Journal of Microbiology

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

59 View
0 Download
6 Web of Science
6 Crossref

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

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 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

54 View
0 Download
24 Web of Science
28 Crossref

Abstract

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

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
Increased bacterial load of Filifactor alocis in deep periodontal pockets discriminate between periodontitis stage 3 and 4
Reem H. Faisal, Alaa O. Ali
Frontiers in Oral Health.2025;[Epub] CrossRef
Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake
Rongbing Guo, Yuguang Chang, Dandan Wang, Hanxue Sun, Tiantian Gu, Yibo Zong, Shiheng Zhou, Zhizhou Huang, Li Chen, Yong Tian, Wenwu Xu, Lizhi Lu, Tao Zeng
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
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

First
Prev
Page of 1
Next
Last

Search