List of works - Dirk Gevers

A Microbiome Foundation for the Study of Crohn's Disease

scientific article published on March 2017

A catalog of reference genomes from the human microbiome

scientific article

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy

scientific article published in 2012

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

scientific article

Advancing the microbiome research community

scientific article

Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer

scientific article published on 15 December 2017

Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes

scientific article published in July 2005

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

scientific article published on 8 April 2015

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque

scientific article

Bioinformatics for the Human Microbiome Project

scientific article

Biphasic kinetics of growth and bacteriocin production with Lactobacillus amylovorus DCE 471 occur under stress conditions

scientific article published in April 2003

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development

scientific article

Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus

scientific article

Complex host genetics influence the microbiome in inflammatory bowel disease

scientific article

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

scientific article

ConStrains identifies microbial strains in metagenomic datasets

scientific article

Conservation of the chitin utilization pathway in the Vibrionaceae

scientific article

Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

scientific article published on 2 March 2015

Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas

scientific article published on 18 August 2020

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

scientific article published on 14 September 2015

Dirk Gevers

scientific article

Disease-specific alterations in the enteric virome in inflammatory bowel disease

scientific article

Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis ⬇️

scientific article published on September 15, 2010

Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting

scientific article

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

scientific article (publication date: 16 April 2012)

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

scientific article published on 16 April 2013

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

scientific article published in October 2017

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

scientific article

Experimental and analytical tools for studying the human microbiome

scientific article

Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study

scientific article

Gene duplication and biased functional retention of paralogs in bacterial genomes

scientific article published in April 2004

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

scientific article published on 10 October 2013

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

scientific article

Genomic and phenotypic comparison of Bacillus fumarioli isolates from geothermal Antarctic soil and gelatine

scientific article

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

scientific article

High-quality draft genome sequences of 28 Enterococcus sp. isolates

scientific article

Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats

scientific article published in 2007

Host genetic variation impacts microbiome composition across human body sites

scientific article

Identification of Bifidobacterium species using rep-PCR fingerprinting

scientific article published in November 2003

Identification of lactobacilli by pheS and rpoA gene sequence analyses

scientific article published in December 2007

Identifying personal microbiomes using metagenomic codes

scientific article published on 11 May 2015

In vitro conjugal transfer of tetracycline resistance from Lactobacillus isolates to other Gram-positive bacteria

scientific article published in August 2003

Inflammatory bowel disease microbiotas alter gut CD4 T-cell homeostasis and drive colitis in mice

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

scientific article published on 8 October 2016

Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012.

scientific article

MetaRef: a pan-genomic database for comparative and community microbial genomics

scientific article

Metabolic reconstruction for metagenomic data and its application to the human microbiome

scientific article published in 2012

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease

scientific article published on 26 May 2016

Metagenomic biomarker discovery and explanation

scientific article published on 24 June 2011

Microbial community function and biomarker discovery in the human microbiome

scientific article published on 19 September 2011

Microbial community function and biomarker discovery in the human microbiome

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.

scientific article

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Molecular characterization of tet(M) genes in Lactobacillus isolates from different types of fermented dry sausage

scientific article

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

scientific article published on June 2016

Nitric oxide reductase (norB) gene sequence analysis reveals discrepancies with nitrite reductase (nir) gene phylogeny in cultivated denitrifiers

scientific article

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease

scientific article

Opinion: Re-evaluating prokaryotic species

scientific article

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

scientific article

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

scientific article

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

scientific article published on September 2017

Prevalence and diversity of tetracycline resistant lactic acid bacteria and their tet genes along the process line of fermented dry sausages

scientific article published in June 2003

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

scientific article

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

scientific article

Relating the metatranscriptome and metagenome of the human gut.

scientific article

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

scientific article published in May 2008

Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome

scientific article

Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses

scientific article

Stepping stones towards a new prokaryotic taxonomy

scientific article

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

scientific article published in February 2018

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

scientific article published on 17 February 2016

Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov.

scientific article

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

scholarly article published by Päivi Pöhö in 2016

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids

scientific article published on 10 September 2015

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters ⬇️

scientific article published on November 19, 2012

The Human Microbiome Project: a community resource for the healthy human microbiome

scientific article

The classroom microbiome and asthma morbidity in children attending 3 inner-city schools

scholarly article by Peggy S Lai et al published June 2018 in The Journal of Allergy and Clinical Immunology

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes

scientific article published on 5 February 2015

The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment

scientific article

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571

scientific article published in 2008

The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers

scientific article published in November 2006

The influence of a short-term gluten-free diet on the human gut microbiome

scientific article

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites

scientific article published in May 2012

The microbiome in inflammatory bowel disease: current status and the future ahead

scientific article

The treatment-naive microbiome in new-onset Crohn's disease

scientific article

Towards a prokaryotic genomic taxonomy

scientific article

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

scientific article published on May 2016

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

scientific article

Vibrio chromosomes share common history

scientific article

List of works by Dirk Gevers

A Microbiome Foundation for the Study of Crohn's Disease

A catalog of reference genomes from the human microbiome

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

Advancing the microbiome research community

Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer

Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque

Bioinformatics for the Human Microbiome Project

Biphasic kinetics of growth and bacteriocin production with Lactobacillus amylovorus DCE 471 occur under stress conditions

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development

Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus

Complex host genetics influence the microbiome in inflammatory bowel disease

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

ConStrains identifies microbial strains in metagenomic datasets

Conservation of the chitin utilization pathway in the Vibrionaceae

Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

Dirk Gevers

Disease-specific alterations in the enteric virome in inflammatory bowel disease

Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis ⬇️

Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

Experimental and analytical tools for studying the human microbiome

Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study

Gene duplication and biased functional retention of paralogs in bacterial genomes

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

Genomic and phenotypic comparison of Bacillus fumarioli isolates from geothermal Antarctic soil and gelatine

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

High-quality draft genome sequences of 28 Enterococcus sp. isolates

Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats

Host genetic variation impacts microbiome composition across human body sites

Identification of Bifidobacterium species using rep-PCR fingerprinting

Identification of lactobacilli by pheS and rpoA gene sequence analyses

Identifying personal microbiomes using metagenomic codes

In vitro conjugal transfer of tetracycline resistance from Lactobacillus isolates to other Gram-positive bacteria

Inflammatory bowel disease microbiotas alter gut CD4 T-cell homeostasis and drive colitis in mice

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012.

MetaRef: a pan-genomic database for comparative and community microbial genomics

Metabolic reconstruction for metagenomic data and its application to the human microbiome

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease

Metagenomic biomarker discovery and explanation

Microbial community function and biomarker discovery in the human microbiome

Microbial community function and biomarker discovery in the human microbiome

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Molecular characterization of tet(M) genes in Lactobacillus isolates from different types of fermented dry sausage

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

Nitric oxide reductase (norB) gene sequence analysis reveals discrepancies with nitrite reductase (nir) gene phylogeny in cultivated denitrifiers

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease

Opinion: Re-evaluating prokaryotic species

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

Prevalence and diversity of tetracycline resistant lactic acid bacteria and their tet genes along the process line of fermented dry sausages

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

Relating the metatranscriptome and metagenome of the human gut.

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome

Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses

Stepping stones towards a new prokaryotic taxonomy

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov.

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

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters ⬇️

The Human Microbiome Project: a community resource for the healthy human microbiome

The classroom microbiome and asthma morbidity in children attending 3 inner-city schools

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes

The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment