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Massive-scale genomic analysis reveals SARS-CoV-2 mutation characteristics and evolutionary trends. 大规模基因组分析揭示了严重急性呼吸系统综合征冠状病毒2型的突变特征和进化趋势。
mLife Pub Date : 2022-09-01 Epub Date: 2022-09-26 DOI: 10.1002/mlf2.12040
Yamin Sun, Min Wang, Wenchao Lin, Wei Dong, Jianguo Xu
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引用次数: 0
Distinct gut microbiota and health outcomes in asymptomatic infection, viral nucleic acid test re-positive, and convalescent COVID-19 cases. 无症状感染者、病毒核酸检测重阳性和恢复期新冠肺炎病例的不同肠道微生物群和健康结果。
mLife Pub Date : 2022-06-01 Epub Date: 2022-06-15 DOI: 10.1002/mlf2.12022
Ruqin Lin, Mingzhong Xiao, Shanshan Cao, Yu Sun, Linhua Zhao, Xiaoxiao Mao, Peng Chen, Xiaolin Tong, Zheyuan Ou, Hui Zhu, Dong Men, Xiaodong Li, Yiqun Deng, Xian-En Zhang, Jikai Wen
{"title":"Distinct gut microbiota and health outcomes in asymptomatic infection, viral nucleic acid test re-positive, and convalescent COVID-19 cases.","authors":"Ruqin Lin, Mingzhong Xiao, Shanshan Cao, Yu Sun, Linhua Zhao, Xiaoxiao Mao, Peng Chen, Xiaolin Tong, Zheyuan Ou, Hui Zhu, Dong Men, Xiaodong Li, Yiqun Deng, Xian-En Zhang, Jikai Wen","doi":"10.1002/mlf2.12022","DOIUrl":"10.1002/mlf2.12022","url":null,"abstract":"<p><p>Gut microbiota composition is suggested to associate with coronavirus disease 2019 (COVID-19) severity, but the impact of gut microbiota on health outcomes is largely unclear. We recruited 81 individuals from Wuhan, China, including 13 asymptomatic infection cases (Group A), 24 COVID-19 convalescents with adverse outcomes (Group C), 31 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) re-positive cases (Group D), and 13 non-COVID-19 healthy controls (Group H). The microbial features of Groups A and D were similar and exhibited higher gut microbial diversity and more abundant short-chain fatty acid (SCFA)-producing species than Group C. Group C was enriched with opportunistic pathogens and virulence factors related to adhesion and toxin production. The abundance of SCFA-producing species was negatively correlated, while <i>Escherichia coli</i> was positively correlated with adverse outcomes. All three groups (A, C, and D) were enriched with the mucus-degrading species <i>Akkermansia muciniphila</i>, but decreased with <i>Bacteroides</i>-encoded carbohydrate-active enzymes. The pathways of vitamin B6 metabolic and folate biosynthesis were decreased, while selenocompound metabolism was increased in the three groups. Specifically, the secondary bile acid (BA) metabolic pathway was enriched in Group A. Antibiotic resistance genes were common among the three groups. Conclusively, the gut microbiota was related to the health outcomes of COVID-19. Dietary supplementations (SCFAs, BA, selenium, folate, vitamin B6) may be beneficial to COVID-19 patients.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"1 2","pages":"183-197"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9349603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41167995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
gcCov: Linked open data for global coronavirus studies. gcCov:全球冠状病毒研究的关联开放数据。
mLife Pub Date : 2022-03-01 Epub Date: 2022-03-16 DOI: 10.1002/mlf2.12008
Wenyu Shi, Guomei Fan, Zhihong Shen, Chuan Hu, Juncai Ma, Yuanchun Zhou, Zhen Meng, Songnian Hu, Yuhai Bi, Liang Wang, Haiying Yu, Siru Lin, Xiuqiang Sun, Xinjiao Zhang, Dongmei Liu, Qinlan Sun, Linhuan Wu
{"title":"gcCov: Linked open data for global coronavirus studies.","authors":"Wenyu Shi, Guomei Fan, Zhihong Shen, Chuan Hu, Juncai Ma, Yuanchun Zhou, Zhen Meng, Songnian Hu, Yuhai Bi, Liang Wang, Haiying Yu, Siru Lin, Xiuqiang Sun, Xinjiao Zhang, Dongmei Liu, Qinlan Sun, Linhuan Wu","doi":"10.1002/mlf2.12008","DOIUrl":"10.1002/mlf2.12008","url":null,"abstract":"<p><p>We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework (RDF) and implement a server to publish linked open data (LOD). As one of the largest and most comprehensive semantic databases about coronaviruses, the resulted gcCov database demonstrates the capability of using data in the LOD framework to promote correlations between genotypes and phenotypes. These correlations will be helpful for future research on fundamental viral mechanisms and drug and vaccine designs. These LOD with 62,168,127 semantic triplets and their visualizations are freely accessible through gcCov at https://nmdc.cn/gccov/.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"1 1","pages":"92-95"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9088579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41168004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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