Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner

ARGminer: A web platform for crowdsourcing based curation of antibiotic resistance genes

(2020) G A Arango-Argoty et al.   BIOINFORMATICS

sraX: A Novel Comprehensive Resistome Analysis Tool

(2020) Leonardo G. Panunzi   Frontiers in Microbiology

Potential Elimination of Human Gut Resistome by Exploiting the Benefits of Functional Foods

(2020) Christina Tsigalou et al.   Frontiers in Microbiology

Revealing antibiotic resistance in therapeutic and dietary probiotic supplements

(2020) Joseph Selvin et al.   Journal of Global Antimicrobial Resistance

Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage

(2020) Jiachao Zhang et al.   Gut Microbes

The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

(2020) Tayte P. Campbell et al.   ISME Journal

Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut

(2020) Luís Leónidas Cardoso et al.   Nature Ecology & Evolution

Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study)

(2020) Yifei Zhang et al.   Nature Communications

The pros, cons, and many unknowns of probiotics

(2019) Jotham Suez et al.   NATURE MEDICINE

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

(2019) G. A. Arango-Argoty et al.   Microbiome

Probiotics in the next-generation sequencing era

(2019) Jotham Suez et al.   Gut Microbes

Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome

(2019) Andrew J. Gasparrini et al.   Nature Microbiology

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Indexed variation graphs for efficient and accurate resistome profiling

(2018) Will P M Rowe et al.   BIOINFORMATICS

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

(2018) Xiaole Yin et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

(2018) Jotham Suez et al.   CELL

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

(2018) Niv Zmora et al.   CELL

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults

(2018) Chad W. MacPherson et al.   Scientific Reports

Multicenter Trial of a Combination Probiotic for Children with Gastroenteritis

(2018) Stephen B. Freedman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Lactobacillus rhamnosus GG versus Placebo for Acute Gastroenteritis in Children

(2018) David Schnadower et al.   NEW ENGLAND JOURNAL OF MEDICINE

Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants

(2018) Eirin Esaiassen et al.   Frontiers in Pediatrics

A randomized synbiotic trial to prevent sepsis among infants in rural India

(2017) Pinaki Panigrahi et al.   NATURE

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

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes

(2016) Chenhong Zhang et al.   ISME Journal

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

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

In Vivo Horizontal Gene Transfer of the Carbapenemase OXA-48 During a Nosocomial Outbreak

(2015) S. Gottig et al.   CLINICAL INFECTIOUS DISEASES

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption

(2015) Emiley A. Eloe-Fadrosh et al.   mBio

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Metagenomic insights into the human gut resistome and the forces that shape it

(2014) Kristoffer Forslund et al.   BIOESSAYS

Antibiotic resistance among commercially available probiotics

(2014) Poonam Sharma et al.   FOOD RESEARCH INTERNATIONAL

Lactobacilli and bifidobacteria in the prevention of antibiotic-associated diarrhoea and Clostridium difficile diarrhoea in older inpatients (PLACIDE): a randomised, double-blind, placebo-controlled, multicentre trial

(2013) Stephen J Allen et al.   LANCET

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Nosocomial outbreak of carbapenem-resistant Enterobacter cloacae highlighting the interspecies transferability of the blaOXA-48 gene in the gut flora

(2012) L. Cremet et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

High-level resistance to gentamicin: genetic transfer between Enterococcus faecalis isolated from food of animal origin and human microbiota

(2011) M. Sparo et al.   LETTERS IN APPLIED MICROBIOLOGY

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Transfer of antimicrobial resistance plasmids from Klebsiella pneumoniae to Escherichia coli in the mouse intestine

(2008) S. Schjorring et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY