Article
Gastroenterology & Hepatology
Siwen Bao, Hao Wang, Wang Li, Haisheng Wu, Chunying Lu, Liang Yong, Qing Zhang, Xiang Lu, Min Zhao, Juan Lu, Jia Liu, Chukwudozie Kingsley Ikechukwu, Juan Xu, Ping Ni, Ying Xiong, Wen Zhang, Chenglin Zhou
Summary: This study aimed to investigate the differences in the gut virome between diarrheal children and healthy controls. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, but the beta diversity had a significant difference. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae, while the healthy virome also contains phages, including Microviridae and Caudovirales.
Article
Microbiology
Shiraz A. Shah, Ling Deng, Jonathan Thorsen, Anders G. Pedersen, Moira B. Dion, Josue L. Castro-Mejia, Ronalds Silins, Fie O. Romme, Romain Sausset, Leon E. Jessen, Eric Olo Ndela, Mathis Hjelmso, Morten A. Rasmussen, Tamsin A. Redgwell, Cristina Leal Rodriguez, Gisle Vestergaard, Yichang Zhang, Bo Chawes, Klaus Bonnelykke, Soren J. Sorensen, Hans Bisgaard, Francois Enault, Jakob Stokholm, Sylvain Moineau, Marie-Agnes Petit, Dennis S. Nielsen
Summary: Deep sequencing of faecal viromes from 647 healthy infants identified over 230 previously unknown gut virus families, expanding our understanding of the diversity in the human infant gut virome. The findings highlight the importance of the gut microbiome in infancy for the development of the immune system and long-term protection against chronic diseases. This study provides valuable insights into the viral diversity in the infant gut virome and expands phage taxonomy, serving as a resource for future research.
NATURE MICROBIOLOGY
(2023)
Editorial Material
Microbiology
Tanmay Tanna, Randall J. Platt
Summary: Researchers have created an intelligent bacterial strain that can detect and monitor inflammation biomarkers in the gut. It responds by releasing an immunomodulator, allowing for diagnosis and therapy for intestinal inflammation.
CELL HOST & MICROBE
(2023)
Article
Biotechnology & Applied Microbiology
Xiang Lu, Xiuguo Hua, Yan Wang, Dong Zhang, Shengyao Jiang, Shixing Yang, Xiaochun Wang, Quan Shen, Tianji Zhou, Zhibing Lin, Wen Zhang, Li Cui
Summary: Calf diarrhoea is a major cause of economic losses in the global dairy industry, with factors such as pathogen infections contributing to the condition. The study found that calves with diarrhoea had significantly lower diversity of viruses compared to healthy calves, with certain viruses being associated with calf diarrhoea. The research identified specific viral families and genomic sequences that may play a role in gut virus community ecology in healthy hosts and provide a theoretical basis for understanding enteric pathogens related to calf diarrhoea.
JOURNAL OF GENERAL VIROLOGY
(2021)
Review
Immunology
Tasha M. Santiago-Rodriguez, Emily B. Hollister
Summary: Viruses are essential components of the microbiome and play important roles in various fields such as immunology, evolution, and health. The discovery of viral dark matter, which refers to unknown viruses or distantly related species, provides insights into novel viruses and their potential in different environments.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Endocrinology & Metabolism
Bharath Chelluboina, Kristopher Kieft, Adam Breister, Karthik Anantharaman, Raghu Vemuganti
Summary: This study shows that the gut virome responds acutely to stroke, with changes in viral taxa abundances observed following focal ischemia.
JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM
(2022)
Review
Medicine, General & Internal
Zhirui Cao, Naoki Sugimura, Elke Burgermeister, Matthias P. Ebert, Tao Zuo, Ping Lan
Summary: This study reviews the current literature on the human gut virome, highlighting the significant functional differences across different populations. It reveals the roles of gut viruses in health and disease, as well as their potential as therapeutic targets and diagnostic markers.
Article
Cell Biology
Kun Zuo, Jing Li, Chen Fang, Jiuchang Zhong, Li Xu, Xinchun Yang
Summary: This study finds an association between gut viruses and atrial fibrillation (AF). AF patients have increased gut viral diversity and specific alterations in the intestinal viral population. The connections between viruses and bacteria become increasingly disordered in AF cases with severe AF progression. Furthermore, a viral score built from selected discriminative taxa is significantly associated with recurrence after ablation.
Article
Biochemical Research Methods
Lin Liu, Qin Shen, Nan Li, Yuwen He, Na Han, Xianyue Wang, Jinxin Meng, Yousong Peng, Mei Pan, Yuting Jin, Taijiao Jiang, Wenjie Tan, Jinglin Wang, Aiping Wu
Summary: Through studying mosquitoes and Culicoides in Yunnan, China, it was found that they usually share similar viral diversity, with important pathogenic viruses detected in Culicoides and many new viruses discovered. This highlights the importance of studying and monitoring Culicoides for potential emerging viruses.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
Xiang Lu, Hao Wang, Jingqi Zhang, Kexin Jin, Ling Ma, Yan Wang, Shixing Yang, Xiaochun Wang, Quan Shen, Tianji Zhou, Hui Xu, Wen Zhang
Summary: The imbalance of gut microbiota affects the immune development and regulation of individuals, leading to immune dysregulation and the development of atopic dermatitis (AD). This study assessed the composition of the virome in the gut of AD patients and healthy controls, revealing differences in diversity between the two groups. Finds provide a new perspective for understanding the effect of the gut microecological environment on AD.
FRONTIERS IN MEDICINE
(2022)
Article
Cell Biology
Kun Zuo, Jing Li, Chen Fang, Jiuchang Zhong, Li Xu, Xinchun Yang
Summary: This study found an association between gut viruses and atrial fibrillation (AF), with specific alterations of the intestinal viral population observed in AF patients. The study also revealed increasingly disordered virus-bacteria linkages in AF cases, suggesting the involvement of gut viruses in AF progression. Furthermore, a viral score built using selected discriminative taxa was significantly associated with recurrence after ablation, indicating its potential as a predictor of ablation outcomes.
Review
Immunology
Barbara N. Porto
Summary: The virome refers to the viral component of the microbiome, including all viruses that inhabit the human body. Despite previous limitations in accurately characterizing viruses, recent advancements in methods such as deep sequencing and metagenomics have allowed for a better understanding of the diverse viral species present in the human body.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Fang Chen, Shenghui Li, Ruochun Guo, Fanghua Song, Yue Zhang, Xifan Wang, Xiaokui Huo, Qingbo Lv, Hayan Ullah, Guangyang Wang, Yufang Ma, Qiulong Yan, Xiaochi Ma
Summary: This study reveals the changes in gut virome composition in colorectal cancer and adenoma patients and identifies viral markers associated with disease risk. The findings suggest that gut viral signatures may serve as new targets for colorectal cancer treatment and potential biomarkers for non-invasive diagnostic tests.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Virology
Ilya Plyusnin, Olli Vapalahti, Tarja Sironen, Ravi Kant, Teemu Smura
Summary: Viruses are the main cause of emerging and re-emerging infectious diseases. Metagenomic next-generation sequencing (mNGS) is a high-throughput technology that can detect known or novel divergent viruses without prior assumptions. The Lazypipe 2 mNGS pipeline has significant improvements in code stability and transparency, with added functionality and support for new software components.
Article
Veterinary Sciences
Ying Shi, Jie Tao, Benqiang Li, Xiaohui Shen, Jinghua Cheng, Huili Liu
Summary: This study utilized metagenomics to investigate the gut virome of 45 domestic healthy dogs, revealing a diverse range of virus families. Canine coronavirus was particularly prevalent in all samples, posing a potential risk for cross-species transmission to humans. The findings contribute valuable insights into the role of companion animals in public health through viral diversity studies.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Environmental Sciences
Kang Ning, Lei Ji, Lu Zhang, Xue Zhu, Huimin Wei, Maozhen Han, Zhi Wang
Summary: The study evaluated the eco-friendliness of rice-crayfish co-culture compared to other aquaculture models in terms of antibiotic resistance profiles. Results showed that rice-crayfish co-culture model had significantly lower diversity of ARGs and lower potential risks when compared to other aquaculture models. Environmental factors such as nutrient and antibiotic concentrations played a role in shaping ARG patterns, but the effects of mobile genes and bacterial community were stronger in the proliferation and transmission of ARGs.
ENVIRONMENTAL POLLUTION
(2022)
Article
Engineering, Environmental
Maozhen Han, Lu Zhang, Na Zhang, Yujie Mao, Zhangjie Peng, Binbin Huang, Yan Zhang, Zhi Wang
Summary: The study investigated the characteristics and influencing factors of antibiotic resistance genes in urban drinking water sources, proposing an antibiotic resistome risk index (ARRI) to estimate the potential risks of ARGs. The interactions among mobile genetic elements, human bacterial pathogens, and ARGs were considered in determining the spread of ARGs. Overall, the research provides insights into managing similar lakes by analyzing ARG compositions and associated factors.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Pengshuo Yang, Shiguang Hao, Maozhen Han, Junjie Xu, Shaojun Yu, Chaoyun Chen, Houjin Zhang, Kang Ning
Summary: By reanalyzing metagenomic datasets from the Tara Oceans project, the study reveals the role of antibiotic resistance genes (ARGs) in shaping the ocean microbial community structure. ARGs are found to be more abundant and diverse in the mesopelagic zone, potentially due to limited resources. The study also identifies horizontal gene transfer events between protists and prokaryotes involving ARGs.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Lu Zhang, Lei Ji, Xi Liu, Xue Zhu, Kang Ning, Zhi Wang
Summary: The abundance and diversity of antibiotic resistance genes (ARGs) in surface water and groundwater were found to vary inconsistently with seasonal changes. The relationship between ARGs in surface water and groundwater was stronger during the rainy season. Additionally, land use had a greater impact on ARGs in surface water, especially during the dry season. Stochastic mechanisms mediated by mobile gene elements (MGEs) significantly contributed to ARG assemblages, particularly in groundwater.
Article
Multidisciplinary Sciences
Qi Yao, Xue Zhu, Maozhen Han, Chaoyun Chen, Wei Li, Hong Bai, Kang Ning
Summary: With the development of high-throughput sequencing technology, the multi-barcode sequencing approach has been successfully used to identify biological ingredients in Traditional Chinese Medicine (TCM) preparations. In this study, the approach was applied to four representative TCM preparations, and the results showed good universality, sensitivity, and reliability in decoding the herbal materials in these preparations.
SCIENTIFIC REPORTS
(2022)
Letter
Gastroenterology & Hepatology
Nan Wang, Mingyue Cheng, Kang Ning
Letter
Gastroenterology & Hepatology
Maozhen Han, Yixuan Huang, Hongya Gui, Yixuan Xiao, Maozhang He, Jiling Liu, Xiujing Cao, Meijuan Zheng, Min Lu, Weihua Jia, Hui Li, Xiaoyan Wang, Na Zhang, Shu-an Kong, Xiaohui Liu, Yonggui Wu, Fengchang Wu, Shenghai Huang
Article
Biochemical Research Methods
Haohong Zhang, Hui Chong, Qingyang Yu, Yuguo Zha, Mingyue Cheng, Kang Ning
Summary: The gut microbial communities are highly plastic throughout life, but the association between gut microbial communities and time-related factors is unclear. In this study, a novel computational approach called microDELTA was used to track longitudinal human gut microbial communities and demonstrated accurate predictions of infant age and the influence of delivery mode. The application of microDELTA to different cohorts revealed the connections between dietary shifts, seasonal variations, and aging on gut microbial communities.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Engineering, Environmental
Junwei Chen, Lei Ji, Guangzhou Xiong, Kang Ning
Summary: This study examines the different bacterial communities in ICU and Non-ICU hospital wards and clarifies their transmission patterns. It finds that ICU settings have more routes for pathogen transmission from the environment to patients, and identifies several pathogenic genera that are likely to cause nosocomial infections.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Review
Pharmacology & Pharmacy
Xue Zhu, Qi Yao, Pengshuo Yang, Dan Zhao, Ronghua Yang, Hong Bai, Kang Ning
Summary: This article reviews the application and importance of multi-omics approaches in traditional Chinese medicine (TCM) research, including TCM quality assessment, therapeutic mechanism deciphering, network analysis, and database evaluation. With the accumulation of omics data and data-mining resources, deeper understandings of the therapeutic mechanism of TCM have been acquired.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemical Research Methods
Wei Xu, Teng Wang, Nan Wang, Haohong Zhang, Yuguo Zha, Lei Ji, Yuwen Chu, Kang Ning
Summary: Microbiome-based diagnosis of cancer is a necessary addition to genomics approach, but current models face challenges in generalization to different cancer types and sample sources. DeepMicroCancer, an AI-based diagnosis model built on random forest models, shows superior performance on various cancer types' tissue samples. By utilizing transfer learning techniques, improved accuracy can be achieved, especially for cancer types with limited samples, meeting clinical requirements. The model also enables high diagnosis accuracy for blood samples. These results demonstrate the potential of using advanced artificial techniques to uncover complex differences between cancers and healthy individuals. DeepMicroCancer provides a new avenue for accurate cancer diagnosis based on tissue and blood materials in clinical settings.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Microbiology
Guangzhou Xiong, Lei Ji, Mingyue Cheng, Kang Ning
Summary: We analyzed the microbiota assemblage of urban transit systems (UTS) across 16 cities worldwide. The dominant process in UTS microbiota assemblages was found to be stochastic, with the neutral community model (NCM) explaining over 70% of the variation. City characteristics were found to predominantly drive the assemblages, accounting for 50.1% of the variation in stochasticity ratio. Furthermore, the ability of UTS microbes to discriminate between cities was strongly influenced by city characteristics, particularly climate and continent.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Xue Zhu, Pengshuo Yang, Guangzhou Xiong, Huimin Wei, Lu Zhang, Zhi Wang, Kang Ning
Summary: Aquaculture has the potential to feed the growing global population, but it also leads to environmental pollution. Rice-cray-fish co-culture models (RCFP) in China are eco-friendly, but little is known about their microbiome pattern. This study reveals that RCFP has advantages in nitrogen assimilation and sulfur pollutants removal, while non-RCFP produces hazardous pollutants. RCFP plays a crucial role in balancing aquaculture productivity and environmental protection.
Article
Biology
Pengshuo Yang, Xue Zhu, Kang Ning
Summary: Microbes in different habitats exhibit specific species and gene enrichment patterns, reflecting the biome-species-function relationship influenced by ecological and evolutionary principles. However, a comprehensive understanding of these patterns and the driving factors behind them remains limited. In this study, enrichment patterns were examined in 1705 microbiome samples from four representative biomes, and an enrichment sphere model was constructed to reveal the regulatory principles. Case studies demonstrated the enrichment of copper-resistance genes in soil biomes due to contamination and horizontal gene transfer, and the enrichment of flagellum-related genes in freshwater biomes due to fluidity and vertical gene accumulation. The enrichment sphere model has practical applications in biome identification and protein structure modeling. Overall, the model aims to provide a comprehensive understanding of the biome-species-function relationships.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Yuxue Li, Mingyue Cheng, Yuguo Zha, Kun Yang, Yigang Tong, Song Wang, Qunwei Lu, Kang Ning
Summary: Regular high-intensity exercise can cause changes in athletes' gut microbiota, and the extent and nature of these changes may be affected by the athletes' exercise patterns. Different types of athletes have distinct gut microbiome profiles, and these profiles are associated with inflammation, diet, and anaerobic performance. The effects of sport types and exercise intensity on the gut microbiota are sex-dependent.