Article
Multidisciplinary Sciences
Taichi A. Suzuki, J. Liam Fitzstevens, Victor T. Schmidt, Hagay Enav, Kelsey E. Huus, Mirabeau Mbong Ngwese, Anne Griesshammer, Anne Pfleiderer, Bayode R. Adegbite, Jeannot F. Zinsou, Meral Esen, Thirumalaisamy P. Velavan, Ayola A. Adegnika, Le Huu Song, Timothy D. Spector, Amanda L. Muehlbauer, Nina Marchi, Hyena Kang, Lisa Maier, Ran Blekhman, Laure Segurel, GwangPyo Ko, Nicholas D. Youngblut, Peter Kremsner, Ruth E. Ley
Summary: The gut microbiomes of human populations worldwide have common core microbial species. However, within a species, certain strains show population specificity. This study suggests that humans and their gut microbes have experienced parallel evolutionary history, and specific microbial strains may play a crucial role in microbiome-mediated disease phenotypes.
Article
Multidisciplinary Sciences
Carl-Philipp Hackstein, Dana Costigan, Linnea Drexhage, Claire Pearson, Samuel Bullers, Nicholas Ilott, Hossain Delowar Akther, Yisu Gu, Michael E. B. FitzPatrick, Oliver J. Harrison, Lucy C. Garner, Elizabeth H. Mann, Sumeet Pandey, Matthias Friedrich, Nicholas M. Provine, Holm H. Uhlig, Emanuele Marchi, Fiona Powrie, Paul Klenerman, Emily E. Thornton
Summary: Interactions between commensal microbes and the host have a significant impact on the host's immune system and are crucial in human health and disease. Certain T cells in the colon exhibit innate-like characteristics and are reactive to commensal microbes. These cells are increased in ulcerative colitis patients and may contribute to the pathogenesis of colitis.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Jicheng Wang, Jiachao Zhang, Wenjun Liu, Heping Zhang, Zhihong Sun
Summary: This study reveals that ingested probiotics alter their transcription patterns to survive and adapt in the human gut, indicating a highly dynamic cross-talk between probiotics and the human gut microbiome.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Biochemistry & Molecular Biology
Lin Lyu, Xue Li, Ru Feng, Xin Zhou, Tuhin K. Guha, Xiaofei Yu, Guo Qiang Chen, Yufeng Yao, Bing Su, Duowu Zou, Michael P. Snyder, Lei Chen
Summary: We developed an analysis pipeline called spatial metatranscriptome (SMT) that extracts microbial sequences from spatial transcriptomic (ST) data, assigns taxonomic labels, and generates a spatial microbial abundance matrix. The pipeline was applied to human and murine intestinal sections and validated with alternative assays. This work provides biological insights into host-microbe interactions at different spatial scales and demonstrates the feasibility of SMT analysis.
Article
Multidisciplinary Sciences
Yi Yang, Mytien Nguyen, Varnica Khetrapal, Nicole D. Sonnert, Anjelica L. Martin, Haiwei Chen, Martin A. Kriegel, Noah W. Palm
Summary: This study reveals that within-host evolution of gut commensal bacteria plays a critical role in bacterial translocation and initiation of inflammation. Gut microbiota strains can adapt and evolve, affecting their propensity to elicit inflammatory diseases. The changes in bacterial behavior are associated with genetic mutations, altered microbial gene expression programs, and remodelled cell wall structures.
Article
Nutrition & Dietetics
Bridgette Wilson, Oezge Eyice, Ioannis Koumoutsos, Miranda C. Lomer, Peter M. Irving, James O. Lindsay, Kevin Whelan
Summary: Prebiotics may not reduce clinical scores or inflammation in patients with active ulcerative colitis, but can normalize stools. The increase in proportions of Bifidobacterium and Christensenellaceae only occurred in patients with less active diseases, suggesting that the prebiotic effect may depend on disease activity.
Article
Fisheries
Jianbo Zheng, Yongyi Jia, Fei Li, Meili Chi, Shun Cheng, Shili Liu, Wenping Jiang, Yinuo Liu
Summary: This study investigated the immune response mechanism of Decapod iridescent virus 1 (DIV1) infection in crayfish. The results showed that DIV1 infection led to upregulation of immune-related genes and significant changes in gut microbiota composition and function. These findings provide new insights into the immune response to DIV1 infection in crustaceans.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jingjing Liu, Wei Dong, Jian Zhao, Jing Wu, Jinqiang Xia, Shaofei Xie, Xiaofeng Song
Summary: Through statistical analysis and correlation analysis, the study found that the intestinal flora of mice with colorectal inflammation or colorectal cancer significantly changed compared with healthy mice, with Muribaculaceae and Bacteroidaceae showing strong excluding interactions. The functional changes of the gut microbiota include the up-regulation of the cancers pathway and the down-regulation of the replication and repair pathways.
Article
Biochemistry & Molecular Biology
Aspen T. Reese, Sarah R. Phillips, Leah A. Owens, Emily M. Venable, Kevin E. Langergraber, Zarin P. Machanda, John C. Mitani, Martin N. Muller, David P. Watts, Richard W. Wrangham, Tony L. Goldberg, Melissa Emery Thompson, Rachel N. Carmody
Summary: Research found significant variations in gut microbiota of wild chimpanzees at different ages, different from the patterns observed in humans. Chimpanzee infants have similar microbial compositions to human infants, but show higher diversity compared to older conspecifics.
Article
Agriculture, Multidisciplinary
Chenyu Xue, Hao Lv, Ying Li, Na Dong, Yanhui Wang, Jiale Zhou, Baoming Shi, Anshan Shan
Summary: This study investigated the effects of oleanolic acid on gut health, including gut microbiota and intestinal epithelial immunity, using Illumina MiSeq sequencing and Illumina HiSeq (RNA-seq) technology. The results showed that oleanolic acid can improve intestinal health by optimizing gut microbiota and altering the immune function of intestinal epithelial cells.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2022)
Review
Biotechnology & Applied Microbiology
Gerald W. Tannock
Summary: The microbial community in the human colon, known as the gut microbiota, is essential for human health by deriving energy from plant polysaccharides and supporting physiological processes. Dietary interventions with specific plant glycans can modulate the microbiota, correcting dysbiosis and enhancing functional resilience.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
El-Sayed M. Abdel-Kafy, Sabbah F. F. Youssef, Mahmoud Magdy, Shereen S. S. Ghoneim, Hesham A. A. Abdelatif, Randa A. A. Deif-Allah, Yasmein Z. Z. Abdel-Ghafar, Hoda M. A. Shabaan, Huazhen Liu, Abdelmotaleb Elokil
Summary: This study aimed to investigate the growth mechanism in a local breed of chickens by comparing the highest weight and the lowest weight in their microbiota, histological characteristics, and gene expression. The results showed that the highest weight chickens had significant histological changes and a different microbial community in the gut compared to the lowest weight chickens, which may improve intestinal functions.
Review
Food Science & Technology
Pan Yang, Jinbiao Zhao
Summary: Dietary fibers play a crucial role in promoting intestinal health by modulating gut microbiota and SCFA production. However, different types of dietary fibers from edible sources may have divergent impacts on gut health, energy metabolism, and microbial composition. More attention should be focused on the varying responses of different dietary fibers intake on host metabolism and health.
FOOD SCIENCE & NUTRITION
(2021)
Review
Microbiology
Michiel Van de Vliet, Marie Joossens
Summary: Understanding the initial colonization process of the human intestines is crucial for preventing microbiota-associated diseases and improving microbial therapies. Due to a lack of standardization, current insights are largely based on deduction and assumption. Comparing research in piglets, which have similar intestinal tracts to humans, it is found that the colonization process is similar and the bacterial community itself plays a major role in colonization success.
Article
Biochemistry & Molecular Biology
Dandan Yu, Xiaomin Yu, Aifang Ye, Chunquan Xu, Xiaolong Li, Wujun Geng, Liqing Zhu
Summary: This study found significant differences in gut microbiota between ML patients and healthy subjects, indicating a potential role of gut microbiota in the pathogenesis of ML and suggesting the development of novel therapeutic strategies for ML treatment.
Article
Biotechnology & Applied Microbiology
Yu-Hang Zhang, ShiJian Ding, Lei Chen, Tao Huang, Yu-Dong Cai
Summary: This study developed a predictive model for subcellular localization by using protein-protein interaction networks, functional enrichment analysis, and proteins with confirmed localization. Various machine learning algorithms and feature selection methods were utilized to identify key features and understand their biological functions.
BIOMED RESEARCH INTERNATIONAL
(2022)
Article
Chemistry, Multidisciplinary
Lei Chen, Kuangshi Sun, Donghao Hu, Xianlong Su, Linna Guo, Jiamiao Yin, Yuetian Pei, Yiwei Fan, Qian Liu, Ming Xu, Wei Feng, Fuyou Li
Summary: Photochemical afterglow systems have attracted significant attention for their adjustable photophysical properties and potential applications. However, conventional photochemical afterglow lacks repeatability due to the consumption of energy cache units. In this study, we propose a novel strategy to achieve repeatable photochemical afterglow through the reversible storage of O-1(2). This strategy enables the generation of near-infrared afterglow with a lifetime over 10 s, and its initial intensity remains stable over 50 excitation cycles. Mechanism study confirms the repeatable photochemical afterglow is realized through singlet oxygen-sensitized fluorescence emission. The generality of this strategy is demonstrated, allowing for tunable afterglow lifetimes and colors through rational design. Furthermore, the repeatable photochemical afterglow is applied for attacker-misleading information encryption, providing repeatable readout.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biotechnology & Applied Microbiology
FeiMing Huang, QingLan Ma, JingXin Ren, JiaRui Li, Fen Wang, Tao Huang, Yu-Dong Cai
Summary: Long-term cigarette smoking is associated with various human diseases, and this study used advanced machine learning methods to identify specific isoforms and pathways that play important roles in distinguishing smokers from former smokers. The study evaluated multiple feature selection algorithms and utilized a decision tree approach to establish high-performance classification models. The identified isoforms and classification rules were validated through previous research. The results highlight the relevance of isoforms such as ENST00000464835, ENST00000622663, and ENST00000284311, as well as pathways related to smoking response.
BIOMED RESEARCH INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Yu-Hang Zhang, Michael H. Cho, Jarrett D. Morrow, Peter J. Castaldi, Craig P. Hersh, Mukul K. Midha, Michael R. Hoopmann, Sharon M. Lutz, Robert L. Moritz, Edwin K. Silverman
Summary: The integration of lung tissue transcriptomic and proteomic data with COPD-associated genetic variants provides insight into the biological mechanisms of COPD. Low correlations were observed between transcriptomics and proteomics, but higher correlations were found for COPD-associated proteins. Regulatory cis-QTLs were identified through the integration of COPD risk SNPs or SNPs near COPD-associated proteins with lung transcripts and proteins. Multiple COPD-associated biomarkers were found to be regulated by significant expression QTLs (eQTLs) and protein QTLs (pQTLs). Colocalization analysis, mediation analysis, and correlation-based network analysis identified key genes and proteins working together to influence COPD pathogenesis.
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Organic
Alma R. Perez, Evan C. Bornowski, Lei Chen, John P. Wolfe
Summary: The synthesis of indanes containing substituted cyanomethyl groups at C2 has been achieved through Pd-catalyzed coupling reactions. Alkenyl triflates were used to generate partially saturated analogues via similar transformations. The use of a preformed BrettPhosPd(allyl)(Cl) complex as a precatalyst was crucial for the success of these reactions.
Article
Biology
Jingxin Ren, Yuhang Zhang, Wei Guo, Kaiyan Feng, Ye Yuan, Tao Huang, Yu-Dong Cai
Summary: COVID-19 can cause impairment of smell and taste, and this study used machine learning to analyze gene expression levels in COVID-19 patient samples to identify important biomarkers associated with this loss of sensory ability. The study suggests potential mechanisms for COVID-19 complications and provides biomarkers for predicting olfactory and gustatory impairment.
Article
Biology
Yaochen Xu, Qinglan Ma, Jingxin Ren, Lei Chen, Wei Guo, Kaiyan Feng, Zhenbing Zeng, Tao Huang, Yudong Cai
Summary: COVID-19 not only damages the respiratory system, but also puts strain on the cardiovascular system. This study analyzed the gene expression levels of vascular endothelial cells and cardiomyocytes in COVID-19 patients and healthy controls using a machine learning-based workflow. The findings suggest that COVID-19 affects the gene expression levels in cardiac cells, providing insights into the pathogenesis of COVID-19 and potential therapeutic targets.
Article
Biology
Qinglan Ma, FeiMing Huang, Wei Guo, KaiYan Feng, Tao Huang, Yudong Cai
Summary: Phase-separation proteins (PSPs) play a role in liquid-liquid phase separation and have implications for cellular biology and disease development. Identifying PSPs and their functions can provide valuable insights.
Article
Biology
Qing-Lan Ma, Fei-Ming Huang, Wei Guo, Kai-Yan Feng, Tao Huang, Yu-Dong Cai
Summary: Vaccines elicit an immune response involving B and T cells, with B cells producing antibodies. The immunity to SARS-CoV-2 diminishes over time after vaccination. This study aimed to identify important changes in antigen-reactive antibodies post-vaccination to enhance vaccine efficacy.
Article
Biology
Jing-Xin Ren, Qian Gao, Xiao-Chao Zhou, Lei Chen, Wei Guo, Kai-Yan Feng, Lin Lu, Tao Huang, Yu-Dong Cai
Summary: A machine-learning-based method was used to analyze the scRNA-seq data of B cells, T cells, and myeloid cells from patients with COVID-19. Key genes related to SARS-CoV-2 infection were identified. The study revealed the dynamic changes in the immune system of COVID-19 patients at different stages, providing valuable insights into the ongoing effect of COVID-19 development on the immune system.
Article
Biology
Yong Yang, Yuhang Zhang, Jingxin Ren, Kaiyan Feng, Zhandong Li, Tao Huang, Yudong Cai
Summary: This study analyzed single-cell RNA sequencing data from a normal colon to identify genetic markers of 25 immune cell types and reveal quantitative differences between them. Machine learning-based methods were used to analyze the importance of gene features and classify the most important genetic markers. The results provide a reference for exploring the cell composition of the colon cancer microenvironment and clinical immunotherapy.