[HTML][HTML] A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

C Yang, D Chowdhury, Z Zhang, WK Cheung… - Computational and …, 2021 - Elsevier
Metagenomic sequencing provides a culture-independent avenue to investigate the
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …

[HTML][HTML] Bioinformatics for NGS-based metagenomics and the application to biogas research

S Jünemann, N Kleinbölting, S Jaenicke, C Henke… - Journal of …, 2017 - Elsevier
Metagenomics has proven to be one of the most important research fields for microbial
ecology during the last decade. Starting from 16S rRNA marker gene analysis for the …

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

RD Stewart, MD Auffret, A Warr, AH Wiser… - Nature …, 2018 - nature.com
The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a
task largely performed by enzymes encoded by the rumen microbiome. Here we present …

MG-RAST, a metagenomics service for analysis of microbial community structure and function

KP Keegan, EM Glass, F Meyer - Microbial environmental genomics (MEG), 2016 - Springer
Approaches in molecular biology, particularly those that deal with high-throughput
sequencing of entire microbial communities (the field of metagenomics), are rapidly …

NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

Q Tu, L Lin, L Cheng, Y Deng, Z He - Bioinformatics, 2019 - academic.oup.com
Motivation The nitrogen (N) cycle is a collection of important biogeochemical pathways in
the Earth ecosystem and has gained extensive foci in ecology and environmental studies …

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

K Moon, JH Jeon, I Kang, KS Park, K Lee, CJ Cha… - Microbiome, 2020 - Springer
Background Antibiotic resistance developed by bacteria is a significant threat to global
health. Antibiotic resistance genes (ARGs) spread across different bacterial populations …

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming

K Xue, M M. Yuan, Z J. Shi, Y Qin, YE Deng… - Nature Climate …, 2016 - nature.com
Microbial decomposition of soil carbon in high-latitude tundra underlain with permafrost is
one of the most important, but poorly understood, potential positive feedbacks of …

Ecophysiological Examination of the Lake Erie Microcystis Bloom in 2014: Linkages between Biology and the Water Supply Shutdown of Toledo, OH

MM Steffen, TW Davis, RML McKay… - … science & technology, 2017 - ACS Publications
Annual cyanobacterial blooms dominated by Microcystis have occurred in western Lake Erie
(US/Canada) during summer months since 1995. The production of toxins by bloom-forming …

Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

KD Brumfield, A Huq, RR Colwell, JL Olds, MB Leddy - PLoS One, 2020 - journals.plos.org
Microorganisms are ubiquitous in the biosphere, playing a crucial role in both
biogeochemistry of the planet and human health. However, identifying these …

An evaluation of the accuracy and speed of metagenome analysis tools

S Lindgreen, KL Adair, PP Gardner - Scientific reports, 2016 - nature.com
Metagenome studies are becoming increasingly widespread, yielding important insights into
microbial communities covering diverse environments from terrestrial and aquatic …