Results 81 to 90 of about 537,462 (223)

A Metagenome‐Assembled Genome Catalog From the Global Ruminant Microbiomes

Animal Research and One Health, EarlyView.
The Ruminant Gastrointestinal MAG Catalog (RGMC) is a comprehensive global resource offering 40,812 strain‐level genomes across 53 bacterial and 4 archaeal classes. It greatly surpasses prior efforts in scale and diversity, serving as an essential foundation for research in ruminant nutrition, microbial function, and methane mitigation.
Shizhe Zhang, Qiushuang Li, Bingzi Ouyang, Wenxing Wang, Xiang Zhou, Xiumin Zhang, Rong Wang, Zhiliang Tan, Min Wang   +8 more
wiley   +1 more source

Augmenting microbial phylogenomic signal with tailored marker gene sets

Nature Communications
Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes representing major microbial phyla, covering only a small fraction of gene families.
Henry Secaira-Morocho, Xiaofang Jiang, Qiyun Zhu   +2 more
doaj   +1 more source

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

BMC Bioinformatics, 2020
Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for ...
Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski, Lee Ann McCue   +4 more
doaj   +1 more source

Gut microbiome seasonality is associated with dietary plasticity and coexistence in three sympatric Pamir ungulates

iMetaOmics, EarlyView.
This graphical abstract outlines a multi‐omics framework investigating the seasonal dietary composition and gut microbial communities of three coexisting ungulate species inhabiting the extreme high‐altitude Pamir Plateau (Ovis ammon polii, Capra sibirica, and Pseudois nayaur). By integrating dietary DNA metabarcoding, 16S rRNA gene sequencing, shotgun
Dilala Tuoliu, Lijiao Zhang, Muyang Wang, Wenxuan Xu, Kathreen Ruckstuhl, António Alves da Silva, Joana Alves, Hongchen Jiang, Weikang Yang   +8 more
wiley   +1 more source

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

, 2022
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

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

Metagenomic comparison of gut communities between wild and captive Himalayan griffons

Frontiers in Veterinary Science
IntroductionHimalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem.
You Wang, You Wang, Jundie Zhai, Jundie Zhai, Boyu Tang, Boyu Tang, Yonggang Dong, Yonggang Dong, Shengzhen Sun, Shunfu He, Wenxin Zhao, Zhuoma Lancuo, Qiangqiang Jia, Wen Wang   +13 more
doaj   +1 more source

viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data

Genome Biology, 2022
Although the use of long-read sequencing improves the contiguity of assembled viral genomes compared to short-read methods, assembling complex viral communities remains an open problem.
Dmitry Antipov, Mikhail Rayko, Mikhail Kolmogorov, Pavel A. Pevzner   +3 more
doaj   +1 more source

zhouyunyan/PIGC: The construction of reference gene catalog and metagenome-assembled genomes

, 2020
This directory contains scripts related to the manuscript "Expanded catalogue of microbial genes and metagenome-assembled genomes from the pig gut microbiome"
yyz
core   +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