Resistome expansion in disease-associated human gut microbiomes

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing

(2023) David Calderón-Franco et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Development of the oral resistome during the first decade of life

(2023) Smitha Sukumar et al.   Nature Communications

Impact of long-term dietary habits on the human gut resistome in the Dutch population

(2022) Paul B. Stege et al.   Scientific Reports

The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome

(2022) Shengzhi Yang et al.   Microbiome

Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge

(2022) Dongjuan Dai et al.   Microbiome

Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections

(2022) Mathew Stracy et al.   SCIENCE

Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults

(2022) Andrew Oliver et al.   mBio

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

(2022) Lajos Kalmar et al.   PLoS Genetics

Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome

(2022) Alexander Crits-Christoph et al.   Gut Microbes

Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli

(2022) Matthew Davies et al.   Gut Microbes

Inflammatory Endotype-Associated Airway Resistome in Chronic Obstructive Pulmonary Disease

(2022) Xinzhu Yi et al.   Microbiology Spectrum

Host gut resistome in Gulf War chronic multisymptom illness correlates with persistent inflammation

(2022) Dipro Bose et al.   Communications Biology

Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador

(2021) Maria J. Soto-Girón et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Identifying biases and their potential solutions in human microbiome studies

(2021) Jacob T. Nearing et al.   Microbiome

Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis

(2021) Nazreen F. Hadjirin et al.   BMC BIOLOGY

The Human Gut Resistome up to Extreme Longevity

(2021) Teresa Tavella et al.   mSphere

Diet and the Human Gut Microbiome: An International Review

(2020) Annette S. Wilson et al.   DIGESTIVE DISEASES AND SCIENCES

Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease

(2020) Micheál Mac Aogáin et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms

(2020) Jian Sun et al.   Nature Communications

Metagenome-wide association of gut microbiome features for schizophrenia

(2020) Feng Zhu et al.   Nature Communications

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

(2020) Yu Pan et al.   mSystems

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

(2020) Tanya M. Monaghan et al.   Gut Microbes

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

(2020) Santiago Redondo-Salvo et al.   Nature Communications

Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study

(2020) Liese Van Gompel et al.   ENVIRONMENT INTERNATIONAL

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

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

The human respiratory tract microbial community structures in healthy and cystic fibrosis infants

(2020) Marie-Madlen Pust et al.   npj Biofilms and Microbiomes

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing

(2019) You Che et al.   Microbiome

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

Global Geographic Trends in Antimicrobial Resistance: The Role of International Travel

(2019) Isabel Frost et al.   JOURNAL OF TRAVEL MEDICINE

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

(2019) Andrew Maltez Thomas et al.   NATURE MEDICINE

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

(2019) Shinichi Yachida et al.   NATURE MEDICINE

The evolution of antibiotic resistance

(2019) R. Craig MacLean et al.   SCIENCE

Defining and combating antibiotic resistance from One Health and Global Health perspectives

(2019) Sara Hernando-Amado et al.   Nature Microbiology

Sick Individuals and Sick (Microbial) Populations: Challenges in Epidemiology and the Microbiome

(2019) Audrey Renson et al.   Annual Review of Public Health

Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer

(2019) Mingyang Song et al.   GASTROENTEROLOGY

Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India

(2019) Ankit Gupta et al.   mSystems

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

Bangladeshi children with acute diarrhea show fecal microbiomes with increased Streptococcus abundance, irrespective of diarrhea etiology

(2018) Silas Kieser et al.   ENVIRONMENTAL MICROBIOLOGY

Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae

(2018) M Rozwandowicz et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

(2018) Stephen Baker et al.   SCIENCE

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research

(2018) Patrick D. Schloss   mBio

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Defining antimicrobial resistance in cystic fibrosis

(2018) Timothy J. Kidd et al.   Journal of Cystic Fibrosis

A metagenomic study of the gut microbiome in Behcet’s disease

(2018) Zi Ye et al.   Microbiome

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

(2018) Geoffrey D. Hannigan et al.   mBio

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

(2017) R. Balfour Sartor et al.   GASTROENTEROLOGY

Effects of short- and long-course antibiotics on the lower intestinal microbiome as they relate to traveller’s diarrhea

(2017) Lawrence Clifford McDonald   JOURNAL OF TRAVEL MEDICINE

The Threat of Antimicrobial Resistance on the Human Microbiome

(2017) Lauren Brinkac et al.   MICROBIAL ECOLOGY

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

Inflammation boosts bacteriophage transfer between Salmonella spp.

(2017) Médéric Diard et al.   SCIENCE

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome

(2017) Dorottya Nagy-Szakal et al.   Microbiome

Gut microbiota dysbiosis contributes to the development of hypertension

(2017) Jing Li et al.   Microbiome

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

(2016) Emily Vogtmann et al.   PLoS One

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

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

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma

(2015) Krithivasan Sankaranarayanan et al.   CURRENT BIOLOGY

Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

(2015) Jun Yu et al.   GUT

The human gut resistome

(2015) W. van Schaik   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward

(2015) F. M. Aarestrup   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans

(2015) Lawrence A. David et al.   mBio

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

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

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

Antibiotic resistance and its cost: is it possible to reverse resistance?

(2010) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

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

Resistance in bacteria of the food chain: epidemiology and control strategies

(2008) Frank M Aarestrup et al.   Expert Review of Anti-Infective Therapy