Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

(2020) Edoardo Pasolli et al.   Nature Communications

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

The neuroactive potential of the human gut microbiota in quality of life and depression

(2019) Mireia Valles-Colomer et al.   Nature Microbiology

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Viruses as key reservoirs of antibiotic resistance genes in the environment

(2019) Didier Debroas et al.   ISME Journal

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans

(2019) Michael L. Patnode et al.   CELL

High proportions of bacteria and archaea across most biomes remain uncultured

(2019) Andrew D. Steen et al.   ISME Journal

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

(2019) Robert D. Stewart et al.   NATURE BIOTECHNOLOGY

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut

(2019) Yoshihiko Suzuki et al.   Microbiome

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Single-cell metagenomics: challenges and applications

(2018) Yuan Xu et al.   Protein & Cell

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

(2018) Aaron M. Walsh et al.   Microbiome

Abundance determines the functional role of bacterial phylotypes in complex communities

(2018) Damian W. Rivett et al.   Nature Microbiology

High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage

(2018) Akintunde Emiola et al.   Nature Communications

Microbial nutrient niches in the gut

(2017) Fátima C. Pereira et al.   ENVIRONMENTAL MICROBIOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

(2017) John Beaulaurier et al.   NATURE BIOTECHNOLOGY

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

Dietary Fiber and the Human Gut Microbiota: Application of Evidence Mapping Methodology

(2017) Caleigh Sawicki et al.   Nutrients

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach

(2017) Bonnie L. Brown et al.   GigaScience

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

The role of short chain fatty acids in appetite regulation and energy homeostasis

(2015) C S Byrne et al.   INTERNATIONAL JOURNAL OF OBESITY

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

(2015) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS