Dispersal strategies shape persistence and evolution of human gut bacteria

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

Strain inheritance and neonatal gut microbiota development: A meta-analysis

(2021) Daniel Podlesny et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Low mutational load and high mutation rate variation in gut commensal bacteria

(2020) Ricardo S. Ramiro et al.   PLOS BIOLOGY

Succession of Bifidobacterium longum Strains in Response to a Changing Early Life Nutritional Environment Reveals Dietary Substrate Adaptations

(2020) Magdalena Kujawska et al.   iScience

Antibiotics-induced monodominance of a novel gut bacterial order

(2019) Falk Hildebrand et al.   GUT

Transmission of human-associated microbiota along family and social networks

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

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

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

Adaptive Evolution within Gut Microbiomes of Healthy People

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

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

(2019) Dongwan D. Kang et al.   PeerJ

Evolutionary and Ecological Consequences of Gut Microbial Communities

(2019) Nancy A. Moran et al.   Annual Review of Ecology Evolution and Systematics

Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

(2019) Yan Shao et al.   NATURE

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

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

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

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Metagenomic analysis of gut microbial communities from a Central Asian population

(2018) Almagul Kushugulova et al.   BMJ Open

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

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster 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

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

(2017) Derrick M Chu et al.   NATURE MEDICINE

Transmission of the gut microbiota: spreading of health

(2017) Hilary P. Browne et al.   NATURE REVIEWS MICROBIOLOGY

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

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

(2017) Francesco Asnicar et al.   mSystems

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

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

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

(2016) Daniel R. Mende et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

(2016) Doyle V. Ward et al.   Cell Reports

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

(2016) Hailiang Xie et al.   Cell Systems

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics

(2015) Matthias Willmann et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents

(2015) Johan Bengtsson-Palme et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

(2015) Valeria Montano et al.   GENETICS

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

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

The initial state of the human gut microbiome determines its reshaping by antibiotics

(2015) Frédéric Raymond et al.   ISME Journal

A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies

(2015) Fernando Puente-Sánchez et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Measuring Asymmetry in Time-Stamped Phylogenies

(2015) Bethany L. Dearlove et al.   PLoS Computational Biology

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

(2015) Valeria Montano et al.   GENETICS

Temporal and technical variability of human gut metagenomes

(2015) Anita Y Voigt et al.   GENOME BIOLOGY

Lambda: the local aligner for massive biological data

(2014) Hannes Hauswedell et al.   BIOINFORMATICS

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

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

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Genomic evolution and transmission ofHelicobacter pyloriin two South African families

(2013) Xavier Didelot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC 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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS