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List of works by Joël Doré

753 Identification of a Gut Microbial Signature Linked to Severity of Irritable Bowel Syndrome

A Data Integration Multi-Omics Approach to Study Calorie Restriction-Induced Changes in Insulin Sensitivity

scientific article published on 01 January 2018

A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation.

scientific article published on 20 June 2019

A catalog of the mouse gut metagenome

scientific article published on 28 September 2015

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

scientific article

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic

scientific article (publication date: 16 January 2017)

A human gut microbial gene catalogue established by metagenomic sequencing

scientific article

A marker of endotoxemia is associated with obesity and related metabolic disorders in apparently healthy Chinese

scientific article

A metagenomic insight into our gut's microbiome

scientific article

A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome.

scientific article

A new era in gut research concerning interactions between microbiota and human health ⬇️

scientific article published on 01 September 2010

A reference gene catalogue of the pig gut microbiome

scientific article published on 19 September 2016

A robust and adaptable high throughput screening method to study host-microbiota interactions in the human intestine

scientific article

ANGPTL4 expression induced by butyrate and rosiglitazone in human intestinal epithelial cells utilizes independent pathways

scientific article published on 21 March 2013

Acetogenic coccoid spore-forming bacteria isolated from the rumen ⬇️

scientific article published on November 1, 1996

Akkermansia muciniphila abundance is lower in severe obesity, but its increased level after bariatric surgery is not associated with metabolic health improvement

scientific article published on 02 July 2019

Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology

scientific article

Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon

scientific article published on February 2003

Altered gut microbiota composition in immune-impaired Nod2(-/-) mice

article

Altered host-gut microbes symbiosis in severely malnourished anorexia nervosa (AN) patients undergoing enteral nutrition: An explicative factor of functional intestinal disorders?

scientific article published on 09 October 2018

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation

article

Alternative stable states in the intestinal ecosystem: proof of concept in a rat model and a perspective of therapeutic implications

scientific article published on 06 November 2020

Amendments: Author Correction: A catalog of the mouse gut metagenome

scientific article published on 01 January 2019

An integrated catalog of reference genes in the human gut microbiome

scientific article

An iterative workflow for mining the human intestinal metaproteome

scientific article

Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data

scientific article published on 21 September 2020

Anti-inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract.

scientific article

Anti-inflammatory properties of dairy lactobacilli

scientific article

Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine.

scientific article

Bacterial imprinting of the neonatal immune system: lessons from maternal cells?

scientific article

Bacterial protein signals are associated with Crohn's disease

scientific article

Bioavailability of lignans in human subjects

scientific article

Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD.

scientific article

Brussels sprouts, inulin and fermented milk alter the faecal microbiota of human microbiota-associated rats as shown by PCR-temporal temperature gradient gel electrophoresis using universal, Lactobacillus and Bifidobacterium 16S rRNA gene primers

scientific article published in May 2005

Butyrate produced by commensal bacteria potentiates phorbol esters induced AP-1 response in human intestinal epithelial cells

scientific article

Cellular and physiological effects of probiotics and prebiotics

scientific article

Clostridium difficile and Clostridium perfringens species detected in infant faecal microbiota using 16S rRNA targeted probes

scientific article published on 02 May 2006

Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition

scientific article

Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside

scientific article published in January 2007

Colonic microbiota signatures across five northern European countries

scientific article

Commensal Streptococcus salivarius Modulates PPARγ Transcriptional Activity in Human Intestinal Epithelial Cells

scientific article published on 6 May 2015

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells.

scientific article published on 7 March 2017

Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR.

scientific article published on 19 March 2009

Comparative study of bacterial groups within the human cecal and fecal microbiota

scientific article

Comparison of the faecal microflora of patients with ankylosing spondylitis and controls using molecular methods of analysis

scientific article published on 01 December 2002

Composition and metabolism of the intestinal microbiota in consumers and non-consumers of yogurt.

scientific article published in January 2007

Contribution of C. beijerinckii and C. sporogenes in association with C. tyrobutyricum to the butyric fermentation in Emmental type cheese.

scientific article

Correction: Functional Metagenomics: A High Throughput Screening Method to Decipher Microbiota-Driven NF-κB Modulation in the Human Gut

scholarly article by Omar Lakhdari et al published 12 October 2010 in PLOS ONE

Correction: Functional Metagenomics: A High Throughput Screening Method to Decipher Microbiota-Driven NF-κB Modulation in the Human Gut.

scientific article

Corrigendum: Dietary intervention impact on gut microbial gene richness

scientific article published in Nature

Design and Evaluation of a 16S rRNA-Targeted Oligonucleotide Probe for Specific Detection and Quantitation of Human Faecal Bacteroides Populations ⬇️

scientific article published on 01 March 1998

Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota.

scientific article published in July 2005

Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres

scientific article published on 17 February 2011

Development and validation of PCR primers to assess the diversity of Clostridium spp. in cheese by temporal temperature gradient gel electrophoresis

scientific article

Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth

scientific article

Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome

scientific article published on 26 March 2021

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

scientific article published on 10 July 2015

Dietary intervention impact on gut microbial gene richness

scientific article

Dietary patterns differently associate with inflammation and gut microbiota in overweight and obese subjects

scientific article

Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study

scientific article

Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs

scientific article

Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers ⬇️

scientific article

Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.

scientific article

Diversity of Bifidobacterium and Lactobacillus spp. in Breast-Fed and Formula-Fed Infants as Assessed by 16S rDNA Sequence Differences

article

Diversity of H2/CO2-utilizing acetogenic bacteria from feces of non-methane-producing humans.

scientific article published in August 1996

Diversity ofBifidobacteriumandLactobacillusspp. in Breast-Fed and Formula-Fed Infants as Assessed by 16S rDNA Sequence Differences

article

Does our food (environment) change our gut microbiome ('in-vironment'): a potential role for inflammatory bowel disease?

scientific article published on January 2012

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

scholarly article by Patricia Lepage et al published 1 March 2008 in Gut

Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray

scientific article

Early-life establishment of the swine gut microbiome and impact on host phenotypes

scientific article published on 6 May 2015

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

scientific article published on 08 March 2016

Effect of amoxicillin-clavulanic acid on human fecal flora in a gnotobiotic mouse model assessed with fluorescence hybridization using group-specific 16S rRNA probes in combination with flow cytometry

scientific article published on April 2004

Effect of fecal water on an in vitro model of colonic mucosal barrier function

scientific article

Effects of orally administered Lactobacillus casei DN-114 001 on the composition or activities of the dominant faecal microbiota in healthy humans

scientific article published on 01 February 2006

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis

scientific article

Enterotypes of the human gut microbiome

scientific article

Enterotypes of the human gut microbiome

scientific article published in Nature

Enumeration of Bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16S rRNA probes.

scientific article published in March 2003

Enumeration of bacteria from the Clostridium leptum subgroup in human faecal microbiota using Clep1156 16S rRNA probe in combination with helper and competitor oligonucleotides

scientific article published on 01 July 2005

Erratum: Addendum: Enterotypes of the human gut microbiome

scientific article published in Nature

Establishment of hydrogen-utilizing bacteria in the rumen of the newborn lamb

scientific article published on 01 April 1994

Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing

scientific article

Faecal microbiota and short-chain fatty acid levels in faeces from infants with cow's milk protein allergy

scientific article published on 29 June 2011

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

scientific article (publication date: 28 October 2008)

Fate and effects of Camembert cheese micro-organisms in the human colonic microbiota of healthy volunteers after regular Camembert consumption.

scientific article published on 14 April 2008

Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects

scientific article published in Scientific Reports

Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies

scientific article published on 8 September 2015

Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes

scientific article published on March 2003

Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria

scientific article

Functional metagenomics to decipher food-microbe-host crosstalk

scientific article

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

scientific article

Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut

scientific article (publication date: 30 September 2010)

Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora

scientific article published on 01 April 2001

Gastrointestinal tract and the elderly: functional foods, gut microflora and healthy ageing

scientific article published on 01 September 2002

Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission

scientific article published on 21 January 2020

Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention

scientific article published on 15 September 2020

Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon.

scientific article published on 22 November 2012

Gut health: predictive biomarkers for preventive medicine and development of functional foods

scientific article published on 07 April 2010

Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes

scientific article

Gut microbiota and gastrointestinal health: current concepts and future directions

scientific article

Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults

scientific article published on 31 July 2015

High gastrointestinal microbial diversity and clinical outcome in graft-versus-host disease patients

scientific article published on 14 June 2018

Highlighting new phylogenetic specificities of Crohn's disease microbiota.

scientific article

Hot topics in gut microbiota

scientific article

Human gut microbes impact host serum metabolome and insulin sensitivity

scientific article

Human intestinal metagenomics: state of the art and future

scientific article

Humans as holobionts: implications for prevention and therapy.

scientific article

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

scientific article published on 6 July 2014

Identification of NF-κB modulation capabilities within human intestinal commensal bacteria

scientific article published on 14 June 2011

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome

scientific article

Impact of newly developed metagenomic tools on our knowledge of the gut microbiota and its role in human health: diagnostic and therapeutic issues

scientific article

Influence of Camembert consumption on the composition and metabolism of intestinal microbiota: a study in human microbiota-associated rats

scientific article published on 01 September 2004

Inhibition of the NF-kappaB pathway in human intestinal epithelial cells by commensal Streptococcus salivarius

scientific article

Insulin resistance and inflammation predict kinetic body weight changes in response to dietary weight loss and maintenance in overweight and obese subjects by using a Bayesian network approach

scientific article published on 30 October 2013

Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans

scientific article

Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics

scientific article published in July 2010

Introduction to host microbiome symbiosis in health and disease

Investigating host-microbiome interactions by droplet based microfluidics

scientific article published on 01 October 2020

Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept

scientific article published on December 2011

Isoflavones and functional foods alter the dominant intestinal microbiota in postmenopausal women

scientific article published on 01 December 2005

Isolation and characterization of a new hydrogen-utilizing bacterium from the rumen

scientific article published on 01 January 1995

Isolation from the rumen of a new acetogenic bacterium phylogenetically closely related to Clostridium difficile

scientific article published on 01 April 1998

Isolation of an anaerobic intestinal bacterium capable of cleaving the C-ring of the isoflavonoid daidzein.

scientific article

Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species.

scientific article

Lactobacillus rhamnosus CNCMI-4317 Modulates Fiaf/Angptl4 in Intestinal Epithelial Cells and Circulating Level in Mice.

scientific article published on 6 October 2015

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets

scientific article published on 16 January 2020

Lipid growth requirement and influence of lipid supplement on fatty acid and aldehyde composition of Syntrophococcus sucromutans

scientific article

Low counts of Faecalibacterium prausnitzii in colitis microbiota.

scientific article

Major microbiota dysbiosis in severe obesity: fate after bariatric surgery

scientific article published on 13 June 2018

Mathematical modelling of carbohydrate degradation by human colonic microbiota.

scientific article published on 16 June 2010

Metabolic fate of polyphenols in the human superorganism

scientific article

Metabolism of One-Carbon Compounds by the Ruminal Acetogen Syntrophococcus sucromutans.

scientific article

Metagenomic species profiling using universal phylogenetic marker genes

scientific article

Microbial ecology perturbation in human IgA deficiency

scientific article published on 01 May 2018

Microbiome-Based Diagnostics: Ready for Applications in Laboratory Medicine?

scientific article published on 7 September 2017

Microbiote intestinal : qu’en attendre au plan physiologique et thérapeutique ?

scientific article published on 11 January 2017

Modulation of Lactobacillus casei in ileal and fecal samples from healthy volunteers after consumption of a fermented milk containing Lactobacillus casei DN-114 001Rif.

scientific article

Molecular analysis of the digestive microbiota in a gnotobiotic mouse model during antibiotic treatment: Influence of Saccharomyces boulardii

scientific article published on 22 April 2008

Molecular biological methods for studying the gut microbiota: the EU human gut flora project

scientific article published in May 2002

Molecular comparison of dominant microbiota associated with injured versus healthy mucosa in ulcerative colitis.

scientific article published on January 2007

Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity

scientific article published on 21 December 2009

Molecular inventory of faecal microflora in patients with Crohn's disease

scientific article published in October 2004

Most probable number enumeration of H2-utilizing acetogenic bacteria from the digestive tract of animals and man

scientific article published on 01 July 1995

Mucosal Healing and Bacterial Composition in Response to Enteral Nutrition Vs Steroid-based Induction Therapy-A Randomised Prospective Clinical Trial in Children With Crohn's Disease

scientific article published on 01 July 2019

Occurrence and activity of human intestinal bacteria involved in the conversion of dietary lignans

scientific article published on 15 December 2005

Patchy distribution of mucosal lesions in ileal Crohn's disease is not linked to differences in the dominant mucosa-associated bacteria: a study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis

scientific article

Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside

scientific article published in March 2006

Potential role of the intestinal microbiota of the mother in neonatal immune education

scientific article published on 15 July 2010

Prediction of the intestinal resistome by a three-dimensional structure-based method

scientific article published on 26 November 2018

Probiotics, prebiotics, and the host microbiome: the science of translation ⬇️

scientific article (publication date: December 2013)

Processing faecal samples: a step forward for standards in microbial community analysis

scientific article

Quality control of microbiota metagenomics by k-mer analysis

scientific article

Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization

scientific article

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome.

scientific article

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

scientific article published in 2023

Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach

scientific article (publication date: February 2006)

Replication of obesity and associated signaling pathways through transfer of microbiota from obese-prone rats

scientific article published on 15 January 2014

Reply to C Matuchansky

scientific article published on 01 March 2014

Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge

scientific article

Review article: gut flora and inflammatory bowel disease.

scientific article published in October 2004

Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease

scientific article published in October 2006

Richness of human gut microbiome correlates with metabolic markers

scientific article (publication date: 29 August 2013)

Roseburia, a decreased bacterial taxon in the gut microbiota of patients suffering from anorexia nervosa

scientific article published in 2022

SCFAs strongly stimulate PYY production in human enteroendocrine cells.

scientific article

Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA.

scientific article published in September 2005

Separation of bacteria of the Clostridium leptum subgroup from the human colonic microbiota by fluorescence-activated cell sorting or group-specific PCR using 16S rRNA gene oligonucleotides

scientific article

Specificities of the fecal microbiota in inflammatory bowel disease

scholarly article by Harry Sokol et al published February 2006 in Inflammatory Bowel Diseases

Statement of Retraction. Replication of Obesity and Associated Signaling Pathways Through Transfer of Microbiota From Obese-Prone Rats. Diabetes 2014;63:1624-1636. DOI: 10.2337/db13-1526

scientific article published on 01 May 2016

Storage conditions of intestinal microbiota matter in metagenomic analysis

scientific article

Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery

scientific article

Survival of Bifidobacterium animalis DN-173 010 in the Faecal Microbiota after Administration in Lyophilised Form or in Fermented Product – A Randomised Study in Healthy Adults

scientific article published on 24 October 2007

Survival of Lactobacillus casei in the human digestive tract after consumption of fermented milk

scientific article

TLR ligands and butyrate increase Pyy expression through two distinct but inter-regulated pathways.

scientific article published on 12 July 2016

Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis

scientific article

Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice

scientific article published on 23 May 2012

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age.

scientific article

The NF-κB binding site located in the proximal region of the TSLP promoter is critical for TSLP modulation in human intestinal epithelial cells

scientific article published on 11 February 2013

The SURMetaGIT study: Design and rationale for a prospective pan-omics examination of the gastrointestinal response to Roux-en-Y gastric bypass surgery.

scientific article published on 10 November 2016

The clinical Pseudomonas fluorescens MFN1032 strain exerts a cytotoxic effect on epithelial intestinal cells and induces Interleukin-8 via the AP-1 signaling pathway

scientific article

The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation

scientific article

The human gut microbiome and its dysfunctions

scientific article

The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?

scientific article published on 3 January 2017

The human intestinal microbiota ⬇️

scientific article published on September 1, 2010

The importance of the gut microbiota after bariatric surgery

scientific article published on 28 August 2012

The inflammatory status of old age can be nurtured from the intestinal environment

scientific article

The influence of diet on the gut microbiota and its consequences for health

scientific article published on 20 January 2015

The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide

scientific article

Three glycosylated serine-rich repeat proteins play a pivotal role in adhesion and colonization of the pioneer commensal bacterium, Streptococcus salivarius.

scientific article published on 11 July 2017

Towards standards for human fecal sample processing in metagenomic studies.

scientific article

Towards the human intestinal microbiota phylogenetic core

scientific article

Transcriptional interactions suggest niche segregation among microorganisms in the human gut.

scientific article

Transformation of (sup14)C-Lignin-Labeled Cell Walls of Wheat by Syntrophococcus sucromutans, Eubacterium oxidoreducens, and Neocallimastix frontalis.

scientific article published on January 1995

Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice.

scientific article

Translating the human microbiome

scientific article published in April 2013

Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis

scientific article

Validation of fluorescent in situ hybridization combined with flow cytometry for assessing interindividual variation in the composition of human fecal microflora during long-term storage of samples

scientific article published in November 2004

[Expanding the known diversity and environmental distribution of cultured and uncultured bacteria].

scientific article published in March 2005

[Molecular analysis of the colonic microflora]

scientific article published on 01 September 2001

[Role and integration of the intestinal microbiota in clinical management of other diseases]

scientific article published on 01 September 2019

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