Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

(2020) Till R. Lesker et al.   Cell Reports

Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia

(2020) Silke Rath et al.   Frontiers in Microbiology

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

Adjusting for age improves identification of gut microbiome alterations in multiple diseases

(2020) Tarini S Ghosh et al.   eLife

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

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

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

(2019) Edoardo Pasolli et al.   CELL

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms

(2019) Matthew R. Olm et al.   Microbiome

CAMISIM: simulating metagenomes and microbial communities

(2019) Adrian Fritz et al.   Microbiome

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

(2019) Takeshi Tanoue et al.   NATURE

Human contamination in bacterial genomes has created thousands of spurious proteins

(2019) Florian P. Breitwieser et al.   GENOME RESEARCH

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

(2019) Andrew Maltez Thomas et al.   NATURE MEDICINE

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

(2019) Almut Heinken et al.   Microbiome

Multiple levels of the unknown in microbiome research

(2019) Andrew Maltez Thomas et al.   BMC BIOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

(2019) Shinichi Yachida et al.   NATURE MEDICINE

Benchmarking Metagenomics Tools for Taxonomic Classification

(2019) Simon H. Ye et al.   CELL

Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

(2019) Yan Shao et al.   NATURE

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

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

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

(2019) Adrian Tett et al.   Cell Host & Microbe

Detecting contamination in viromes using ViromeQC

(2019) Moreno Zolfo et al.   NATURE BIOTECHNOLOGY

Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India

(2019) Ankit Gupta et al.   mSystems

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

(2019) Qiyun Zhu et al.   Nature Communications

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

(2018) Moran Yassour et al.   Cell Host & Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

(2018) Pamela Ferretti et al.   Cell Host & Microbe

Selective maternal seeding and environment shape the human gut microbiome

(2018) Katri Korpela et al.   GENOME RESEARCH

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin

(2018) Lulu Sun et al.   NATURE MEDICINE

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii

(2017) Indrani Mukhopadhya et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome

(2017) Francesco Beghini et al.   ISME Journal

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Genomic history of the seventh pandemic of cholera in Africa

(2017) François-Xavier Weill et al.   SCIENCE

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Uncovering the trimethylamine-producing bacteria of the human gut microbiota

(2017) Silke Rath et al.   Microbiome

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

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

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

(2017) Francesco Asnicar et al.   mSystems

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges

(2016) Martin J. Blaser et al.   mBio

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Elevated trimethylamine-N-oxide (TMAO) is associated with poor prognosis in primary sclerosing cholangitis patients with normal liver function

(2016) Martin Kummen et al.   United European Gastroenterology Journal

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

(2016) Emily Vogtmann et al.   PLoS One

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

(2015) Monika Schaubeck et al.   GUT

Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

(2015) Jun Yu et al.   GUT

Structure and Function of CutC Choline Lyase from Human Microbiota BacteriumKlebsiella pneumoniae

(2015) Gints Kalnins et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

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

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

A unified initiative to harness Earth's microbiomes

(2015) A. P. Alivisatos et al.   SCIENCE

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

(2015) Stephen Nayfach et al.   PLoS Computational Biology

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Bioboxes: standardised containers for interchangeable bioinformatics software

(2015) Peter Belmann et al.   GigaScience

Conducting Meta-Analyses inRwith themetaforPackage

(2015) Wolfgang Viechtbauer   Journal of Statistical Software

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

(2014) Weili Xiong et al.   JOURNAL OF PROTEOME RESEARCH

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Intestinal Microbial Metabolism of Phosphatidylcholine and Cardiovascular Risk

(2013) W.H. Wilson Tang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Database resources of the National Center for Biotechnology Information

(2013)   NUCLEIC ACIDS RESEARCH

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Biodiversity and functional genomics in the human microbiome

(2012) Xochitl C. Morgan et al.   TRENDS IN GENETICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Analysis of 16S rRNA environmental sequences using MEGAN

(2011) Suparna Mitra et al.   BMC GENOMICS

Chronic Intestinal Inflammation Induces Stress-Response Genes in Commensal Escherichia coli

(2011) Laura G. Patwa et al.   GASTROENTEROLOGY

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

(2011) Nicola Segata et al.   PLoS One

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH