Meta-Analysis
- Exploring COVID-19 Pandemic Disparities with Transcriptomic Meta-analysis from the Perspective of Personalized Medicine
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Medi Kori, Ceyda Kasavi, Kazim Yalcin Arga
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J. Microbiol. 2024;62(9):785-798. Published online July 9, 2024
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DOI: https://doi.org/10.1007/s12275-024-00154-9
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Abstract
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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
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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
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J. Microbiol. 2022;60(12):1178-1190. Published online November 24, 2022
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DOI: https://doi.org/10.1007/s12275-022-2416-1
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57
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Abstract
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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.
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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
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Kwangmin Kim , Karpagam Veerappan , Nahyun Woo , Bohyeon Park , Sathishkumar Natarajan , Hoyong Chung , Cheolmin Kim , Junhyung Park
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J. Microbiol. 2021;59(12):1150-1156. Published online October 26, 2021
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DOI: https://doi.org/10.1007/s12275-021-1329-8
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50
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6
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6
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Abstract
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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.
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Citations
Citations to this article as recorded by

- 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
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Hyojung Kim , Sora Kim , Sungwon Jung
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J. Microbiol. 2020;58(3):193-205. Published online February 27, 2020
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DOI: https://doi.org/10.1007/s12275-020-9556-y
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47
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23
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24
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Abstract
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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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Citations
Citations to this article as recorded by

- 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
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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
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Zhuoning Tang, Sen Yang, Zilong He
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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
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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
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- Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
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Jihoon Jo , Jooseong Oh , Chungoo Park
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J. Microbiol. 2020;58(3):176-192. Published online February 27, 2020
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DOI: https://doi.org/10.1007/s12275-020-9525-5
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44
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Abstract
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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.
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Citations
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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
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O.S. Lavrukova, N.A. Sidorova
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Mohamed Ait-El-Mokhtar, Abdelilah Meddich, Marouane Baslam
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Olga Mineeva, Daniel Danciu, Bernhard Schölkopf, Ruth E. Ley, Gunnar Rätsch, Nicholas D. Youngblut, Luis Pedro Coelho
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Ji-Ming Wu, Wang-Ren Qiu, Zi Liu, Zhao-Chun Xu, Shou-Hua Zhang
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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
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Weifang Xu, Tao Sun, Jiahui Du, Shuqing Jin, Ying Zhang, Guofa Bai, Wanyu Li, Dengke Yin
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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
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Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang, Yang Bai
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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
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Jang-Cheon Cho
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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
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DOI: https://doi.org/10.1007/s12275-018-8238-5
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49
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Abstract
-
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.
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- MINIREVIEW] On the study of microbial transcriptomes using second- and third-generation sequencing technologies
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Sang Chul Choi
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J. Microbiol. 2016;54(8):527-536. Published online August 2, 2016
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DOI: https://doi.org/10.1007/s12275-016-6233-2
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48
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11
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Abstract
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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.
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Amir Shmaryahu , Margarita Carrasco , Pablo D.T. Valenzuela
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DOI: https://doi.org/10.1007/s12275-014-3658-3
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47
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17
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Abstract
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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.
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Inae Hur , Jongsik Chun
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DOI: https://doi.org/2008 [pii]
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Abstract
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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/.