Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

(2018) Aaron M. Walsh et al.   Microbiome

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

Microbiome Composition and Diversity of the Ice-Dwelling Sea Anemone,Edwardsiella andrillae

(2016) Alison E. Murray et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

(2016) Jun Wang et al.   NATURE GENETICS

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

(2016) Andrew W. Brooks et al.   PLOS BIOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Analyses of Intestinal Microbiota: Culture versus Sequencing: Figure 1

(2015) Andreas Hiergeist et al.   ILAR JOURNAL

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Which is more important for classifying microbial communities: who’s there or what they can do?

(2014) Zhenjiang Xu et al.   ISME Journal

Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness

(2014) Joseph M. Pickard et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The chemistry of negotiation: Rhythmic, glycan-driven acidification in a symbiotic conversation

(2014) Julia A. Schwartzman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel O-linked glycan modulates Campylobacter jejuni major outer membrane protein-mediated adhesion to human histo-blood group antigens and chicken colonization

(2014) J. Mahdavi et al.   Open Biology

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

Molecular Timetrees Reveal a Cambrian Colonization of Land and a New Scenario for Ecdysozoan Evolution

(2013) Omar Rota-Stabelli et al.   CURRENT BIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

Fast filtering for RNA homology search

(2011) D. L. Kolbe et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

(2011) P. Rausch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaorganisms as the new frontier

(2011) Thomas C.G. Bosch et al.   ZOOLOGY

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

(2010) Jin-Ya Wu et al.   BMC MICROBIOLOGY

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

The origins of modern biodiversity on land

(2010) M. J. Benton   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

(2009) Chih-Horng Kuo et al.   Biology Direct

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

Capsular glucan and intracellular glycogen ofMycobacterium tuberculosis: biosynthesis and impact on the persistence in mice

(2008) Tounkang Sambou et al.   MOLECULAR MICROBIOLOGY

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH