Results 91 to 100 of about 503,920 (237)

ExMODE: A comprehensive resource for extremophile genomic and functional exploration

iMetaOmics, EarlyView.
ExMODE (https://db.genomics.cn/exmode/) integrates 3518 samples to build a unified extremophile resource, which hosts 1.35 billion habitat‐specific non‐redundant genes, 5.25 million representative protein structures, 67,026 metagenome‐assembled genomes (MAGs), and 164,132 biosynthetic gene clusters (BGCs). By combining sequence‐, structure‐, and genome‐
Denghui Li, Kailong Ma, Xiaoqiang Li, Jieni Wang, Zhen Cui, Yulu Zhang, Weiwen Wang, Jiawei Tong, Yang Guo, Zongan Wang, Peiyun Zeng, Jieyu Wang, Xiaokai Xu, Nannan Zhang, Yingying Zhang, Jing Chen, Qingjiang Hu, Wenzhen Yang, Zhiyong Li, Tao Yang, Wensi Du, Zhicheng Xu, Zhen Yue, Jian Wang, Guangyi Fan, Weijia Zhang, Xun Xu, Liujie Huo, Xiaofeng Wei, Liang Meng, Shanshan Liu   +30 more
wiley   +1 more source

Multi‐omics reveals gastrointestinal metabolic disorder‐induced diarrhea in postpartum dairy cows

iMetaOmics, EarlyView.
Nutritional diarrhea is a pervasive, costly challenge in dairy production. Using integrated metagenomic and metabolomic profiling, we identified coordinated microbial and metabolic alterations across the rumen, hindgut, and serum. In the rumen, enrichment of Prevotella sp.
Weixuan Tang, Yangyi Hao, Jiawei Zhang, Yajing Wang, Zhijun Cao, Hongjian Yang, Wei Wang, Shengli Li   +7 more
wiley   +1 more source

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Nature Communications, 2022
Reference genomes for gut microbiomes help unravel microbial “dark matter” and serve as valuable resource for disease-focused studies. Here, the authors perform short and long read metagenomics and metagenome-assembled genomes analyses to profile the gut
Jean-Sebastien Gounot, Minghao Chia, Denis Bertrand, Woei-Yuh Saw, Aarthi Ravikrishnan, Adrian Low, Yichen Ding, Amanda Hui Qi Ng, Linda Wei Lin Tan, Yik-Ying Teo, Henning Seedorf, Niranjan Nagarajan   +11 more
doaj   +1 more source

Metagenomic and culture‐based insights into host and plasmid contexts of high‐risk ARGs in poultry farm environments

iMetaOmics, EarlyView.
Shotgun metagenomics and culture‐based isolate genomics revealed position‐associated high‐risk antibiotic resistance genes (ARGs) signals across poultry manure piles and surrounding soils. Culture‐confirmed Enterobacteriaceae and IncHI2A‐related blaNDM‐5 plasmid backgrounds further highlight priority host‐ARG‐plasmid contexts for farm antimicrobial ...
Yaling Wang, Lianwei Ye, Linan He, Zhenlong Wu, Yiwen Yang, Sheng Chen   +5 more
wiley   +1 more source

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes

Genome Biology
Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs).
Guo Ye, Hao Hong, Ting Li, Jin Li, Jia-Qi Wu, Shuai Jiang, Zhi-Tong Meng, He-Tian Yuan, Wen Xue, Ai-Ling Li, Tao Zhou, Ting-Ting Li, Tao Li   +12 more
doaj   +1 more source

Multi‐omics–driven precision medicine

iMeta, EarlyView.
Multi‐omics‐driven precision medicine (MODPM) provides a multiscale, continuously learnable framework that integrates genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome profiles, and clinical data. Powered by artificial intelligence and foundation models, MODPM enables cross‐modal representation learning, contextual modeling ...
Huibo Li, Zhe Zhao, Yifan Zhang, Yao Ma, Gaofei Hu, Min Zeng, Zhanqun Yang, Zixuan Zhao, Xin Zhou, Wei Hu, Yuxuan Sun, Meng Su, Jun Li, Matthew Whiteman, Wei Fu, Chao Zhong, Lemin Zheng, Long Chen, Hairong Lv, Rongsheng Zhao, Yi Zhun Zhu   +20 more
wiley   +1 more source

The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences [version 1; peer review: 2 approved]

Wellcome Open Research
We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases.
Eerik Aunin, Victoria McKenna, Ute Hentschel, Sergi Taboada, Carles Galià, Kathrin Busch, Elizabeth Sinclair, Ana Riesgo, Graeme Oatley, Camilla Santos, Haoyu Niu, Dirk Erpenbeck, Noah Gettle, Michael Paulini, Rebecca O’Brien   +14 more
doaj   +1 more source

Quality metrics for metagenome-assembled genomes of Alnus viridis spp. Fruticose nodules

, 2023
Quality metrics for metagenome-assembled genomes of Alnus viridis spp. Fruticose nodules. Binning methods are MaxBin2 v2.2.5,MetaBAT version 2.12.1, CONCOCT v 1.1.0 ,CheckM v1.1.10  , GTDB database R06-RS202, GTDB-tk version v1.5 ...
Neslihan Tas (12964601)
core   +1 more source

Zinc‐stabilized stannous fluoride modulates the periodontal microbiome, reducing Fusobacteria, key Gram‐negative species, and overall inflammation within an experimental gingivitis clinical trial

Journal of Periodontology, EarlyView.
Abstract Background This study aimed to evaluate the effects of a dentifrice containing stannous fluoride stabilized with zinc phosphate on subgingival microbiome composition and clinical inflammation during experimental gingivitis, compared with a sodium fluoride control. Methods This investigation was conducted as a secondary analysis of a randomized,
Kristopher A. Kerns, Allison A. Naumann, Lay Y. Soon, Erik L. Hendrickson, Abdelahhad Barbour, Dandan Chen, Harsh M. Trivedi, Michael Glogauer, Jeffrey S. McLean   +8 more
wiley   +1 more source

The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences [version 2; peer review: 2 approved, 1 approved with reservations]

Wellcome Open Research
We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases.
Jose Victor Lopez, Eerik Aunin, Ute Hentschel, Martha Alejandra Durán Canché, Rinat Bar-Shalom, Micha Ilan, Victoria McKenna, Laura Steindler, Elizabeth Sinclair, Graeme Oatley, Camilla Santos, Haoyu Niu, Noah Gettle, Michael Paulini, Rebecca O’Brien   +14 more
doaj   +1 more source