi.org/10.1007/s12275-024-00154-9
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  • 1 Web of Science
AbstractAbstract
Infection with SARS-CoV2, which is responsible for COVID-19, can lead to differences in disease development, severity and mortality rates depending on gender, age or the presence of certain diseases. Considering that existing studies ignore these differences, this study aims to uncover potential differences attributable to gender, age and source of sampling as well as viral load using bioinformatics and multi-omics approaches. Differential gene expression analyses were used to analyse the phenotypic differences between SARS-CoV-2 patients and controls at the mRNA level. Pathway enrichment analyses were performed at the gene set level to identify the activated pathways corresponding to the differences in the samples. Drug repurposing analysis was performed at the protein level, focusing on host-mediated drug candidates to uncover potential therapeutic differences. Significant differences (i.e. the number of differentially expressed genes and their characteristics) were observed for COVID-19 at the mRNA level depending on the sample source, gender and age of the samples. The results of the pathway enrichment show that SARS-CoV-2 can be combated more effectively in the respiratory tract than in the blood samples. Taking into account the different sample sources and their characteristics, different drug candidates were identified. Evaluating disease prediction, prevention and/or treatment strategies from a personalised perspective is crucial. In this study, we not only evaluated the differences in COVID-19 from a personalised perspective, but also provided valuable data for further experimental and clinical efforts. Our findings could shed light on potential pandemics.
Journal Article
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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  • 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
Randomized Controlled Trial
Ulmus macrocarpa Hance extract modulates intestinal microbiota in healthy adults: a randomized, placebo-controlled clinical trial
Kwangmin Kim , Karpagam Veerappan , Nahyun Woo , Bohyeon Park , Sathishkumar Natarajan , Hoyong Chung , Cheolmin Kim , Junhyung Park
J. Microbiol. 2021;59(12):1150-1156.   Published online October 26, 2021
DOI: https://doi.org/10.1007/s12275-021-1329-8
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  • 6 Crossref
AbstractAbstract
The stem and root bark of Ulmus macrocarpa Hance has been used as traditional pharmacological agent against inflammation related disorders. The objective of this study was to explore the impact of Ulmus macrocarpa Hance extract (UME) on human gut microbiota. A randomized placebo-controlled clinical study was conducted in healthy adults. The study subjects were given 500 mg/day of UME or placebo orally for 4 weeks. Eighty fecal samples were collected at baseline and 4 weeks of UME or placebo intervention. The gut microbiota variation was evaluated by 16S rRNA profiling. The microbial response was highly personalized, and no statistically significant differences was observed in both species richness and abundance. The number of bacterial species identified in study subjects ranged from 86 to 182 species. The analysis for taxonomical changes revealed an increase in Eubacterium ventriosum, Blautia faecis, Ruminococcus gnavus in the UME group. Functional enrichment of bacterial genes showed an increase in primary and secondary bile acid biosynthesis in UME group. Having known from previous studies Eubacterium regulated bile acid homeostasis in protecting gut microbial architecture and immunity, we suggest that UME supplementation might enhance host immunity by modulating gut microbiota. This is the first stage study and forthcoming clinical studies with larger participants are needed to confirm these findings.

Citations

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  • Catechin and flavonoid glycosides from the Ulmus genus: Exploring their nutritional pharmacology and therapeutic potential in osteoporosis and inflammatory conditions
    Chanhyeok Jeong, Chang Hyung Lee, Jiwon Seo, Jung Han Yoon Park, Ki Won Lee
    Fitoterapia.2024; 178: 106188.     CrossRef
  • Comparative transcriptomes of four Elm species provide insights into the genetic features and adaptive evolution of Ulmus spp.
    Shijie Wang, Lihui Zuo, Yichao Liu, Lianxiang Long, Jianghao Wu, Mengting Yuan, Jinmao Wang, Minsheng Yang
    Forest Ecology and Management.2024; 553: 121560.     CrossRef
  • Dietary Supplementation with Popped Amaranth Modulates the Gut Microbiota in Low Height-for-Age Children: A Nonrandomized Pilot Trial
    Oscar de Jesús Calva-Cruz, Cesaré Ovando-Vázquez, Antonio De León-Rodríguez, Fabiola Veana, Eduardo Espitia-Rangel, Samuel Treviño, Ana Paulina Barba-de la Rosa
    Foods.2023; 12(14): 2760.     CrossRef
  • Potential lipid-lowering effects of Ulmus macrocarpa Hance extract in adults with untreated high low-density lipoprotein cholesterol concentrations: A randomized double-blind placebo-controlled trial
    Ye Li Lee, Sang Yeoup Lee
    Frontiers in Medicine.2022;[Epub]     CrossRef
  • Research progress on the relationship between intestinal microecology and intestinal bowel disease
    Qianhui Fu, Tianyuan Song, Xiaoqin Ma, Jian Cui
    Animal Models and Experimental Medicine.2022; 5(4): 297.     CrossRef
  • The current status of old traditional medicine introduced from Persia to China
    Jinmin Shi, Yifan Yang, Xinxin Zhou, Lijun Zhao, Xiaohua Li, Abdullah Yusuf, Mohaddeseh S. M. Z. Hosseini, Fatemeh Sefidkon, Xuebo Hu
    Frontiers in Pharmacology.2022;[Epub]     CrossRef
Journal Articles
Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing
Hyojung Kim , Sora Kim , Sungwon Jung
J. Microbiol. 2020;58(3):193-205.   Published online February 27, 2020
DOI: https://doi.org/10.1007/s12275-020-9556-y
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  • 23 Web of Science
  • 24 Crossref
AbstractAbstract
Recent studies on microbiome highlighted their importance in various environments including human, where they are involved in multiple biological contexts such as immune mechanism, drug response, and metabolism. The rapid increase of new findings in microbiome research is partly due to the technological advances in microbiome identification, including the next-generation sequencing technologies. Several applications of different next-generation sequencing platforms exist for microbiome identification, but the most popular method is using short-read sequencing technology to profile targeted regions of 16S rRNA genes of microbiome because of its low-cost and generally reliable performance of identifying overall microbiome compositions. The analysis of targeted 16S rRNA sequencing data requires multiple steps of data processing and systematic analysis, and many software tools have been proposed for such procedures. However, properly organizing and using such software tools still require certain level of expertise with computational environments. The purpose of this article is introducing the concept of computational analysis of 16S rRNA sequencing data to microbiologists and providing easy-to-follow and step-by-step instructions of using recent software tools of microbiome analysis. This instruction may be used as a quick guideline for general next-generation sequencing-based microbiome studies or a template of constructing own software pipelines for customized analysis.

Citations

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  • PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts
    Yin-Cheng Chen, Yin-Yuan Su, Tzu-Yu Chu, Ming-Fong Wu, Chieh-Chun Huang, Chen-Ching Lin
    npj Biofilms and Microbiomes.2025;[Epub]     CrossRef
  • Microbial Population Analysis Based on 16S rRNA Detection and Its Application in Epidemic Disease Warning
    逸欣 王
    Advances in Microbiology.2024; 13(03): 216.     CrossRef
  • The microbial composition of pancreatic ductal adenocarcinoma: a systematic review of 16S rRNA gene sequencing
    Nabeel Merali, Tarak Chouari, Casie Sweeney, James Halle-Smith, Maria-Danae Jessel, Bing Wang, James O’ Brien, Satoshi Suyama, José I. Jiménez, Keith J. Roberts, Eirini Velliou, Shivan Sivakumar, Timothy A. Rockall, Ayse Demirkan, Virginia Pedicord, Dongm
    International Journal of Surgery.2024; 110(10): 6771.     CrossRef
  • Effect of the 16S rRNA Gene Hypervariable Region on the Microbiome Taxonomic Profile and Diversity in the Endangered Fish Totoaba macdonaldi
    Itzel Soledad Pérez-Bustamante, Roberto Cruz-Flores, Jesús Antonio López-Carvallo, Samuel Sánchez-Serrano
    Microorganisms.2024; 12(11): 2119.     CrossRef
  • The Synergistic Impact of a Novel Plant Growth-Promoting Rhizobacterial Consortium and Ascophyllum nodosum Seaweed Extract on Rhizosphere Microbiome Dynamics and Growth Enhancement in Oryza sativa L. RD79
    Pisit Thamvithayakorn, Cherdchai Phosri, Louisa Robinson-Boyer, Puenisara Limnonthakul, John H. Doonan, Nuttika Suwannasai
    Agronomy.2024; 14(11): 2698.     CrossRef
  • Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome
    Hamidreza Taherkhani, Azadeh KavianFar, Sargol Aminnezhad, Hossein Lanjanian, Ali Ahmadi, Sadegh Azimzadeh, Ali Masoudi-Nejad
    Heliyon.2024; 10(4): e24775.     CrossRef
  • Patent Mining on the Use of Antioxidant Phytochemicals in the Technological Development for the Prevention and Treatment of Periodontitis
    Paulo José Lima Juiz, Luiza Teles Barbalho Ferreira, Edilson Araújo Pires, Cristiane Flora Villarreal
    Antioxidants.2024; 13(5): 566.     CrossRef
  • Periodontal Hastalıklar: Başlıca Risk Faktörleri
    Tuba USTAOĞLU, Deniz MIHÇIOĞLU
    Cumhuriyet Üniversitesi Sağlık Bilimleri Enstitüsü Dergisi.2023; 8(3): 501.     CrossRef
  • Potential effects of gut microbiota on host cancers: focus on immunity, DNA damage, cellular pathways, and anticancer therapy
    Jiaao Sun, Feng Chen, Guangzhen Wu
    The ISME Journal.2023; 17(10): 1535.     CrossRef
  • Using microbiome information to understand and improve animal performance
    Jeferson Menezes Lourenco, Christina Breanne Welch
    Italian Journal of Animal Science.2022; 21(1): 899.     CrossRef
  • The Influence of Periodontal Disease on Oral Health Quality of Life in Patients with Cardiovascular Disease: A Cross-Sectional Observational Single-Center Study
    Pompilia Camelia Lazureanu, Florina Georgeta Popescu, Laura Stef, Mircea Focsa, Monica Adriana Vaida, Romeo Mihaila
    Medicina.2022; 58(5): 584.     CrossRef
  • Osteoimmunology in Periodontitis: Local Proteins and Compounds to Alleviate Periodontitis
    Kridtapat Sirisereephap, Tomoki Maekawa, Hikaru Tamura, Takumi Hiyoshi, Hisanori Domon, Toshihito Isono, Yutaka Terao, Takeyasu Maeda, Koichi Tabeta
    International Journal of Molecular Sciences.2022; 23(10): 5540.     CrossRef
  • Effects of oral health intervention strategies on cognition and microbiota alterations in patients with mild Alzheimer's disease: A randomized controlled trial
    Lili Chen, Huizhen Cao, Xiaoqi Wu, Xinhua Xu, Xinli Ji, Bixia Wang, Ping Zhang, Hong Li
    Geriatric Nursing.2022; 48: 103.     CrossRef
  • Lung microbiome in children with hematological malignancies and lower respiratory tract infections
    Yun Zhang, Haonan Ning, Wenyu Zheng, Jing Liu, Fuhai Li, Junfei Chen
    Frontiers in Oncology.2022;[Epub]     CrossRef
  • Defining the baseline of pulmonary microbiota in healthy populations and influencing factors
    Zhuoning Tang, Sen Yang, Zilong He
    Highlights in Science, Engineering and Technology.2022; 11: 38.     CrossRef
  • Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results
    Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo
    BMC Bioinformatics.2022;[Epub]     CrossRef
  • Periodontal Disease: The Good, The Bad, and The Unknown
    Lea M. Sedghi, Margot Bacino, Yvonne Lorraine Kapila
    Frontiers in Cellular and Infection Microbiology.2021;[Epub]     CrossRef
  • Omics-based microbiome analysis in microbial ecology: from sequences to information
    Jang-Cheon Cho
    Journal of Microbiology.2021; 59(3): 229.     CrossRef
  • Microbiome-immune interactions in tuberculosis
    Giorgia Mori, Mark Morrison, Antje Blumenthal, N.Luisa Hiller
    PLOS Pathogens.2021; 17(4): e1009377.     CrossRef
  • Simple Matching Using QIIME 2 and RDP Reveals Misidentified Sequences and an Underrepresentation of Fungi in Reference Datasets
    Lauren E. Eldred, R. Greg Thorn, David Roy Smith
    Frontiers in Genetics.2021;[Epub]     CrossRef
  • Xylanase impact beyond performance: A microbiome approach in laying hens
    Veerle Van Hoeck, Ingrid Somers, Anas Abdelqader, Alexandra L. Wealleans, Sandy Van de Craen, Dany Morisset, Arda Yildirim
    PLOS ONE.2021; 16(9): e0257681.     CrossRef
  • User guides for biologists to learn computational methods
    Dokyun Na
    Journal of Microbiology.2020; 58(3): 173.     CrossRef
  • High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
    Suhyun Kim, Miri S. Park, Jaeho Song, Ilnam Kang, Jang-Cheon Cho
    Journal of Microbiology.2020; 58(11): 893.     CrossRef
  • Microbiome Composition and Borrelia Detection in Ixodes scapularis Ticks at the Northwestern Edge of Their Range
    Janet L. H. Sperling, Daniel Fitzgerald, Felix A. H. Sperling, Katharine E. Magor
    Tropical Medicine and Infectious Disease.2020; 5(4): 173.     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
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  • 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

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  • Current updates on metabolites and its interlinked pathways as biomarkers for diabetic kidney disease: A systematic review
    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
    Sarbanding Sané, Abou Abdallah Malick Diouara, Seynabou Coundoul, Sophie Déli Tene, Alé Kane, Serigne Fallou Wade, Abdoulaye Tamba, Mamadou Diop, Mame Ndew Mbaye, Fatou Thiam, Modou Dieng, Malick Mbengue, Cheikh Momar Nguer, Aminata Diassé Sarr, Ababacar
    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
    Journal of Fungi.2024; 10(6): 389.     CrossRef
  • Use of microbiological data for the purposes of forensic medical examination
    O.S. Lavrukova, N.A. Sidorova
    Forensic Medical Expertise.2024; 67(5): 55.     CrossRef
  • Integrating microbiome and transcriptome analyses to understand the effect of replacing fishmeal with Tenebrio molitor meal in Pacific white shrimp (Litopenaeus vannamei) diets
    Yudong Zheng, Cuihong Hou, Jian Chen, Hongming Wang, Hang Yuan, Naijie Hu, Lili Shi, Shuang Zhang
    Aquaculture.2023; 575: 739818.     CrossRef
  • The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations
    Ana Cláudia-Ferreira, Daniel José Barbosa, Veroniek Saegeman, Amparo Fernández-Rodríguez, Ricardo Jorge Dinis-Oliveira, Ana R. Freitas
    Microorganisms.2023; 11(10): 2509.     CrossRef
  • Plant-microbiome interactions under drought—insights from the molecular machinist’s toolbox
    Mohamed Ait-El-Mokhtar, Abdelilah Meddich, Marouane Baslam
    Frontiers in Sustainable Food Systems.2023;[Epub]     CrossRef
  • ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning
    Olga Mineeva, Daniel Danciu, Bernhard Schölkopf, Ruth E. Ley, Gunnar Rätsch, Nicholas D. Youngblut, Luis Pedro Coelho
    PLOS Computational Biology.2023; 19(5): e1011001.     CrossRef
  • Response of dissolved organic matter (DOM) and microbial community to submerged macrophytes restoration in lakes: A review
    Haoyu Ren, Guoxi Wang, Wanchang Ding, He Li, Xian Shen, Dongbo Shen, Xia Jiang, Abdul Qadeer
    Environmental Research.2023; 231: 116185.     CrossRef
  • Integrative approach for classifying male tumors based on DNA methylation 450K data
    Ji-Ming Wu, Wang-Ren Qiu, Zi Liu, Zhao-Chun Xu, Shou-Hua Zhang
    Mathematical Biosciences and Engineering.2023; 20(11): 19133.     CrossRef
  • Impact of coprophagy prevention on the growth performance, serum biochemistry, and intestinal microbiome of rabbits
    Zhitong Wang, Hui He, Mengjuan Chen, Mengke Ni, Dongdong Yuan, Hanfang Cai, Zhi Chen, Ming Li, Huifen Xu
    BMC Microbiology.2023;[Epub]     CrossRef
  • The roles of gut microbiota and its metabolites in diabetic nephropathy
    Hui Zhao, Cheng-E Yang, Tian Liu, Ming-Xia Zhang, Yan Niu, Ming Wang, Jun Yu
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Structure and ecological function of the soil microbiome associated with ‘Sanghuang’ mushrooms suffering from fungal diseases
    Weifang Xu, Tao Sun, Jiahui Du, Shuqing Jin, Ying Zhang, Guofa Bai, Wanyu Li, Dengke Yin
    BMC Microbiology.2023;[Epub]     CrossRef
  • Analysis of differences in tobacco leaf microbial communities after redrying in Chinese provinces and from abroad
    Yifan Zhang, Qiang Xu, Mengmeng Yang, Yue Yang, Jincun Fu, Chenlin Miao, Guiyao Wang, Liwei Hu, Zongyu Hu
    AMB Express.2023;[Epub]     CrossRef
  • Learning from mistakes: challenges in finding holobiont factors from environmental samples and the importance of methodological consistency
    So Fujiyoshi, Kyoko Yarimizu, Ishara Perera, Michel Abanto, Milko Jorquera, Fumito Maruyama
    Current Opinion in Biotechnology.2023; 80: 102897.     CrossRef
  • Structural and functional characteristics of soil microbial community in a Pinus massoniana forest at different elevations
    Jian Zhang, Ming Xu, Xiao Zou, Jin Chen
    PeerJ.2022; 10: e13504.     CrossRef
  • Does filter pore size introduce bias in DNA sequence-based plankton community studies?
    Guolin Ma, Ramiro Logares, Yuanyuan Xue, Jun Yang
    Frontiers in Microbiology.2022;[Epub]     CrossRef
  • What will polyethylene film mulching bring to the root-associated microbial community of Paeonia ostii?
    Yingdan Yuan, Mengting Zu, Jiajia Zuo, Runze Li, Jun Tao
    Applied Microbiology and Biotechnology.2022; 106(12): 4737.     CrossRef
  • Differences in Supragingival Microbiome in Patients with and without Full-Crown Prostheses
    Manli Guo, Zhidong Zhang, Jiyuan Lu, Di Wang, Yimin Yan, Shen Zhang, Xin Yu, Songhua Su, Lu Yuan, Zhige Li, Baoping Zhang
    Dentistry Journal.2022; 10(8): 152.     CrossRef
  • Recent advances in droplet microfluidics for microbiology
    Ziyi He, Hao Wu, Xianghua Yan, Wu Liu
    Chinese Chemical Letters.2022; 33(4): 1729.     CrossRef
  • The root microbiome: Community assembly and its contributions to plant fitness
    Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang, Yang Bai
    Journal of Integrative Plant Biology.2022; 64(2): 230.     CrossRef
  • Analysis on the Structure and Function of the Bacterial Community in the Replanting Soil of Basswood of Ganoderma lingzhi Medicinal Mushroom (Agaricomycetes)
    Tiantian Wang, Wenxin Liu, Jize Xu, Muhammad Idrees, Yi Zhou, Guangbo Xu, Jian Shen, Chunlan Zhang
    International Journal of Medicinal Mushrooms.2022; 24(10): 45.     CrossRef
  • Ecosystem-specific microbiota and microbiome databases in the era of big data
    Victor Lobanov, Angélique Gobet, Alyssa Joyce
    Environmental Microbiome.2022;[Epub]     CrossRef
  • Omics-based microbiome analysis in microbial ecology: from sequences to information
    Jang-Cheon Cho
    Journal of Microbiology.2021; 59(3): 229.     CrossRef
  • Monitoring of plankton diversity in Dianchi Lake by environmental DNA technology
    Liwei He, Lijuan Zhang, Jianghua Yang, Zheng Zhao, Xiaohua Zhou, Qing Feng, Xiaowei Zhang, Shan Xu
    IOP Conference Series: Earth and Environmental Science.2021; 651(4): 042023.     CrossRef
  • Fecal Microbiome Composition Does Not Predict Diet‐Induced TMAO Production in Healthy Adults
    Marc Ferrell, Peter Bazeley, Zeneng Wang, Bruce S. Levison, Xinmin S. Li, Xun Jia, Ronald M. Krauss, Rob Knight, Aldons J. Lusis, J. C. Garcia‐Garcia, Stanley L. Hazen, W. H. Wilson Tang
    Journal of the American Heart Association.2021;[Epub]     CrossRef
  • Roles of Gut Microbial Metabolites in Diabetic Kidney Disease
    Qing Fang, Na Liu, Binjie Zheng, Fei Guo, Xiangchang Zeng, Xinyi Huang, Dongsheng Ouyang
    Frontiers in Endocrinology.2021;[Epub]     CrossRef
  • A Review of the Molluscan Microbiome: Ecology, Methodology and Future
    Bridget Chalifour, Jingchun Li
    Malacologia.2021;[Epub]     CrossRef
  • Microbial-induced concrete corrosion under high-salt conditions: Microbial community composition and environmental multivariate association analysis
    Jingya Zhou, Shouyi Yin, Qionglin Fu, Qingqing Wang, Qing Huang, Junfeng Wang
    International Biodeterioration & Biodegradation.2021; 164: 105287.     CrossRef
  • User guides for biologists to learn computational methods
    Dokyun Na
    Journal of Microbiology.2020; 58(3): 173.     CrossRef
  • High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
    Suhyun Kim, Miri S. Park, Jaeho Song, Ilnam Kang, Jang-Cheon Cho
    Journal of Microbiology.2020; 58(11): 893.     CrossRef
Reviews
[MINIREVIEW] Progress of analytical tools and techniques for human gut microbiome research
Eun-Ji Song , Eun-Sook Lee , Young-Do Nam
J. Microbiol. 2018;56(10):693-705.   Published online September 28, 2018
DOI: https://doi.org/10.1007/s12275-018-8238-5
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AbstractAbstract
Massive DNA sequencing studies have expanded our insights and understanding of the ecological and functional characteristics of the gut microbiome. Advanced sequencing technologies allow us to understand the close association of the gut microbiome with human health and critical illnesses. In the future, analyses of the gut microbiome will provide key information associating with human individual health, which will help provide personalized health care for diseases. Numerous molecular biological analysis tools have been rapidly developed and employed for the gut microbiome researches; however, methodological differences among researchers lead to inconsistent data, limiting extensive share of data. It is therefore very essential to standardize the current
method
ologies and establish appropriate pipelines for human gut microbiome research. Herein, we review the methods and procedures currently available for studying the human gut microbiome, including fecal sample collection, metagenomic DNA extraction, massive DNA sequencing, and data analyses with bioinformatics. We believe that this review will contribute to the progress of gut microbiome research in the clinical and practical aspects of human health.

Citations

Citations to this article as recorded by  
  • Efficacy of a Postbiotic Formulation Combined With Microneedling for Mild‐to‐Moderate Acne: A Self‐Control Study
    Zhanhong Li, Peihui Li, Yu Xu, Changqing Yan, Xiufen Ma, Huiying Wang, Hong Cheng, Jing Zeng, Ting Li, Xinxian Li, Jia Zhou, Jie Zhang, Jianfeng Zhou, Rongya Yang, Yan Wu, Li Li, Wei Lai, Jiangyun Zhao, Zhe Liu, Qiong Meng
    Journal of Cosmetic Dermatology.2025;[Epub]     CrossRef
  • Changes in the Gastrointestinal Microbiota Induced by Proton Pump Inhibitors—A Review of Findings from Experimental Trials
    Reidar Fossmark, Maya Olaisen
    Microorganisms.2024; 12(6): 1110.     CrossRef
  • Deciphering the gut microbiome: The revolution of artificial intelligence in microbiota analysis and intervention
    Mohammad Abavisani, Alireza Khoshrou, Sobhan Karbas Foroushan, Negar Ebadpour, Amirhossein Sahebkar
    Current Research in Biotechnology.2024; 7: 100211.     CrossRef
  • From the Gut to the Brain: Is Microbiota a New Paradigm in Parkinson’s Disease Treatment?
    Cristiana Vilela, Bruna Araújo, Carla Soares-Guedes, Rita Caridade-Silva, Joana Martins-Macedo, Catarina Teixeira, Eduardo D. Gomes, Cristina Prudêncio, Mónica Vieira, Fábio G. Teixeira
    Cells.2024; 13(9): 770.     CrossRef
  • Gut Microbiome in Alzheimer’s Disease: from Mice to Humans
    Chang Liang, Resel Pereira, Yan Zhang, Olga L. Rojas
    Current Neuropharmacology.2024; 22(14): 2314.     CrossRef
  • Comparative Analysis of Healthy Gut Microbiota in German and Korean Populations: Insights from Large-Scale Cohort Studies
    Min Kee Son, Yuri Song, Jin Chung, Hee Sam Na
    Microbiology Research.2023; 15(1): 109.     CrossRef
  • Changes in the microbiota of the upper airways and intestine in the treatment of acute respiratory infections in preschool children
    Tatiana I. Kurdyukova, Olga N. Krasnorutskaya, Daniil Yu. Bugrimov, Artem N. Shevtsov
    Russian Pediatric Journal.2023; 23(2): 95.     CrossRef
  • Factors Affecting Gut Microbiota of Puppies from Birth to Weaning
    Fatemeh Balouei, Bruno Stefanon, Sandy Sgorlon, Misa Sandri
    Animals.2023; 13(4): 578.     CrossRef
  • Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques
    Saber Khelaifia, Pilliol Virginie, Souad Belkacemi, Herve Tassery, Elodie Terrer, Gérard Aboudharam
    Microorganisms.2023; 11(4): 836.     CrossRef
  • Influence of Microbiota on Vaccine Effectiveness: “Is the Microbiota the Key to Vaccine-induced Responses?”
    So-Hee Hong
    Journal of Microbiology.2023; 61(5): 483.     CrossRef
  • gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions
    Changlu Qi, Yiting Cai, Kai Qian, Xuefeng Li, Jialiang Ren, Ping Wang, Tongze Fu, Tianyi Zhao, Liang Cheng, Lei Shi, Xue Zhang
    Nucleic Acids Research.2023; 51(D1): D717.     CrossRef
  • The impact of environmental toxins on the animal gut microbiome and their potential to contribute to disease
    Dinesh Nalage, Tejswini Sontakke, Ashwini Biradar, Vinod Jogdand, Ravindra Kale, Sanjay Harke, Rahul Kale, Prashant Dixit
    Food Chemistry Advances.2023; 3: 100497.     CrossRef
  • Fecal and cloacal microbiomes of cold-stunned loggerhead Caretta caretta, Kemp’s ridley Lepidochelys kempii, and green sea turtles Chelonia mydas
    ZR Forbes, AK Scro, SH Patel, KM Dourdeville, RL Prescott, RM Smolowitz
    Endangered Species Research.2023; 50: 93.     CrossRef
  • A Two-Step Single Plex PCR Method for Evaluating Key Colonic Microbiota Markers in Young Mexicans with Autism Spectrum Disorders: Protocol and Pilot Epidemiological Application
    Julián Herrera-Mejía, Rocío Campos-Vega, Abraham Wall-Medrano, Florinda Jiménez-Vega
    Diagnostics.2023; 13(14): 2387.     CrossRef
  • Effect of Concurrent Training on Body Composition and Gut Microbiota in Postmenopausal Women with Overweight or Obesity
    MARINE DUPUIT, MÉLANIE RANCE, CLAIRE MOREL, PATRICE BOUILLON, AUDREY BOSCARO, VINCENT MARTIN, EMILIE VAZEILLE, NICOLAS BARNICH, BENOIT CHASSAING, NATHALIE BOISSEAU
    Medicine & Science in Sports & Exercise.2022; 54(3): 517.     CrossRef
  • Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy
    Lucia Boeri, Francesca Donnaloja, Marzia Campanile, Lorenzo Sardelli, Marta Tunesi, Federica Fusco, Carmen Giordano, Diego Albani
    Neurobiology of Disease.2022; 164: 105614.     CrossRef
  • The gut microbiota as a biomarker in epilepsy
    Emilio Russo
    Neurobiology of Disease.2022; 163: 105598.     CrossRef
  • Developing whole cell standards for the microbiome field
    Chrysi Sergaki, Saba Anwar, Martin Fritzsche, Ryan Mate, Robert J. Francis, Kirsty MacLellan-Gibson, Alastair Logan, Gregory C. A. Amos
    Microbiome.2022;[Epub]     CrossRef
  • Changes in Vaginal Microbiome Diversity in Women With Polycystic Ovary Syndrome
    Chaoyi Lu, Hui Wang, Jihong Yang, Xinyue Zhang, Yao Chen, Ruizhi Feng, Yun Qian
    Frontiers in Cellular and Infection Microbiology.2021;[Epub]     CrossRef
  • High-throughput 16S rDNA sequencing assisting in the detection of bacterial pathogen candidates: a fatal case of necrotizing fasciitis in a child
    Dong Qu, Dong-Fang Qiao, Michael Klintschar, Zhi Qu, Xia Yue
    International Journal of Legal Medicine.2021; 135(2): 399.     CrossRef
  • Standardization of microbiome studies for urolithiasis: an international consensus agreement
    Naveen Kachroo, Dirk Lange, Kristina L. Penniston, Joshua Stern, Gregory Tasian, Petar Bajic, Alan J. Wolfe, Mangesh Suryavanshi, Andrea Ticinesi, Tiziana Meschi, Manoj Monga, Aaron W. Miller
    Nature Reviews Urology.2021; 18(5): 303.     CrossRef
  • The Mammalian Metaorganism: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity
    Solveig Runge, Stephan Patrick Rosshart
    Frontiers in Immunology.2021;[Epub]     CrossRef
  • Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health
    Kirsten Berding, Klara Vlckova, Wolfgang Marx, Harriet Schellekens, Catherine Stanton, Gerard Clarke, Felice Jacka, Timothy G Dinan, John F Cryan
    Advances in Nutrition.2021; 12(4): 1239.     CrossRef
  • Interrogation of the perturbed gut microbiota in gouty arthritis patients through in silico metabolic modeling
    Michael A. Henson
    Engineering in Life Sciences.2021; 21(7): 489.     CrossRef
  • A comprehensive review for gut microbes: technologies, interventions, metabolites and diseases
    Changlu Qi, Ping Wang, Tongze Fu, Minke Lu, Yiting Cai, Xu Chen, Liang Cheng
    Briefings in Functional Genomics.2021; 20(1): 42.     CrossRef
  • Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients
    Sofia Sehli, Imane Allali, Rajaa Chahboune, Youssef Bakri, Najib Al Idrissi, Salsabil Hamdi, Chakib Nejjari, Saaïd Amzazi, Hassan Ghazal
    Bioinformatics and Biology Insights.2021;[Epub]     CrossRef
  • Potential role of the skin microbiota in Inflammatory skin diseases
    Pan Chen, Guangwen He, Jingru Qian, Yi Zhan, Rong Xiao
    Journal of Cosmetic Dermatology.2021; 20(2): 400.     CrossRef
  • Current ocular microbiome investigations limit reproducibility and reliability: Critical review and opportunities
    Erin M. Scott, Andrew C. Lewin, Marina L. Leis
    Veterinary Ophthalmology.2021; 24(1): 4.     CrossRef
  • Mining microbes for mental health: Determining the role of microbial metabolic pathways in human brain health and disease
    Simon Spichak, Thomaz F.S. Bastiaanssen, Kirsten Berding, Klara Vlckova, Gerard Clarke, Timothy G. Dinan, John F. Cryan
    Neuroscience & Biobehavioral Reviews.2021; 125: 698.     CrossRef
  • Interactions between immune system and the microbiome of skin, blood and gut in pathogenesis of rosacea
    Marie Isolde Joura, Alexandra Brunner, Éva Nemes-Nikodém, Miklós Sárdy, Eszter Ostorházi
    Acta Microbiologica et Immunologica Hungarica.2021; 68(1): 1.     CrossRef
  • The gut microbiome in drug‐resistant epilepsy
    Simela Chatzikonstantinou, Georgia Gioula, Vasilios K. Kimiskidis, Jack McKenna, Ioannis Mavroudis, Dimitrios Kazis
    Epilepsia Open.2021; 6(1): 28.     CrossRef
  • Estimating included animal species in mixed crude drugs derived from animals using massively parallel sequencing
    Hiroaki Nakanishi, Katsumi Yoneyama, Masaaki Hara, Aya Takada, Kazuyuki Saito
    Scientific Reports.2021;[Epub]     CrossRef
  • Effects of Xylo-Oligosaccharide on the Gut Microbiota of Patients With Ulcerative Colitis in Clinical Remission
    Zongwei Li, Zhengpeng Li, Liying Zhu, Ning Dai, Gang Sun, Lihua Peng, Xin Wang, Yunsheng Yang
    Frontiers in Nutrition.2021;[Epub]     CrossRef
  • Recent advances in modulating the microbiome
    Eamonn M.M Quigley, Prianka Gajula
    F1000Research.2020; 9: 46.     CrossRef
  • Tools for Analysis of the Microbiome
    Jessica Galloway-Peña, Blake Hanson
    Digestive Diseases and Sciences.2020; 65(3): 674.     CrossRef
  • The potential role of interventions impacting on gut-microbiota in epilepsy
    Luigi F Iannone, Maria Gómez-Eguílaz, Rita Citaro, Emilio Russo
    Expert Review of Clinical Pharmacology.2020; 13(4): 423.     CrossRef
  • State of the Art in the Culture of the Human Microbiota: New Interests and Strategies
    Maryam Tidjani Alou, Sabrina Naud, Saber Khelaifia, Marion Bonnet, Jean-Christophe Lagier, Didier Raoult
    Clinical Microbiology Reviews.2020;[Epub]     CrossRef
  • Database limitations for studying the human gut microbiome
    Camila K Dias, Robert Starke, Victor S. Pylro, Daniel K. Morais
    PeerJ Computer Science.2020; 6: e289.     CrossRef
  • Machine learning methods for microbiome studies
    Junghyun Namkung
    Journal of Microbiology.2020; 58(3): 206.     CrossRef
  • Gut Microbiome Reveals Specific Dysbiosis in Primary Osteoporosis
    Zhiming Xu, Zheng Xie, Jianguang Sun, Shilei Huang, Yangyang Chen, Chengxiang Li, Xing Sun, Bicheng Xia, Lingyang Tian, Caijuan Guo, Feng Li, Guofu Pi
    Frontiers in Cellular and Infection Microbiology.2020;[Epub]     CrossRef
  • Evaluation of cutaneous, oral and intestinal microbiota in patients affected by pemphigus and bullous pemphigoid: A pilot study
    Giovanni Luca Scaglione, Luca Fania, Elisa De Paolis, Maria De Bonis, Cinzia Mazzanti, Giovanni Di Zenzo, Stefania Lechiancole, Serena Messinese, Ettore Capoluongo
    Experimental and Molecular Pathology.2020; 112: 104331.     CrossRef
  • Microecology research: a new target for the prevention of asthma
    Hong-Lei Shi, Yu-Hao Lan, Zheng-Chuan Hu, Zi-Ning Yan, Ze-Zhong Liu, Xiriaili Kadier, Li Ma, Jin-Yan Yu, Jing Liu
    Chinese Medical Journal.2020; 133(22): 2712.     CrossRef
  • Omics Biomarkers in Obesity: Novel Etiological Insights and Targets for Precision Prevention
    Krasimira Aleksandrova, Caue Egea Rodrigues, Anna Floegel, Wolfgang Ahrens
    Current Obesity Reports.2020; 9(3): 219.     CrossRef
  • Microbiome and colorectal cancer: Roles in carcinogenesis and clinical potential
    Ester Saus, Susana Iraola-Guzmán, Jesse R. Willis, Anna Brunet-Vega, Toni Gabaldón
    Molecular Aspects of Medicine.2019; 69: 93.     CrossRef
  • Dietary quality and the colonic mucosa–associated gut microbiome in humans
    Yanhong Liu, Nadim J Ajami, Hashem B El-Serag, Clark Hair, David Y Graham, Donna L White, Liang Chen, Zhensheng Wang, Sarah Plew, Jennifer Kramer, Rhonda Cole, Ruben Hernaez, Jason Hou, Nisreen Husain, Maria E Jarbrink-Sehgal, Fasiha Kanwal, Gyanprakash K
    The American Journal of Clinical Nutrition.2019; 110(3): 701.     CrossRef
MINIREVIEW] On the study of microbial transcriptomes using second- and third-generation sequencing technologies
Sang Chul Choi
J. Microbiol. 2016;54(8):527-536.   Published online August 2, 2016
DOI: https://doi.org/10.1007/s12275-016-6233-2
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AbstractAbstract
Second-generation sequencing technologies transformed the study of microbial transcriptomes. They helped reveal the transcription start sites and antisense transcripts of microbial species, improving the microbial genome annotation. Quantification of genome-wide gene expression levels allowed for functional studies of microbial research. Ever-evolving sequencing technologies are reshaping approaches to studying microbial transcriptomes. Recently, Oxford Nanopore Technologies delivered a sequencing platform called MinION, a third-generation sequencing technology, to the research community. We expect it to be the next sequencing technology that enables breakthroughs in life science fields. The studies of microbial transcriptomes will be no exception. In this paper, we review microbial transcriptomics studies using second- generation sequencing technology. We also discuss the prospect of microbial transcriptomics studies with thirdgeneration sequencing.

Citations

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  • TPX2 upregulates MMP13 to promote the progression of lipopolysaccharide-induced osteoarthritis
    Jingtao Yu, Weiqi Wang, Zenghui Jiang, Huashun Liu
    PeerJ.2024; 12: e17032.     CrossRef
  • Gut Microbiota in Children with Hand Foot and Mouth Disease on 16S rRNA Gene Sequencing
    Yan Zhuang, Yiyan Lin, Hongxia Sun, Zaiting Zhang, Tao Wang, Rongjun Fan, Lu Han
    Current Microbiology.2023;[Epub]     CrossRef
  • Advances in Nanopore and Photoelectron-Based High-Throughput Sequencing Technology for Single-Molecule Sequencing
    Yunqi Huang, Yutong Lu, Cailing Song, Yican Wei, Yuxi Yang, Jie Ren, Meiling Wang, Congli Tang, Aayesha Riaz, Muhammad Ali Shah, Yan Deng, Hongna Liu, Wenjing Pan, Song Li
    Journal of Nanoelectronics and Optoelectronics.2023; 18(4): 381.     CrossRef
  • Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature
    Chongchong Yan, Nan Zhang, Qianqian Wang, Yuying Fu, Hongyuan Zhao, Jiajia Wang, Gang Wu, Feng Wang, Xueyan Li, Huajun Liao
    BMC Plant Biology.2022;[Epub]     CrossRef
  • Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
    Felix Grünberger, Sébastien Ferreira-Cerca, Dina Grohmann
    RNA.2022; 28(3): 400.     CrossRef
  • Full-length transcriptome sequences of ridgetail white prawn Exopalaemon carinicauda provide insight into gene expression dynamics during thermal stress
    Kunpeng Shi, Jitao Li, Jianjian Lv, Ping Liu, Jian Li, Sedong Li
    Science of The Total Environment.2020; 747: 141238.     CrossRef
  • A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa
    Ao Li, Ai Liu, Xin Du, Jin-Yuan Chen, Mou Yin, Hong-Yin Hu, Nawal Shrestha, Sheng-Dan Wu, Hai-Qing Wang, Quan-Wen Dou, Zhi-Peng Liu, Jian-Quan Liu, Yong-Zhi Yang, Guang-Peng Ren
    Horticulture Research.2020;[Epub]     CrossRef
  • Next-generation technologies for studying host–pathogen interactions: a focus on dual transcriptomics, CRISPR/Cas9 screening and organs-on-chips
    Buket Baddal
    Pathogens and Disease.2019;[Epub]     CrossRef
  • Prospects for the use of third generation sequencers for quantitative profiling of transcriptome
    S.P. Radko, L.K. Kurbatov, K.G. Ptitsyn, Y.Y. Kiseleva, E.A. Ponomarenko, A.V. Lisitsa, A.I. Archakov
    Biomedical Chemistry: Research and Methods.2018; 1(4): e00086.     CrossRef
  • Two's company: studying interspecies relationships with dual RNA-seq
    Thomas Wolf, Philipp Kämmer, Sascha Brunke, Jörg Linde
    Current Opinion in Microbiology.2018; 42: 7.     CrossRef
  • Taxonomy and systematics of plant probiotic bacteria in the genomic era
    Lorena Carro, Imen Nouioui
    AIMS Microbiology.2017; 3(3): 383.     CrossRef
Research Support, Non-U.S. Gov'ts
Prediction of Bacterial microRNAs and Possible Targets in Human Cell Transcriptome
Amir Shmaryahu , Margarita Carrasco , Pablo D.T. Valenzuela
J. Microbiol. 2014;52(6):482-489.   Published online May 29, 2014
DOI: https://doi.org/10.1007/s12275-014-3658-3
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AbstractAbstract
Recent studies have examined gene transfer from bacteria to humans that would result in vertical inheritance. Bacterial DNA appears to integrate into the human somatic genome through an RNA intermediate, and such integrations are detected more frequently in tumors than normal samples and in RNA than DNA samples. Also, vertebrate viruses encode products that interfere with the RNA silencing machinery, suggesting that RNA silencing may indeed be important for antiviral responses in vertebrates. RNA silencing in response to virus infection could be due to microRNAs encoded by either the virus or the host. We hypothesized that bacterial expression of RNA molecules with secondary structures is potentially able to generate miRNA molecules that can interact with the human host mRNA during bacterial infection. To test this hypothesis, we developed a pipelinebased bioinformatics approach to identify putative micro-RNAs derived from bacterial RNAs that may have the potential to regulate gene expression of the human host cell. Our results suggest that 68 bacterial RNAs predicted from 37 different bacterial genomes have predicted secondary structures potentially able to generate putative microRNAs that may interact with messenger RNAs of genes involved in 47 different human diseases. As an example, we examined the effect of transfecting three putative microRNAs into human embryonic kidney 293 (HEK293) cells. The results show that the bacterially derived microRNA sequence can significantly regulate the expression of the respective target human gene. We suggest that the study of these predicted microRNAs may yield important clues as to how the human host cell processes involved in human diseases like cancer, diabetes, rheumatoid arthritis, and others may respond to a particular bacterial environment.

Citations

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  • Pseudomonas aeruginosa outer membrane vesicle-packed sRNAs can enter host cells and regulate innate immune responses
    Zhen Xie, Xiao Wang, Yangyang Huang, Shukun Chen, Mohua Liu, Fuhua Zhang, Mengyuan Li, Xiao Wang, Yanchao Gu, Yadong Yang, Xihui Shen, Yao Wang, Yang Xu, Lei Xu
    Microbial Pathogenesis.2024; 188: 106562.     CrossRef
  • Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus
    Imrat, Rajendra Kumar Labala, Abhisek Kumar Behara, Kumaraswamy Jeyaram
    Functional & Integrative Genomics.2023;[Epub]     CrossRef
  • Identification of putative microRNAs in the complete genome of Mycobacterium avium and their possible interaction with human transcripts
    Durbba Nath, Supriyo Chakraborty
    Journal of Applied Genetics.2022; 63(1): 169.     CrossRef
  • Biological Functions and Cross-Kingdom Host Gene Regulation of Small RNAs in Lactobacillus plantarum-Derived Extracellular Vesicles
    Siran Yu, Zhehao Zhao, Piliang Hao, Yan Qiu, Meiyi Zhao, Gang Zhou, Chengqian Zhang, Jiuhong Kang, Ping Li
    Frontiers in Microbiology.2022;[Epub]     CrossRef
  • The neglected nutrigenomics of milk: What is the role of inter-species transfer of small non-coding RNA?
    Laura Bordoni, Rosita Gabbianelli
    Food Bioscience.2021; 39: 100796.     CrossRef
  • Prediction of microRNAs in Pseudomonas syringae pv. tomato DC3000 and their potential target prediction in Solanum lycopersicum
    Yengkhom Sophiarani, Supriyo Chakraborty
    Gene Reports.2021; 25: 101360.     CrossRef
  • Small RNAs Asserting Big Roles in Mycobacteria
    Fatma S. Coskun, Przemysław Płociński, Nicolai S. C. van Oers
    Non-Coding RNA.2021; 7(4): 69.     CrossRef
  • Genome wide analysis of Mycobacterium leprae for identification of putative microRNAs and their possible targets in human
    Durbba Nath, Supriyo Chakraborty
    Biologia.2021; 76(8): 2437.     CrossRef
  • Potential Mechanisms Linking Food-Derived MicroRNAs, Gut Microbiota and Intestinal Barrier Functions in the Context of Nutrition and Human Health
    Ester Díez-Sainz, Silvia Lorente-Cebrián, Paula Aranaz, José I. Riezu-Boj, J. Alfredo Martínez, Fermín I. Milagro
    Frontiers in Nutrition.2021;[Epub]     CrossRef
  • From Gene to Protein—How Bacterial Virulence Factors Manipulate Host Gene Expression During Infection
    Lea Denzer, Horst Schroten, Christian Schwerk
    International Journal of Molecular Sciences.2020; 21(10): 3730.     CrossRef
  • Editorial commentary: Wanted: MicroRNAs to the aid of the diabetic foot
    Louise T. Dalgaard, Eugenia Carvalho
    Trends in Cardiovascular Medicine.2019; 29(3): 138.     CrossRef
  • MicroRNA expression profiles of bovine monocyte-derived macrophages infected in vitro with two strains of Streptococcus agalactiae
    Anna Monika Lewandowska-Sabat, Silje Furre Hansen, Trygve Roger Solberg, Olav Østerås, Bjørg Heringstad, Preben Boysen, Ingrid Olsaker
    BMC Genomics.2018;[Epub]     CrossRef
  • Core non-coding RNAs of Piscirickettsia salmonis
    Cristopher Segovia, Raul Arias-Carrasco, Alejandro J. Yañez, Vinicius Maracaja-Coutinho, Javier Santander, Igor B. Rogozin
    PLOS ONE.2018; 13(5): e0197206.     CrossRef
  • Mammalian microRNAs and long noncoding RNAs in the host-bacterial pathogen crosstalk
    Mélodie Duval, Pascale Cossart, Alice Lebreton
    Seminars in Cell & Developmental Biology.2017; 65: 11.     CrossRef
  • A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles
    Katja Koeppen, Thomas H. Hampton, Michael Jarek, Maren Scharfe, Scott A. Gerber, Daniel W. Mielcarz, Elora G. Demers, Emily L. Dolben, John H. Hammond, Deborah A. Hogan, Bruce A. Stanton, Marvin Whiteley
    PLOS Pathogens.2016; 12(6): e1005672.     CrossRef
  • Regulatory role of cellular and viral microRNAs in insect–virus interactions
    Sassan Asgari
    Current Opinion in Insect Science.2015; 8: 104.     CrossRef
  • Wolbachia small noncoding RNAs and their role in cross-kingdom communications
    Jaime G. Mayoral, Mazhar Hussain, D. Albert Joubert, Iñaki Iturbe-Ormaetxe, Scott L. O’Neill, Sassan Asgari
    Proceedings of the National Academy of Sciences.2014; 111(52): 18721.     CrossRef
A Method for Comparing Multiple Bacterial Community Structures from 16S rDNA Clone Library Sequences
Inae Hur , Jongsik Chun
J. Microbiol. 2004;42(1):9-13.
DOI: https://doi.org/2008 [pii]
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AbstractAbstract
Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

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