Results 51 to 60 of about 30,341 (174)

High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly

Frontiers in Microbiology, 2022
Metagenome assembly is a core yet methodologically challenging step for taxonomic classification and functional annotation of a microbiome. This study aims to generate the high-resolution human gut metagenome using both Illumina and Nanopore platforms ...
Lianwei Ye, Ning Dong, Wenguang Xiong, Jun Li, Runsheng Li, Heng Heng, Edward Wai Chi Chan, Sheng Chen, Sheng Chen   +8 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

MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency [PDF]

, 2014
Grouping large fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions.
Kang, Dongwan D., Kang, Dongwan, Froula, Jeff, Egan, Rob, Wang, Zhong   +4 more
core  

Cloud-SPAN NERC Metagenomics Course Session 5: Binning & Functional Annotation

, 2023
<p>In this lesson we will finish off our analysis by separating out the individual genomes into metagenome-assembled genomes (MAGs) using a process called binning. Binning can be done in lots of different ways but the general idea is to put all the
Forrester, Sarah, Greeves, Evelyn, Cansdale, Annabel   +2 more
core   +1 more source

An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs

Frontiers in Genetics, 2019
Here, we describe MetaErg, a standalone and fully automated metagenome and metaproteome annotation pipeline. Annotation of metagenomes is challenging. First, metagenomes contain sequence data of many organisms from all domains of life.
Xiaoli Dong, Marc Strous
doaj   +1 more source

Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes

mSystems, 2022
Long-read sequencing offers the potential to improve metagenome assemblies and provide more robust assessments of microbial community composition and function than short-read sequencing.
N. V. Patin, K. D. Goodwin
doaj   +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

Metagenome-assembled genomes of Cyanobacteria in cryoconite

, 2022
These data are associated with the manuscript "Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light harvesting mechanisms in glacier cryoconite".
Takumi Murakami (10828728)
core   +1 more source

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs

BMC Bioinformatics, 2021
Background Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the fragmented
Zhenmiao Zhang, Lu Zhang
doaj   +1 more source

Characterization of the dynamic microbiome evolution across thrips species

Insect Science, EarlyView.
Comprehensive survey of the microbiome in thrips. The dominant bacterial genera found in thrips include intracellular ones, such as Wolbachia and Spiroplasma, and extracellular ones, including Serratia, Pantoea, and Acinetobacter. We isolated and sequenced high‐quality genomes of two dominant symbionts, Pantoea dispersa and Serratia marcescens.
Xiaodi Hu, Zhaohui Shi, Yangwei Gao, Hanze Zheng, Lin Lin, Jian‐Ping Chen, Yong Chen, Chuan‐Xi Zhang, Yiyuan Li   +8 more
wiley   +1 more source