Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

AE Pérez-Cobas, L Gomez-Valero… - Microbial …, 2020 - microbiologyresearch.org
Metagenomics and marker gene approaches, coupled with high-throughput sequencing
technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture …

New approaches for metagenome assembly with short reads

M Ayling, MD Clark, RM Leggett - Briefings in bioinformatics, 2020 - academic.oup.com
In recent years, the use of longer range read data combined with advances in assembly
algorithms has stimulated big improvements in the contiguity and quality of genome …

Improved metagenome binning and assembly using deep variational autoencoders

JN Nissen, J Johansen, RL Allesøe, CK Sønderby… - Nature …, 2021 - nature.com
Despite recent advances in metagenomic binning, reconstruction of microbial species from
metagenomics data remains challenging. Here we develop variational autoencoders for …

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

YW Wu, YH Tang, SG Tringe, BA Simmons, SW Singer - Microbiome, 2014 - Springer
Background Recovering individual genomes from metagenomic datasets allows access to
uncultivated microbial populations that may have important roles in natural and engineered …

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

S Kumar, M Jones, G Koutsovoulos, M Clarke… - Frontiers in …, 2013 - frontiersin.org
Generating the raw data for a de novo genome assembly project for a target eukaryotic
species is relatively easy. This democratization of access to large-scale data has allowed …

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

Y Yue, H Huang, Z Qi, HM Dou, XY Liu, TF Han… - BMC …, 2020 - Springer
Background Shotgun metagenomics based on untargeted sequencing can explore the
taxonomic profile and the function of unknown microorganisms in samples, and complement …

Gut dysbiosis and muscle aging: searching for novel targets against sarcopenia

A Picca, F Fanelli, R Calvani, G Mulè… - Mediators of …, 2018 - Wiley Online Library
Advanced age is characterized by several changes, one of which is the impairment of the
homeostasis of intestinal microbiota. These alterations critically influence host health and …

Metagenome-assembled genomes uncover a global brackish microbiome

LW Hugerth, J Larsson, J Alneberg, MV Lindh… - Genome biology, 2015 - Springer
Background Microbes are main drivers of biogeochemical cycles in oceans and lakes.
Although the genome is a foundation for understanding the metabolism, ecology and …

MetaSim—a sequencing simulator for genomics and metagenomics

DC Richter, F Ott, AF Auch, R Schmid, DH Huson - PloS one, 2008 - journals.plos.org
Background The new research field of metagenomics is providing exciting insights into
various, previously unclassified ecological systems. Next-generation sequencing …

Classification of metagenomic sequences: methods and challenges

SS Mande, MH Mohammed… - Briefings in …, 2012 - academic.oup.com
Characterizing the taxonomic diversity of microbial communities is one of the primary
objectives of metagenomic studies. Taxonomic analysis of microbial communities, a process …