Results 11 to 20 of about 1,840,918 (247)

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes [PDF]

BMC Genomics, 2017
Background Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential.
Bhavya Papudeshi, J. Matthew Haggerty, Michael Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano Thompson, Robert A. Edwards, Elizabeth A. Dinsdale   +11 more
doaj   +5 more sources

Gut microbial community of patients with Parkinson’s disease analyzed using metagenome-assembled genomes

Neural Regeneration Research
Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.
Yi Zhang, Chengjun Mo, Xiaoqin He, Qin Xiao, Xiaodong Yang   +4 more
doaj   +3 more sources

To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities

Briefings in Bioinformatics, 2022
AbstractHigh-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi ...
Jiayin Zhou, Wen Song, Qichao Tu
openaire   +3 more sources

Metagenome-Assembled Genomes from Amazonian Soil Microbial Consortia

Microbiology Resource Announcements, 2022
Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.
Jéssica A. Mandro, Fernanda M. Nakamura, Júlia B. Gontijo, Siu M. Tsai, Andressa M. Venturini   +4 more
openaire   +2 more sources

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome [PDF]

Nature Communications, 2021
AbstractGut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog
Congying Chen, Yunyan Zhou, Hao Fu, Xinwei Xiong, Shaoming Fang, Hui Jiang, Jinyuan Wu, Hui Yang, Jun Gao, Lusheng Huang   +9 more
openaire   +3 more sources

Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome. [PDF]

Mol Ecol Resour
ABSTRACT Strain‐level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain‐level resolution of individual microbes.
Sahil R, Jain M.
europepmc   +2 more sources

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate

Microbiology Resource Announcements, 2022
Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs). These MAGs can inform future studies aimed at generating renewable chemicals
Kevin A. Walters, Kevin S. Myers, Hui Wang, Nathaniel W. Fortney, Abel T. Ingle, Matthew J. Scarborough, Timothy J. Donohue, Daniel R. Noguera   +7 more
openaire   +2 more sources

Metagenome-assembled microbial genomes from Parkinson’s disease fecal samples

Scientific Reports, 2023
AbstractThe human gut microbiome composition has been linked to Parkinson’s disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples).
Ilhan Cem Duru, Alexandre Lecomte, Tânia Keiko Shishido, Pia Laine, Joni Suppula, Lars Paulin, Filip Scheperjans, Pedro A. B. Pereira, Petri Auvinen   +8 more
openaire   +4 more sources

Rainfall Shapes the Diversity of Soil Nitrogen-Fixing Microorganisms Worldwide. [PDF]

Adv Sci (Weinh)
This study reveals the distinctive pattern and mechanism of rainfall driving the global biodiversity and biogeography of soil potential N‐fixing microorganisms, and constructs the theoretical framework. The results guide us on how to maintain ecosystem productivity under future climate changes (e.g., whether a specific region needs more N fertilizers ...
Hua B, Pang S, Li A, Hu Z, Wu H, Zhang S, Fan Y, Wu Y, Yang W, Zhao Y, Guan Y, Ji B, Kong D, Zhao Y, Goncharov AA, Korotkevich AY, Mao R, Zhang Y, Zhang X.   +18 more
europepmc   +2 more sources

A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome

Poultry Science, 2023
The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date.
Xinwei Xiong, Yousheng Rao, Jinge Ma, Zhangfeng Wang, Qin He, Jishang Gong, Wentao Sheng, Jiguo Xu, Xuenong Zhu, Yuwen Tan, Yanbei Yang   +10 more
openaire   +3 more sources