Article
Biotechnology & Applied Microbiology
Shoichiro Kameoka, Daisuke Motooka, Satoshi Watanabe, Ryuichi Kubo, Nicolas Jung, Yuki Midorikawa, Natsuko O. Shinozaki, Yu Sawai, Aya K. Takeda, Shota Nakamura
Summary: The study compared 192 Japanese volunteers' fecal 16S analysis data using modified V1-V2 and standard V3-V4 primers. Results showed that the bacterial composition derived from the V34 region might differ from the actual abundance, suggesting that the modified V12 primer set is more desirable for analyzing the Japanese gut microbiota.
Article
Immunology
Yanyan Que, Man Cao, Jianquan He, Qiang Zhang, Qiongyun Chen, Changsheng Yan, Aiqiang Lin, Luxi Yang, Zezhen Wu, Dan Zhu, Fengwu Chen, Zhangran Chen, Chuanxing Xiao, Kaijian Hou, Bangzhou Zhang
Summary: Research shows significant differences in microbial diversity between individuals with type 2 diabetes mellitus (T2DM) and controls, but not in microbial alpha diversity. Various operational taxonomic units (OTUs) and bacterial genera with significant odds ratios for T2DM were identified. The microbial characteristics of T2DM can be applied to other studies, improving detection accuracy and disease specificity for T2DM through training on multiple research studies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Veterinary Sciences
Li Xi, Yumin Song, Xinxi Qin, Jincheng Han, Yung-Fu Chang
Summary: By comparing the gut microbial composition of healthy and diarrheic giraffes, this study found that diarrhea significantly impacts the diversity and composition of the gut microbiota by increasing the proportion of pathogenic bacteria and decreasing beneficial bacteria. It also identified specific changes in bacterial phyla and genera, providing insights for establishing prevention and treatment strategies for diarrhea in giraffes.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Microbiology
Baiyuan Li, Huahai Chen, Linyan Cao, Yunfei Hu, Dan Chen, Yeshi Yin
Summary: The study investigated the interaction between Escherichia coli exopolysaccharides (EPS-m2) and the human gut microbiota (HGM), finding that EPS-m2 could be degraded by human fecal microbiota and increase the abundance of certain bacteria species, thereby enhancing the production of short-chain fatty acids in the body.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Yoshiyuki Matsuo, Shinnosuke Komiya, Yoshiaki Yasumizu, Yuki Yasuoka, Katsura Mizushima, Tomohisa Takagi, Kirill Kryukov, Aisaku Fukuda, Yoshiharu Morimoto, Yuji Naito, Hidetaka Okada, Hidemasa Bono, So Nakagawa, Kiichi Hirota
Summary: This study demonstrates that full-length 16S rRNA gene sequencing using the MinION(TM) long-read sequencer provides better resolution for bacterial classification, especially in complex gut microbiota.
Article
Immunology
Jie Huang, Shanshan Wei, Chuanhao Jiang, Zijun Xiao, Jian Liu, Weijun Peng, Bikui Zhang, Wenqun Li
Summary: This study reveals that an imbalance in the composition and function of the gut microbiota may be one of the etiological mechanisms underlying Doxorubicin-induced cardiotoxicity (DIC). The gut microbiota may serve as new targets for the treatment of cardiotoxicity and cardiovascular diseases.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Ming -Han Li, Jin-Xin Meng, Wei Wang, Ma He, Zi-Yu Zhao, Ning Ma, Qing-Bo Lv, Yi-Feng Qin, Quan Zhao, Hong -Bo Ni, Xiao-Xuan Zhang
Summary: This study examined the diversity of bacteria and fungi in the gut microbiota of commercial broilers raised in cages. The results showed that the composition of the gut microbiota was influenced by age, with increasing richness and diversity as the broilers grew older. The gut microbiota had a unique structure in the early days after birth, and then underwent significant changes during periods of rapid growth and weight gain. Furthermore, certain bacteria and fungi played key roles in the gut microbiota of broilers, and their loss may impact the intestinal homeostasis of broilers.
Article
Ecology
Jiulin Chan, Daoqiang Geng, Binbin Pan, Qiming Zhang, Qianghua Xu
Summary: Hadal amphipods from different trenches showed distinct differences in gut microbial composition and functional potential. Microbe-microbe correlation analysis revealed that symbiont colonization was host-specific. The study also found enrichment of particular functional pathways in the gut microbiota of different isolated trench amphipods.
Article
Microbiology
Tarek Mazzawi, Trygve Hausken, Per Forde Refsnes, Jan Gunnar Hatlebakk, Gulen Arslan Lied
Summary: This study compared the efficacy and safety of ACHIM suspension, donor-FMT, and placebo in the treatment of IBS. The results showed that all three treatment methods improved the symptoms and gut microbiota profile of IBS patients, but donor-FMT and ACHIM were more significant compared to placebo.
Article
Food Science & Technology
Shimin Gu, Qiang Xie, Chen Chen, Chenglong Liu, Wentong Xue
Summary: This study used 16S rRNA sequencing to analyze the gut microbiota composition of peanut-allergic mice and found several bacterial groups that were significantly associated with peanut allergy, potentially serving as gut microbial signatures for peanut allergy.
Article
Biotechnology & Applied Microbiology
Dong Han, Hongmin Zhen, Xiaoyan Liu, Justyna Zulewska, Zhennai Yang
Summary: This study used both rRNA and gDNA sequencing on mouse cecal contents and found differences in microbial composition and functional predictions between the two methods. rRNA-derived sequencing improved identification capability of specific microorganisms and was more suitable for functional predictions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Xiaqing Yu, Wen Jiang, Russell Oliver Kosik, Yingchun Song, Qiong Luo, Tingting Qiao, Junyu Tong, Simin Liu, Chengwen Deng, Shanshan Qin, Zhongwei Lv, Dan Li
Summary: The study found that patients with thyroid carcinoma show significant changes in gut microbiota compared to healthy controls, with 70% of patients having increased levels of Proteobacteria-types. Microbiota analysis can distinguish thyroid carcinoma patients from healthy controls.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Infectious Diseases
Wenpei Shi, Yi Hu, Zhu Ning, Fan Xia, Meiying Wu, Yue O. O. Hu, Cheng Chen, Stefanie Prast-Nielsen, Biao Xu
Summary: There were significant differences in gut microbiota composition and metabolic pathways between tuberculosis patients and healthy controls. Antibiotic exposure was found to further reduce diversity and deplete beneficial bacteria in the gut microbiota of TB patients. Microbial functional analysis showed lower biosynthesis capacity of amino acids and fatty acids in TB patients compared to healthy controls.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Pharmacology & Pharmacy
Liang Dai, Yingjue Tang, Wenjun Zhou, Yanqi Dang, Qiaoli Sun, Zhipeng Tang, Mingzhe Zhu, Guang Ji
Summary: Mesalamine treatment partially restored the disrupted gut microbiota diversity and community composition in ulcerative colitis (UC) patients. Many genera and metabolites were significantly altered in UC group and reversed by mesalamine, indicating its beneficial role in modulating gut microbiota signature with correlated metabolites in different pathways as potential therapeutic targets and biomarkers for UC.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Taylor A. Breuninger, Nina Wawro, Dennis Freuer, Sandra Reitmeier, Anna Artati, Harald Grallert, Jerzy Adamski, Christa Meisinger, Annette Peters, Dirk Haller, Jakob Linseisen
Summary: Bile acids, neutral sterols, and the gut microbiome are closely related and have an impact on human health and metabolism. This study found significant associations between bile acids and several microbial subgroups, and identified a trend where microbial subgroups associated with healthy factors were inversely related to fecal bile acid levels, while subgroups associated with unhealthy factors were positively related to fecal bile acid levels.
Article
Multidisciplinary Sciences
Jenny Jeong, Nicholas J. Frohberg, Enlu Zhou, Todd Sulchek, Peng Qiu
Article
Biochemical Research Methods
Xingyu Yang, Peng Qiu
Article
Biochemical Research Methods
Qinwei Zhuang, Brandon Alexander Holt, Gabriel A. Kwong, Peng Qiu
PLOS COMPUTATIONAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Peng Qiu
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
William Pilcher, Xingyu Yang, Anastasia Zhurikhina, Olga Chernaya, Yinghan Xu, Peng Qiu, Denis Tsygankov
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemical Research Methods
Hong Seo Lim, Peng Qiu
Summary: With the increasing number of single-cell datasets being generated, computational tools for aligning these datasets are critical for integration and meta-analysis. The JSOM algorithm aligns related datasets with similar clusters and preserves the topology of the datasets, allowing for further analysis like clustering. The algorithm has shown promising results across different technologies, potentially leading to new discoveries.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Marc A. Fernandez-Yague, Lauren A. Hymel, Claire E. Olingy, Claire McClain, Molly E. Ogle, Jose R. Garcia, Dustin Minshew, Sofiya Vyshnya, Hong Seo Lim, Peng Qiu, Andres J. Garcia, Edward A. Botchwey
Summary: Understanding the immune response to hydrogel implantation is crucial for designing immunomodulatory biomaterials. Through the use of advanced techniques such as high-dimensional flow cytometry and intravital imaging, the study found that RGD-presenting hydrogels can promote cellular infiltration and revascularization, and can direct the immune response through controlling macrophage cytokine secretion.
Article
Biology
Yutong Sun, Peng Qiu
Summary: A supervised strategy called SIDA (Supervised Integration using Domain Adaptation) is proposed for scRNA-seq data integration, which utilizes domain adaptation to generate comprehensive reference datasets and improve accuracy in automated cell type mapping. This strategy corrects the nontrivial batch effects that often occur in large-scale scRNA-seq studies. By using cell type annotations as guidance, SIDA demonstrates the ability to generate comprehensive reference datasets and enhance the accuracy of automated cell type mapping analyses.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Lauren A. Hymel, Shannon E. Anderson, Thomas C. Turner, William Y. York, Hongmanlin Zhang, Adrian R. Liversage, Hong Seo Lim, Peng Qiu, Luke J. Mortensen, Young C. Jang, Nick J. Willett, Edward A. Botchwey
Summary: This study investigates the cellular dynamics and immune response in the quadriceps muscle undergoing subcritical or critical volumetric muscle loss (VML) injury. The results show that critical VML leads to the sustained presence of M2-like and CD206(hi)Ly6C(hi) 'hybrid' macrophages, as well as elevated levels of certain T cell subpopulations. These findings provide important insights into the dysregulated immune response and potential therapeutic strategies for VML. Rating: 8/10.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Hong Seo Lim, Peng Qiu
Summary: In this study, a computational pipeline is presented to quantify cell-type-specific differences and identify genes responsible for these differences by comparing multiple single-cell datasets. The algorithm quantifies differences observed in a low-dimensional space and uses SHapley Additive exPlanations to determine the genes driving the differences. The algorithm is applied to different datasets and successfully quantifies cell-type-specific differences and identifies the relevant genes.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Oncology
John C. G. Spainhour, Hong Seo Lim, Soojin Yi, Peng Qiu
CANCER INFORMATICS
(2019)
Article
Multidisciplinary Sciences
T. C. Turner, M. C. P. Sok, L. A. Hymel, F. S. Pittman, W. Y. York, Q. D. Mac, S. Vyshnya, H. S. Lim, G. A. Kwong, P. Qiu, E. A. Botchwey