Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

(2020) Alexander Crits-Christoph et al.   ISME Journal

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

(2020) Soumaya Zlitni et al.   Genome Medicine

Within-Host Viral Diversity: A Window into Viral Evolution

(2020) Adam S. Lauring   Annual Review of Virology

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

(2020) Alyssa G. Kent et al.   Nature Communications

Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut

(2019) Xiaofang Jiang et al.   SCIENCE

Gut microbiota density influences host physiology and is shaped by host and microbial factors

(2019) Eduardo J Contijoch et al.   eLife

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

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs

(2019) Katharine Michelle Ng et al.   Cell Host & Microbe

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

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

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

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

Selective maternal seeding and environment shape the human gut microbiome

(2018) Katri Korpela et al.   GENOME RESEARCH

Automated annotation of mobile antibiotic resistance in Gram-negative bacteria: the Multiple Antibiotic Resistance Annotator (MARA) and database

(2018) Sally R Partridge et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Experimental Studies of Evolutionary Dynamics in Microbes

(2018) Ivana Cvijović et al.   TRENDS IN GENETICS

Evolution of a Dominant Natural Isolate of Escherichia coli in the Human Gut over the Course of a Year Suggests a Neutral Evolution with Reduced Effective Population Size

(2018) Mohamed Ghalayini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics

(2018) David C. Danko et al.   GENOME RESEARCH

High-quality genome sequences of uncultured microbes by assembly of read clouds

(2018) Alex Bishara et al.   NATURE BIOTECHNOLOGY

Microbiome as a tool and a target in the effort to address antimicrobial resistance

(2018) David A. Relman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

(2018) Bálint Kintses et al.   Nature Microbiology

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

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

(2017) Freeman Lan et al.   NATURE BIOTECHNOLOGY

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

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

(2017) Francesco Asnicar et al.   mSystems

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

Genome assembly from synthetic long read clouds

(2016) Volodymyr Kuleshov et al.   BIOINFORMATICS

The Central Nervous System and the Gut Microbiome

(2016) Gil Sharon et al.   CELL

Bayesian Inference of Natural Selection from Allele Frequency Time Series

(2016) Joshua G. Schraiber et al.   GENETICS

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

The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism

(2016) Peter Spanogiannopoulos et al.   NATURE REVIEWS MICROBIOLOGY

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

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

Bayesian Inference of Natural Selection from Allele Frequency Time Series

(2016) Joshua G. Schraiber et al.   GENETICS

Frenemies: Signaling and Nutritional Integration in Pathogen-Microbiota-Host Interactions

(2015) Elizabeth A. Cameron et al.   Cell Host & Microbe

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut

(2015) Jinbao Yin et al.   ECOTOXICOLOGY

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

(2015) Frédéric Raymond et al.   ISME Journal

No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens

(2015) Martina Sassone-Corsi et al.   JOURNAL OF IMMUNOLOGY

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces

(2015) E. Zaura et al.   mBio

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

A novel spectral method for inferring general diploid selection from time series genetic data

(2014) Matthias Steinrücken et al.   Annals of Applied Statistics

Effects of Antibiotics on Human Microbiota and Subsequent Disease

(2014) Kristie M. Keeney et al.   Annual Review of Microbiology

A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

(2014) J. D. O'Brien et al.   GENETICS

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Cryptic genetic variation: evolution's hidden substrate

(2014) Annalise B. Paaby et al.   NATURE REVIEWS GENETICS

Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation

(2013) Richard A. Neher   Annual Review of Ecology Evolution and Systematics

Identifying Signatures of Selection in Genetic Time Series

(2013) A. F. Feder et al.   GENETICS

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes 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

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Regulated Virulence Controls the Ability of a Pathogen to Compete with the Gut Microbiota

(2012) N. Kamada et al.   SCIENCE

Long-term impacts of antibiotic exposure on the human intestinal microbiota

(2010) C. Jernberg et al.   MICROBIOLOGY-SGM

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimation of 2Nes From Temporal Allele Frequency Data

(2008) J. P. Bollback et al.   GENETICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal