Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems

(2020) Jesse R. Willis et al.   Microorganisms

Gender-associated differences in oral microbiota and salivary biochemical parameters in response to feeding

(2020) M. Minty et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Assessment of fecal DNA extraction protocols for metagenomic studies

(2020) Fangming Yang et al.   GigaScience

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

(2019) Edoardo Pasolli et al.   CELL

Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors

(2019) Stephen S. Dominy et al.   Science Advances

Transmission of human-associated microbiota along family and social networks

(2019) Ilana L. Brito et al.   Nature Microbiology

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

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

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

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Extensive transmission of microbes along the gastrointestinal tract

(2019) Thomas SB Schmidt et al.   eLife

Microbiome therapeutics go small molecule

(2019) Megan Cully   NATURE REVIEWS DRUG DISCOVERY

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

(2019) Dongwan D. Kang et al.   PeerJ

A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis

(2019) Hudan Pan et al.   Microbiome

Vancomycin relieves mycophenolate mofetil–induced gastrointestinal toxicity by eliminating gut bacterial β-glucuronidase activity

(2019) Michael R. Taylor et al.   Science Advances

OUP accepted manuscript

(2018)   BIOINFORMATICS

A gene catalogue of the Sprague-Dawley rat gut metagenome

(2018) Hudan Pan et al.   GigaScience

A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses

(2018) Mo Han et al.   Microbiome

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

(2018) Daniela S. Aliaga Goltsman et al.   GENOME RESEARCH

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

(2018) Imen Nouioui et al.   Frontiers in Microbiology

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

(2018) Isabel F. Escapa et al.   mSystems

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

On the ecosystemic network of saliva in healthy young adults

(2017) Egija Zaura et al.   ISME Journal

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

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

Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

(2017) Florent Lassalle et al.   MOLECULAR ECOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

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

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

(2017) Koji Atarashi et al.   SCIENCE

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

(2017) Chao Fang et al.   GigaScience

High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

(2017) Julia L. Drewes et al.   npj Biofilms and Microbiomes

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Microbial genome-wide association studies: lessons from human GWAS

(2016) Robert A. Power et al.   NATURE REVIEWS GENETICS

Metagenome-wide association studies: fine-mining the microbiome

(2016) Jun Wang et al.   NATURE REVIEWS MICROBIOLOGY

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat

(2015) Rong Xu et al.   BMC GENOMICS

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

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

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

(2015) Jun Yu et al.   GUT

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

Environment and Colonisation Sequence Are Key Parameters Driving Cooperation and Competition between Pseudomonas aeruginosa Cystic Fibrosis Strains and Oral Commensal Streptococci

(2015) Robert A. Whiley et al.   PLoS One

Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis

(2015) Baochen Shi et al.   mBio

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

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

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

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

(2012) Bo Liu et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS