Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

(2022) Silas Kieser et al.   PLoS Computational Biology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

(2022) Gianluca Ianiro et al.   NATURE MEDICINE

Improved metagenome binning and assembly using deep variational autoencoders

(2021) Jakob Nybo Nissen et al.   NATURE BIOTECHNOLOGY

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

(2021) Francesco Asnicar et al.   NATURE MEDICINE

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk

(2021) Dong D. Wang et al.   NATURE MEDICINE

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit

(2021) Fernando Meyer et al.   Nature Protocols

The long-term genetic stability and individual specificity of the human gut microbiome

(2021) Lianmin Chen et al.   CELL

Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data

(2021) Sara Saheb Kashaf et al.   Nature Protocols

Diversity and functional landscapes in the microbiota of animals in the wild

(2021) Doron Levin et al.   SCIENCE

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

(2021) Francesco Beghini et al.   eLife

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

(2021) Donovan H Parks et al.   NUCLEIC ACIDS RESEARCH

Variation and transmission of the human gut microbiota across multiple familial generations

(2021) Mireia Valles-Colomer et al.   Nature Microbiology

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

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

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

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

(2020) Francesco Asnicar et al.   Nature Communications

Metagenome-wide association of gut microbiome features for schizophrenia

(2020) Feng Zhu et al.   Nature Communications

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

(2020) Silas Kieser et al.   BMC BIOINFORMATICS

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

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease

(2020) Francesca De Filippis et al.   CURRENT BIOLOGY

Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma

(2020) Gianluca Ianiro et al.   Nature Communications

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

(2019) Edoardo Pasolli et al.   CELL

Transmission of human-associated microbiota along family and social networks

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

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

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

New approaches for metagenome assembly with short reads

(2019) Martin Ayling et al.   BRIEFINGS IN BIOINFORMATICS

Longitudinal multi-omics of host–microbe dynamics in prediabetes

(2019) Wenyu Zhou 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

Multiple levels of the unknown in microbiome research

(2019) Andrew Maltez Thomas et al.   BMC BIOLOGY

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

(2019) Dongwan D. Kang et al.   PeerJ

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

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces

(2019) Richard W. Hagan et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

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

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

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

A metagenomic study of the gut microbiome in Behcet’s disease

(2018) Zi Ye et al.   Microbiome

Species-level functional profiling of metagenomes and metatranscriptomes

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

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults

(2018) Lea B. S. Hansen et al.   Nature Communications

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

(2018) Chirag Jain et al.   Nature Communications

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

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

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

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

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

(2017) Francesco Asnicar et al.   mSystems

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis

(2017) Adrian Tett et al.   npj Biofilms and Microbiomes

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

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

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

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

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

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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

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

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

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

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Update of the Healthy Eating Index: HEI-2010

(2013) Patricia M. Guenther et al.   Journal of the Academy of Nutrition and Dietetics

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   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

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH