Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria

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

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

Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century

(2018) Bethany M. Henrick et al.   mSphere

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

(2018) Katariina Pärnänen et al.   Nature Communications

GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets

(2018) Matthew D Czajkowski et al.   BIOINFORMATICS

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Antibiotic resistance potential of the healthy preterm infant gut microbiome

(2017) Graham Rose et al.   PeerJ

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

(2017) Steven A. Frese et al.   mSphere

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota

(2017) Jasmine C. C. Davis et al.   Scientific Reports

Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria

(2016) Sabrina Duranti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

(2016) María X. Maldonado-Gómez et al.   Cell Host & Microbe

Metagenomic Comparison of Antibiotic Resistance Genes Associated with Liquid and Dewatered Biosolids

(2016) Crystal A. McCall et al.   JOURNAL OF ENVIRONMENTAL QUALITY

Translational metagenomics and the human resistome: confronting the menace of the new millennium

(2016) Matthias Willmann et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

(2016) M. P. Francino   Frontiers in Microbiology

Why Don't All Infants Have Bifidobacteria in Their Stool?

(2016) Gerald W. Tannock et al.   Frontiers in Microbiology

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

(2016) Molly K. Gibson et al.   Nature Microbiology

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

(2015) Dennis Versluis et al.   Scientific Reports

Multidrug Efflux Pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus Bacterial Food Pathogens

(2015) Jody Andersen et al.   International Journal of Environmental Research and Public Health

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut

(2014) Mark A. Underwood et al.   PEDIATRIC RESEARCH

Stool Microbiota and Vaccine Responses of Infants

(2014) M. N. Huda et al.   PEDIATRICS

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library

(2014) Fiona Fouhy et al.   PLoS One

Bacteriophage therapy: a potential solution for the antibiotic resistance crisis

(2014) Zhabiz Golkar et al.   Journal of Infection in Developing Countries

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

(2014) Brandon Brooks et al.   Microbiome

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Tetracycline resistance genes acquired at birth

(2013) Angela M. Alicea-Serrano et al.   ARCHIVES OF MICROBIOLOGY

Exploring Variation of Antibiotic Resistance Genes in Activated Sludge over a Four-Year Period through a Metagenomic Approach

(2013) Ying Yang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

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

(2013) Yongfei Hu et al.   Nature Communications

Strategies to Minimize Antibiotic Resistance

(2013) Chang-Ro Lee et al.   International Journal of Environmental Research and Public Health

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome

(2013) Michael R. Gillings   Frontiers in Microbiology

The human microbiome as a reservoir of antimicrobial resistance

(2013) John Penders et al.   Frontiers in Microbiology

Human-Associated Extended-Spectrum β-Lactamase in the Antarctic

(2012) Jorge Hernández et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Different Functions of MdtB and MdtC Subunits in the Heterotrimeric Efflux Transporter MdtB2C Complex of Escherichia coli

(2012) Hong-Suk Kim et al.   BIOCHEMISTRY

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

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

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

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

Genotypic-Phenotypic Discrepancies between Antibiotic Resistance Characteristics of Escherichia coli Isolates from Calves in Management Settings with High and Low Antibiotic Use

(2011) Margaret A. Davis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Acquired Antibiotic Resistance: Are We Born with It?

(2011) Lu Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Occurrence of oligosaccharides in feces of breast-fed babies in their first six months of life and the corresponding breast milk

(2011) Simone Albrecht et al.   CARBOHYDRATE RESEARCH

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements

(2011) Erik Kristiansson et al.   PLoS One

Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge

(2011) Tong Zhang et al.   PLoS One

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

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

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

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

Constitutive SoxS Expression in a Fluoroquinolone-Resistant Strain with a Truncated SoxR Protein and Identification of a New Member of the marA-soxS-rob Regulon, mdtG

(2009) A. Fabrega et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Structural and functional aspects of the multidrug efflux pump AcrB

(2009) Thomas Eicher et al.   BIOLOGICAL CHEMISTRY

Strategies for managing today's infections

(2008) Y. Carmeli   CLINICAL MICROBIOLOGY AND INFECTION

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA