Unveiling microbial diversity: harnessing long-read sequencing technology

DP Agustinho, Y Fu, VK Menon, GA Metcalf… - Nature …, 2024 - nature.com
Long-read sequencing has recently transformed metagenomics, enhancing strain-level
pathogen characterization, enabling accurate and complete metagenome-assembled …

Effect of dietary components on the gut microbiota of aquatic animals. A never‐ending story?

E Ringø, Z Zhou, JLG Vecino, S Wadsworth… - Aquaculture …, 2016 - Wiley Online Library
It is well known that healthy gut microbiota is essential to promote host health and well‐
being. The intestinal microbiota of endothermic animals as well as fish are classified as …

[HTML][HTML] Anvi'o: an advanced analysis and visualization platform for 'omics data

AM Eren, ÖC Esen, C Quince, JH Vineis, HG Morrison… - PeerJ, 2015 - peerj.com
Advances in high-throughput sequencing and 'omics technologies are revolutionizing
studies of naturally occurring microbial communities. Comprehensive investigations of …

Next‐generation sequencing technologies for environmental DNA research

S Shokralla, JL Spall, JF Gibson… - Molecular …, 2012 - Wiley Online Library
Since 2005, advances in next‐generation sequencing technologies have revolutionized
biological science. The analysis of environmental DNA through the use of specific gene …

The human microbiome: our second genome

EA Grice, JA Segre - Annual review of genomics and human …, 2012 - annualreviews.org
The human genome has been referred to as the blueprint of human biology. In this review
we consider an essential but largely ignored overlay to that blueprint, the human …

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

T Riaz, W Shehzad, A Viari, F Pompanon… - Nucleic acids …, 2011 - academic.oup.com
Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from
complex substrates. In this article, we present ecoPrimers, a software for identifying new …

The metagenomics RAST server–a public resource for the automatic phylogenetic and functional analysis of metagenomes

F Meyer, D Paarmann, M D'Souza, R Olson… - BMC …, 2008 - Springer
Background Random community genomes (metagenomes) are now commonly used to
study microbes in different environments. Over the past few years, the major challenge …

Next-generation DNA sequencing methods

ER Mardis - Annu. Rev. Genomics Hum. Genet., 2008 - annualreviews.org
Recent scientific discoveries that resulted from the application of next-generation DNA
sequencing technologies highlight the striking impact of these massively parallel platforms …

Metagenomics and future perspectives in virus discovery

JL Mokili, F Rohwer, BE Dutilh - Current opinion in virology, 2012 - Elsevier
Monitoring the emergence and re-emergence of viral diseases with the goal of containing
the spread of viral agents requires both adequate preparedness and quick response …

Multivariate analyses in microbial ecology

A Ramette - FEMS microbiology ecology, 2007 - academic.oup.com
Environmental microbiology is undergoing a dramatic revolution due to the increasing
accumulation of biological information and contextual environmental parameters. This will …