Journal of Microbiology

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Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data: Sungwon Jung; J. Microbiol. 2025;63(1):e.2411006. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2411006

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Abstract PDF: This review explores current advancements in microbiome functional analysis enabled by next-generation sequencing technologies, which have transformed our understanding of microbial communities from mere taxonomic composition to their functional potential. We examine approaches that move beyond species identification to characterize microbial activities, interactions, and their roles in host health and disease. Genome-scale metabolic models allow for in-depth simulations of metabolic networks, enabling researchers to predict microbial metabolism, growth, and interspecies interactions in diverse environments. Additionally, computational methods for predicting metabolite profiles offer indirect insights into microbial metabolic outputs, which is crucial for identifying biomarkers and potential therapeutic targets. Functional pathway analysis tools further reveal microbial contributions to metabolic pathways, highlighting alterations in response to environmental changes and disease states. Together, these methods offer a powerful framework for understanding the complex metabolic interactions within microbial communities and their impact on host physiology. While significant progress has been made, challenges remain in the accuracy of predictive models and the completeness of reference databases, which limit the applicability of these methods in under-characterized ecosystems. The integration of these computational tools with multi-omic data holds promise for personalized approaches in precision medicine, allowing for targeted interventions that modulate the microbiome to improve health outcomes. This review highlights recent advances in microbiome functional analysis, providing a roadmap for future research and translational applications in human health and environmental microbiology.

Journal Article

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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24 Web of Science
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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.

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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
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Reem H. Faisal, Alaa O. Ali
Frontiers in Oral Health.2025;[Epub] CrossRef
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Animal Microbiome.2025;[Epub] CrossRef
Understanding the implicit effects of 16S rRNA gene databases on microbial bioindicator studies
Vitória Domingues, Lucy Seldin, Diogo Jurelevicius
Aquatic Toxicology.2025; : 107351. CrossRef
Cyber-Biosecurity Challenges in Next-Generation Sequencing: A Comprehensive Analysis of Emerging Threat Vectors
Nasreen Anjum, Hani Alshahrani, Asadullah Shaikh, Mahreen-Ul-Hassan, Mehreen Kiran, Shah Raz, Abu Alam
IEEE Access.2025; 13: 52006. 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
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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
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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
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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
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Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef
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PLOS Pathogens.2021; 17(4): e1009377. CrossRef
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Lauren E. Eldred, R. Greg Thorn, David Roy Smith
Frontiers in Genetics.2021;[Epub] CrossRef
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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
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Dokyun Na
Journal of Microbiology.2020; 58(3): 173. CrossRef
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Journal of Microbiology.2020; 58(11): 893. CrossRef
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Janet L. H. Sperling, Daniel Fitzgerald, Felix A. H. Sperling, Katharine E. Magor
Tropical Medicine and Infectious Disease.2020; 5(4): 173. CrossRef

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