Review
Pharmacology & Pharmacy
Chenyin Wang, Chaogu Zheng
Summary: Emerging evidence suggests that the interaction between the gut microbiome and the brain plays a critical role in neurodegenerative diseases (NDs). This review highlights the advantages of using C. elegans as a model to study the microbe-host interaction in neurodegeneration. The role of bacterial amyloid proteins in promoting proteotoxicity and neurodegeneration is investigated, and the potential therapeutic strategy of targeting bacterial amyloid production is proposed.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Immunology
Yan Li, Qingshan Ma, Xiaoyuan Shi, Guiqin Liu, Changfa Wang
Summary: This study explored the differences in gut microbiome and differentially expressed genes related to lipid metabolism and the immune system in the donkey hindgut. The study found significant differences in dominant bacteria among different sections of the hindgut, particularly between the cecum and dorsal colon sites. It also identified interesting DEGs related to lipid metabolism and the immune system, with the PPAR pathway being mainly enriched in the cecum. Furthermore, the study revealed a complex relationship between the gut microbiome and gene expression, especially in relation to the immune system.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nahikari Lopez-Lopez, Celia Gil-Campillo, Roberto Diez-Martinez, Junkal Garmendia
Summary: Haemophilus influenzae has played a significant role in key bacterial genome sequencing milestones, contributing to our understanding of the human-adapted pathogen responsible for respiratory infections. The evolving technologies have led to insights into essential genes, virulence factors, and gene regulatory networks, posing challenges in understanding genomic plasticity and identifying clinical targets. Multi-omics approaches have greatly enhanced our knowledge of the interactions between H. influenzae and the human airways, offering strategies for biomedical research and clinical applications.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Editorial Material
Biochemistry & Molecular Biology
Ryan C. Hunter
Summary: Recent research suggests that glycan-based signaling through a carbohydrate-binding sensor kinase plays a crucial role in regulating pathogen behavior at the mucosal interface, providing robust protection against infection.
Review
Biochemistry & Molecular Biology
Julia D. D. Meredith, Michael J. J. Gray
Summary: The pseudohypohalous acid hypothiocyanite/hypothiocyanous acid (OSCN-/HOSCN) has been widely investigated for its antimicrobial properties in mammalian immunity. Generated by peroxidase enzymes from thiocyanate (SCN-) and hydrogen peroxide (H2O2), HOSCN has potential applications in food preservation, pathogen control, and oral care. However, the mechanisms by which bacteria sense and respond to HOSCN remain largely unknown. This review summarizes the current knowledge on the role of HOSCN in host-pathogen interactions and discusses recent findings regarding bacterial responses to this antimicrobial agent, focusing on three model organisms: Escherichia coli, Streptococcus spp., and Pseudomonas aeruginosa.
MOLECULAR MICROBIOLOGY
(2023)
Review
Immunology
Nathan Cruz, George A. Abernathy, Armand E. K. Dichosa, Anand Kumar
Summary: Humans are considered superorganisms with a diverse microbial collective outnumbering human cells 10 to 1. The interactions between host and microbe-microbe play a crucial role in overall well-being, but are still gravely understudied. Current research focuses on identifying and utilizing these interactions to discover beneficial microbes for therapeutic purposes.
INFECTION AND IMMUNITY
(2022)
Article
Engineering, Biomedical
Min Beom Kim, Soonho Hwangbo, Sungho Jang, Yun Kee Jo
Summary: The recent increase in complex physiological host-microbe interactions has led to a demand for in vitro models that replicate the microbial microenvironment in the human body. Organoids, an in vitro culture system that closely mimics the structure, function, and genetic features of human organs, are emerging as a promising tool for studying host-microbe interactions. Co-cultures of organoids with microbes show great potential in simulating complex host-microbe interactions and advancing related fields. This review provides an overview of bioengineering approaches for microbe-co-cultured organoids and highlights the latest developments in their applications for studying human physiology and pathophysiology.
MATERIALS TODAY BIO
(2022)
Review
Immunology
Emily R. Wahlenmayer, Daniel E. Hammers
Summary: The genus Streptococcus encompasses a wide range of bacteria that can colonize hosts and cause diseases. Streptococci produce peptides that manipulate the host immune system and environment, allowing them to survive and cause diseases. Understanding the functions of these peptides is crucial for developing therapeutic approaches against Streptococcal infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Microbiology
Ying Zhao, Yan Zeng, Dong Zeng, Hesong Wang, Mengjia Zhou, Ning Sun, Jinge Xin, Abdul Khalique, Danish Sharafat Rajput, Kangcheng Pan, Gang Shu, Bo Jing, Xueqin Ni
Summary: This paper discusses the roles of probiotics and miRNAs in host-microbe interactions, proposes the association of probiotics with altered miRNAs in intestinal diseases and potential mechanisms, and provides a perspective on the probiotics-miRNA-host/gut microbiota axis for disease management highly associated with the gut microbiome in future studies.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Immunology
Shivani Singh, Jake G. Natalini, Leopoldo N. Segal
Summary: In recent years, our understanding of the microbial world within us has been revolutionized by culture-independent techniques. Advances in bioinformatics have enabled comprehensive analysis of the role of the human microbiome in different conditions. Despite challenges in lower airway research, new approaches will facilitate further progress.
MUCOSAL IMMUNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Kathie A. Mihindukulasuriya, Ruben A. T. Mars, Abigail J. Johnson, Tonya Ward, Sambhawa Priya, Heather R. Lekatz, Krishna R. Kalari, Lindsay Droit, Tenghao Zheng, Ran Blekhman, Mauro D'Amato, Gianrico Farrugia, Dan Knights, Scott A. Handley, Purna C. Kashyap
Summary: The gut virome is stable over time but varies among subsets of patients with IBS. Specific changes in phage populations were identified in different IBS subsets, and they were correlated with bacterial composition and diet.
Article
Oncology
Abdulkadir Elmas, Amaia Lujambio, Kuan-lin Huang
Summary: In this study, proteogenomic analyses were performed on hepatocellular carcinoma (HCC) tumors, revealing overexpressed protein targets that have therapeutic potential even in the absence of clinically actionable mutations. The study demonstrates the importance of proteomics approaches in advancing precision medicine for cancer types lacking druggable mutations.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Hazel McLellan, Sarah E. Harvey, Jens Steinbrenner, Miles R. Armstrong, Qin He, Rachel Clewes, Leighton Pritchard, Wei Wang, Shumei Wang, Thomas Nussbaumer, Bushra Dohai, Qingquan Luo, Priyanka Kumari, Hui Duan, Ana Roberts, Petra C. Boevink, Christina Neumann, Nicolas Champouret, Ingo Hein, Pascal Falter-Braun, Jim Beynon, Katherine Denby, Paul R. J. Birch
Summary: By studying the interaction between pathogen effectors and nonhost plants, we revealed the mechanism behind nonhost resistance and demonstrated the crucial role of disrupting this interaction in immune response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Ming-Wei Lai, Yu-De Chu, Chao-Wei Hsu, Yi-Cheng Chen, Kung-Hao Liang, Chau-Ting Yeh
Summary: Gut dysbiosis and impaired intestinal barrier are associated with different liver diseases, affecting the systemic immune environment through the gut-liver axis. This study identified common network features in patients with liver cirrhosis or hepatocellular carcinoma (HCC), as well as disease-specific signatures. Alterations in gut microbial/viral composition may contribute to pre-HCC disorders, metabolic reprogramming, or inflammatory microenvironments for hepatocarcinogenesis.
Review
Plant Sciences
Danillo O. Alvarenga, Kathrin Rousk
Summary: Mosses play a crucial role in ecosystems, forming symbiotic relationships with bacteria that significantly impact carbon and nitrogen cycles. They can store a large amount of carbon and contribute to nitrogen input in ecosystems through microbial interactions.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Guangzhao Jin, Wenjun Li, Feng Song, Lei Yang, Zhibin Wen, Ying Feng
Summary: This study sequenced and compared the chloroplast genomes of 16 species within the subgenus Seriphidium, revealing genetic consistency and variation in the subgenus. It also identified repetitive sequences and highly variable loci, and found inconsistencies between the molecular phylogeny and traditional taxonomy of subgenus Seriphidium. The whole chloroplast genomes can serve as molecular markers to infer interspecific relationships in this taxon.
Article
Biology
Yanan Wu, Qianqian Qi, Shouliang Qi, Liming Yang, Hanlin Wang, Hui Yu, Jianpeng Li, Gang Wang, Ping Zhang, Zhenyu Liang, Rongchang Chen
Summary: The study proposes a method for accurately distinguishing COVID-19 from CAP using MIP images from CT scans and a capsule network. The method achieves high accuracy and sensitivity in COVID-19 diagnosis and prediction.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Microbiology
Chun-Yan Lu, Lei Dong, Shuai Li, Wen-Hui Lian, Zhi-Liang Lin, Zhuo-Huan Zheng, Lei Gao, Bao-Zhu Fang, Wen-Jun Li
Summary: A new actinobacterium, SYSU T00001(T), was isolated from a tidal flat sediment sample from Guangdong province, China. The isolate exhibited unique characteristics and showed highest similarity to Salinibacterium hongtaonis 194(T) based on phylogenetic analyses. Therefore, a novel species of the genus Salinibacterium, Salinibacterium sedimenticola sp. nov., is proposed, with SYSU T00001(T) as the type strain.
CURRENT MICROBIOLOGY
(2023)
Article
Fisheries
Chong Han, Wenwei Huang, Suhan Peng, Jiangwei Zhou, Huawei Zhan, Wenjun Li, Jian Gong, Qiang Li
Summary: In this study, 11 members of IRFs were identified and their expression patterns in different tissues were analyzed in the zig-zag eel. The results provide valuable information for understanding the antibacterial mechanism of IRFs in teleosts.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2023)
Article
Substance Abuse
Thomas J. Stopka, Marc R. Larochelle, Xiaona Li, Dana Bernson, Wenjun Li, Leland K. Ackerson, Ric Bayly, Olaf Dammann, Cici Bauer
Summary: The study identified significant variations in fatal overdose rates of opioid-related drugs among different populations and geographical locations. These variations and clusters changed over time, providing valuable information to develop targeted public health strategies for high-risk subpopulations.
DRUG AND ALCOHOL DEPENDENCE
(2023)
Article
Multidisciplinary Sciences
Bo Tang, Li Tang, Shengpeng Li, Shuang Liu, Jialin He, Pan Li, Sumin Wang, Min Yang, Longhui Zhang, Yuanyuan Lei, Dianji Tu, Xuefeng Tang, Hua Hu, Qin Ouyang, Xia Chen, Shiming Yang
Summary: Intrahepatic cholestasis of pregnancy (ICP) is a liver disease that sometimes develops during pregnancy and is characterized by increased serum bile acid levels. Here the authors report that the gut microbiome species B. fragilis is enriched in patients with ICP and promotes ICP development in mice via inhibition of signalling though the bile acid receptor FXR.
NATURE COMMUNICATIONS
(2023)
Article
Respiratory System
Shengchuan Feng, Yuqiong Yang, Fengyan Wang, Weijuan Shi, Jiaxuan Xu, Guoyan Tang, Jiaxing Xie, Nanshan Zhong, Zhenyu Liang, Rongchang Chen
Summary: This study aimed to determine the relationship between human beta-defensin-2 (hBD-2) levels and aggravation of COPD. The results showed that patients with exacerbations had significantly lower sputum hBD-2 levels, and low hBD-2 levels were associated with exacerbations. These findings have important implications for future therapies for COPD.
BMC PULMONARY MEDICINE
(2023)
Article
Microbiology
Kun Zhang, Yanling Zhang, Maocheng Deng, Pengcheng Wang, Xiu Yue, Pandeng Wang, Wenjun Li
Summary: In this study, the dynamics of microbial and viral communities in an expanded granular sludge bed (EGSB) reactor were investigated. The results showed that COD, VSS/TSS ratio, and temperature were the main factors affecting the microbial community structure. The study also identified key genes involved in nitrogen cycling, with the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification pathways dominating in the anaerobic system. The findings provide insights for the optimization of engineered systems.
FRONTIERS IN MICROBIOLOGY
(2023)
Editorial Material
Microbiology
Hongchen Jiang, Wen-Jun Li, Nils-Kare Birkeland, Dilfuza Egamberdieva
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Qian Du, Xin Xi, Jie Dong, Tongyan Zhang, Dongxuan Li, Yuzhu Dong, Wenjun Li, Guili Huang, Jun Zhu, Hailong Ran, Jinghui Gou, Cheng Chen, Zhanfeng Bai, Qinglong Liu, Wei Yao, Lei Zhang, Yutian Bi, Songqing Liu
Summary: This study found that early active pharmacy infectious disease consultation can reduce 30-day all-cause mortality and improve clinical outcomes in multidrug-resistant organism patients.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Microbiology
Cale O. Seymour, Marike Palmer, Eric D. Becraft, Ramunas Stepanauskas, Ariel D. Friel, Frederik Schulz, Tanja Woyke, Emiley Eloe-Fadrosh, Dengxun Lai, Jian-Yu Jiao, Zheng-Shuang Hua, Lan Liu, Zheng-Han Lian, Wen-Jun Li, Maria Chuvochina, Brianna K. Finley, Benjamin J. Koch, Egbert Schwartz, Paul Dijkstra, Duane P. Moser, Bruce A. Hungate, Brian P. Hedlund
Summary: The candidate bacterial phylum Omnitrophota is poorly studied. By analyzing genomes and data from the Earth Microbiome Project, researchers found that Omnitrophota are ultra-small cells mainly found in water, sediments, and soils. These bacteria have reduced genomes but retain key metabolic pathways and symbiotic gene clusters, indicating a host-associated lifestyle. Additionally, stable-isotope probing identified certain Omnitrophota families as potential obligate bacterial predators. Overall, most Omnitrophota inhabit various ecosystems as predators or parasites.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Yang-Zhi Rao, Yu-Xian Li, Ze-Wei Li, Yan-Ni Qu, Yan-Ling Qi, Jian-Yu Jiao, Wen-Sheng Shu, Zheng-Shuang Hua, Wen-Jun Li
Summary: By using genome-resolved metagenomics, researchers discovered 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) and identified metabolic differences between Jingweiarchaeales and Parvarchaeales, as well as the adaptation of Parvarchaeales to acidic environments. The study also revealed unique genomic features of Jingweiarchaeum and Haiyanarchaeum that may contribute to their adaptation to high-temperature environments. Overall, this research is important for understanding the strategies and processes of how Candidatus Parvarchaeales microbes adapt to extreme environments.
Article
Multidisciplinary Sciences
Dilinuer Wufuer, Haidiya Aierken, Zhenyu Liang, Jin-Ping Zheng, Li Li
Summary: This study aimed to explore the correlation between depression-related gene polymorphisms and the risk of bronchial asthma combined with depression. A total of 387 patients diagnosed with bronchial asthma were divided into different groups based on depression scales. The study identified 84 gene loci associated with depression and found 18 loci with significant differences among the three groups. Logistic regression analysis revealed that 24 of the depression-associated loci had a relationship with asthmatic prevalence. The study concluded that there may be an important genetic basis for bronchial asthma and depression.
JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES
(2023)
Review
Medicine, General & Internal
Pan Li, Ping Shuai, Sj Shen, Huimin Zheng, Ping Sun, Renfang Zhang, Shanwei Lan, Zixin Lan, Thisun Jayawardana, Yumei Yang, Jianhui Zhao, Yuping Liu, Xia Chen, Emad M. El-Omar, Zhengwei Wan
Summary: This study conducted a systematic review and meta-analysis, and found that gut dysbiosis in PCOS is characterized by decreased diversity and alterations in specific bacteria. The imbalance in gut microbiota may lead to a pro-inflammatory environment due to a reduction in short-chain fatty acid (SCFA)-producing and bile-acid-metabolizing bacteria. These findings provide important insights for further understanding the pathogenesis and treatment of PCOS.
Article
Oncology
Chengzhi Zhou, Yinyin Qin, Wei Zhao, Zhenyu Liang, Min Li, Dan Liu, Li Bai, Yahong Chen, Yan Chen, Yuan Cheng, Tianqing Chu, Qian Chu, Haiyi Deng, Yuchao Dong, Wenfeng Fang, Xiuhua Fu, Beili Gao, Yiping Han, Yong He, Qunying Hong, Jie Hu, Yi Hu, Liyan Jiang, Yang Jin, Fen Lan, Qiang Li, Shuben Li, Wen Li, Yaqing Li, Wenhua Liang, Gen Lin, Xinqing Lin, Ming Liu, Xiaofang Liu, Xiaoju Liu, Zhefeng Liu, Tangfeng Lv, Chuanyong Mu, Ming Ouyang, Jianwen Qin, Shengxiang Ren, Huanzhong Shi, Minhua Shi, Chunxia Su, Jin Su, Dejun Sun, Yongchang Sun, Huaping Tang, Huijuan Wang, Kai Wang, Ke Wang, Mengzhao Wang, Qi Wang, Wei Wang, Xiaoping Wang, Yuehong Wang, Zhijie Wang, Zirui Wang, Lin Wu, Di Wu, Baosong Xie, Min Xie, Xiaohong Xie, Zhanhong Xie, Shufeng Xu, Xiaoman Xu, Xia Yang, Yan Yin, Zongyang Yu, Jian Zhang, Jianqing Zhang, Jing Zhang, Xiaoju Zhang, Yingying Zhang, Diansheng Zhong, Qing Zhou, Xiangdong Zhou, Yanbin Zhou, Bo Zhu, Zhengfei Zhu, Chenxi Zou, Nanshan Zhong, Jianxing He, Chunxue Bai, Chengping Hu, Weimin Li, Yong Song, Jianying Zhou, Baohui Han, Janos Varga, Esther Barreiro, Hye Yun Park, Francesco Petrella, Yuichi Saito, Taichiro Goto, Hitoshi Igai, Sara Bravaccini, Michele Zanoni, Piergiorgio Solli, Satoshi Watanabe, Alfonso Fiorelli, Takeo Nakada, Yoshinobu Ichiki, Rossana Berardi, Nikolaos Tsoukalas, Nicolas Girard, Antonio Rossi, Antonio Passaro, Toyoaki Hida, Shiyue Li, Liang'an Chen, Rongchang Chen
Summary: This study provides consensus recommendations for the diagnosis and treatment of lung cancer combined with chronic obstructive pulmonary disease (LC-COPD), emphasizing the need for concurrent treatment and personalized care.
TRANSLATIONAL LUNG CANCER RESEARCH
(2023)