Elevated rates of horizontal gene transfer in the industrialized human microbiome

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform

(2020) Christian Munck et al.   Nature Communications

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

(2020) Soumaya Zlitni et al.   Genome Medicine

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

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

(2019) Nandita R. Garud et al.   PLOS BIOLOGY

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

(2019) Rene S. Hendriksen 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

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

The ancestral and industrialized gut microbiota and implications for human health

(2019) Erica D. Sonnenburg et al.   NATURE REVIEWS MICROBIOLOGY

Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation

(2019) Ryan Brewster et al.   TRENDS IN MICROBIOLOGY

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

(2019) M. Poyet et al.   NATURE MEDICINE

Global trends in antimicrobial resistance in animals in low- and middle-income countries

(2019) Thomas P. Van Boeckel et al.   SCIENCE

Vulnerability of the industrialized microbiota

(2019) Justin L. Sonnenburg et al.   SCIENCE

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

(2019) Eitan Yaffe et al.   Nature Microbiology

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

(2018) Christopher S. Smillie et al.   Cell Host & Microbe

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki 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

Stability of the human faecal microbiome in a cohort of adult men

(2018) Raaj S. Mehta et al.   Nature Microbiology

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

US Immigration Westernizes the Human Gut Microbiome

(2018) Pajau Vangay et al.   CELL

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

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

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Persistence and reversal of plasmid-mediated antibiotic resistance

(2017) Allison J. Lopatkin et al.   Nature Communications

Two dynamic regimes in the human gut microbiome

(2017) Sean M. Gibbons et al.   PLoS Computational Biology

Antimicrobial Use and Veterinary Care among Agro-Pastoralists in Northern Tanzania

(2017) Mark A. Caudell et al.   PLoS One

RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics

(2016) Frédéric Jauffrit et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mechanisms of inflammation-driven bacterial dysbiosis in the gut

(2016) M Y Zeng et al.   Mucosal Immunology

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

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

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

micropan: an R-package for microbial pan-genomics

(2015) Lars Snipen et al.   BMC BIOINFORMATICS

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

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

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut

(2014) M. J. Coyne et al.   mBio

Gut microbiome of the Hadza hunter-gatherers

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

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

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

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

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

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

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

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

(2011) Chris S. Smillie et al.   NATURE

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION