Joel Dore

Joel Dore
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Microbiologie de l'Alimentation au Service de la Santé Humaine (MICALIS)

PhD

About

497
Publications
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Publications

Publications (497)
Article
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Some cardiometabolic risk factors such as dyslipidemia and insulin resistance are known to be associated with low gut microbiota richness. A link between gut microbiota richness and the diversity of consumed dietary fibers (DF) has also been reported. We introduced a larger diversity of consumed DF by using a daily consumed bread in subjects at car...
Article
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Anorexia nervosa (AN) is a severe eating disorder which can lead to malnutrition and life threatening complications with high mortality rates. We designed our analysis to identify gut microbial taxa differentially abundant between AN and HC across different 16S rRNA gene datasets. We identified a reduced abundance, diversity and richness of Rosebur...
Article
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Scope: An imbalance of the gut microbiota ("dysbiosis") is associated with numerous chronic diseases, and its modulation is a promising novel therapeutic approach. Dietary supplementation with soluble fiber is one of several proposed modulation strategies. This study aimed at confirming the impact of the resistant dextrin NUTRIOSE® (RD), a soluble...
Article
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Background Diosmectite, a natural colloidal clay, has been used worldwide for a number of approved indications, including the treatment of chronic functional diarrhea. Here, we used high-resolution whole metagenome shotgun sequencing to assess the impact of a 5 weeks administration of diosmectite (3 g/sachet, 3 sachets/day) on the fecal microbiota...
Article
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Introduction: Balneotherapy (BT) is the treatment of disease through the use of thermal spring water (TSW). It has been used for centuries and remains a popular form of treatment for dermatologic diseases such as atopic dermatitis (AD). Recent findings highlighted the role of the gut microbiota in AD and the possible crosstalk between gut and skin...
Article
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Background and aims Intestinal microbiota - host interactions play a major role in health and disease. This has been documented at the microbiota level (“dysbiosis” in chronic immune-mediated diseases) and through the study of specific bacteria - host interactions, but rarely at the level of intestinal ecosystem dynamics. Yet, understanding the beh...
Article
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Acute myeloid leukemia (AML) intensive chemotherapy combined with broad-spectrum antibiotics, leads to gut microbiota dysbiosis promoting pathological conditions and an increased incidence of complications. Here we report findings from a phase II single-arm, multicenter study evaluating autologous fecal microbiota transfer (AFMT) in 25 AML patients...
Article
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Background: Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for the treatment of obesity, also improving metabolic and inflammatory status, in patients with mild obesity. The underlying mechanisms have not been fully understood, but gut microbiota is hypothesized to play a key role. Our aim was to evaluate the assoc...
Article
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Background While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially with symptoms. Methods Here, we used a novel approach that combined data from a 4-day food diary, i...
Article
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There is a growing interest in the potentially deleterious impact of antibiotics on gut microbiota. Patients with bone and joint infection (BJI) require prolonged treatment that may impact significantly the gut microbiota. We collected samples from patients with BJI at baseline, end of antibiotics (EOT), and 2 weeks after antibiotic withdrawal (fol...
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The number of indications for fecal microbiota transplantation is expected to rise, thus increasing the needs for production of readily available frozen or freeze-dried transplants. Using shotgun metagenomics, we investigated the capacity of two novel human fecal microbiota transplants prepared in maltodextrin-trehalose solutions (abbreviated MD an...
Article
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Fecal microbiota transplantation (FMT) is an innovative therapy already used in humans to treat Clostridioides difficile infections associated with massive use of antibiotics. Clinical studies are obviously the gold standard to evaluate FMT efficiency but remain limited by regulatory, ethics, and cost constraints. In the present study, an in vitro...
Article
The gut microbiota are increasingly considered as a main partner of human health. Metaproteomics enables us to move from the functional potential revealed by metagenomics to the functions actually operating in the microbiome. However, metaproteome deciphering remains challenging. In particular, confident interpretation of a myriad of MS/MS spectra...
Preprint
Full-text available
Background: Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for the treatment of obesity, also improving metabolic and inflammatory status, in patients with mild obesity. The underlying mechanisms have not been fully understood, but gut microbiota is hypothesized to play a key role. Our aim was to evaluate the associ...
Article
Full-text available
Humans share a core intestinal microbiome and yet human microbiome differs by genes, species, enterotypes (ecology), and gene count (microbial diversity). Achievement of microbiota metagenomic analysis has revealed that the microbiome gene count is a key stratifier of health in several immune disorders and clinical conditions. We review here the pr...
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Background Chronic immune-mediated diseases are rapidly expanding and notoriously difficult to cure. Altered relatively stable intestinal microbiota configurations are associated with several of these diseases, and with a possible pre-disease condition (more susceptible to disease development) of the host-microbiota ecosystem. These observations ar...
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Background Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack...
Article
Background Alterations of gut microbiota may play a role in Anorexia Nervosa (AN) through perturbations of the gut-brain axis. Some studies found differences in the gut microbiota of patients with AN compared to healthy controls, but results are heterogeneous. The aim of this work was to systematically review the existing studies comparing gut mic...
Article
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The gut microbiota is a new frontier in health and disease. Not only many diseases are associated with perturbed microbiota, but an increasing number of studies point to a cause-effect relationship. Defining a healthy microbiota is not possible at the current state of our knowledge mostly because of high interindividual variability. A resilient mic...
Preprint
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Background Fecal microbiota transfer (FMT) is an innovative treatment already successfully used in recurrent Clostridioides difficile infections. Researchers and clinicians are exploring its potential for treating other digestive or extra-intestinal pathologies where gut microbial dysbiosis has been evidenced, such as inflammatory bowel disease, ob...
Article
Introduction Increased adiposity, dyslipidemia and insulin resistance are associated with increased risk of developing cardiometabolic diseases (CM). Such deleterious phenotypes have been shown to be associated with a low gene-richness microbiota that can partly be restored by a short-term dietary intervention (energy-restricted high-protein diet,...
Article
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Over the past years, gut microbiota became a major field of interest with increasing reports suggesting its association with a large number of human diseases. In this context, there is a major interest to develop analysis tools allowing simple and cost-effective population pattern analysis of these complex ecosystems to follow changes over time. Wh...
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Introduction et but de l’étude Le syndrome métabolique est associé à une faible richesse bactérienne du microbiote intestinal. Il a été démontré qu’une intervention alimentaire de courte durée permettait de rétablir partiellement cette richesse du microbiote intestinal et améliorait en parallèle le profil cardiométabolique (CM). Notre objectif est...
Preprint
Full-text available
While several studies have documented associations between dietary habits and microbiota composition and function in healthy subjects, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially in relation to symptoms. Here, we used a novel approach that combined data from 4-day food diary, integrated into...
Article
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Background In pig production systems, weaning is a crucial period characterized by nutritional, environmental, and social stresses. Piglets transition from a milk-based diet to a solid, more complex plant-based diet, and their gut physiology must adapt accordingly. It is well established that piglets weaned later display improved health, better wea...
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Gut microbiota composition is influenced by environmental factors and has been shown to impact body metabolism.OBJECTIVE: To assess the gut microbiota profile before and after Roux-en-Y gastric bypass (RYGB) and the correlation with food intake and postoperative type 2 diabetes remission (T2Dr).DESIGN: Gut microbiota profile from obese diabetic wom...
Article
Role and integration of the intestinal microbiota in clinical management of other diseases. Owing to its numerous functionalities, the microbiota is probably a key player in human health. It is altogether a source of signatures of alteration of host-microbes symbiosis and a potential modulator for prevention and therapy in a number of clinical cond...
Article
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Aims: Exclusive enteral nutrition [EEN] is as efficacious as corticosteroids [CS] to induce remission in Crohn's disease [CD], without their adverse effects. EEN seems to be more efficient than steroids to induce mucosal healing, but the underlying molecular mechanisms are only sparsely understood. We aimed in the present work to study the anti-in...
Article
The gut bacterial species, Akkermansia muciniphila is associated with a healthier clinical profile. The purpose of this study was to determine the association between A. muciniphila and glucose homeostasis in patients undergoing bariatric surgery (BS): gastric banding (GB) or Roux-en-Y gastric bypass (RYGB). This non-randomized prospective study in...
Article
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Owing to the growing recognition of the gut microbiota as a main partner of human health, we are expecting that the number of indications for fecal microbiota transplantation (FMT) will increase. Thus, there is an urgent need for standardization of the entire process of fecal transplant production. This study provides a complete standardized proced...
Chapter
In individuals with IBD, the microbiome occupies an integral juncture between their genetics and disease profile and may participate to the manifestations of the disease and the severity of its course. This chapter will highlight major microbiome research studies showing the pathobionts and symbionts in the human microbiome associated with IBD. It...
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Background: The mechanisms responsible for calorie restriction (CR)-induced improvement in insulin sensitivity (IS) have not been fully elucidated. Greater insight can be achieved through deep biological phenotyping of subjects undergoing CR, and integration of big data. Materials and Methods: An integrative approach was applied to investigate ass...
Article
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The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could poten-tially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and...
Article
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Nat. Biotechnol. 33, 1103–1108 (2015); published online 28 September 2015; corrected after print 18 December 2018 In the version of this article initially published, the y-axis numbering in Figure 1 was high by a factor of 10; the correct range is 0.5 to 2.5 million nonredundant genes. The error hasbeen corrected in the HTML and PDF versions of the...
Article
Le microbiote intestial joue un rôle majeur dans la santé humaine au travers de la relation symbiotique qu’il établit avec son hôte. Dans le cadre de certaines pathologies ou suite à des traitements médicaux comme les chimiothérapies ou les antibiothérapies, le microbiote intestinal peut être fortement altéré, ce qui se traduit souvent par une dimi...
Article
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Introduction. AML standard intensive induction chemotherapy ("3+7" or equivalent) combined with wide spectrum antibiotics can dramatically alter the composition of the gut microbiota, leading to dysbiosis which is characterized by loss of microbial diversity. Such dysbiosis status can promote a pathological condition involving uncontrolled local im...
Article
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Abstract Altered fecal levels of chromogranins (Cg) and secretogranins (Sg) are demonstrated in irritable bowel syndrome (IBS), but their role in IBS pathophysiology remains unknown. This study aimed to determine if granins are associated with bacterial composition, immune activation and IBS symptoms. Protein levels of fecal granins (CgA, CgB, SgII...
Article
Introduction et but de l’étude Alors que l’obésité peut s’expliquer par une surnutrition et l’ingestion de régimes riches en graisses et sucres, l’ingestion de fibres alimentaires est connue pour favoriser la perte de poids [1]. Notre étude vise à déterminer si, en situation d’apport alimentaire supérieur aux besoins (alimentation de type occidenta...
Article
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Background: Functional intestinal disorders (FIDs) are frequently observed in patients with anorexia nervosa (AN). Relationship between FIDs and a potential gut microbiota dysbiosis has been poorly explored. Objective: We aimed to determine an association between FIDs severity and dysbiosis of the intestinal microbiota in a severely malnourished...
Article
Background Immune activity and gut microbiota may impact the pathophysiology of irritable bowel syndrome (IBS). We aimed to determine whether antibacterial gene expression of immune activity‐defined IBS patients differed compared to healthy subjects (HS) and ulcerative colitis (UC) patients and whether antibacterial profiles reflected gut microbiot...
Article
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Objectives: Decreased gut microbial gene richness (MGR) and compositional changes are associated with adverse metabolism in overweight or moderate obesity, but lack characterisation in severe obesity. Bariatric surgery (BS) improves metabolism and inflammation in severe obesity and is associated with gut microbiota modifications. Here, we characte...
Article
Full-text available
The intestinal microbiota plays a key role in human health via the symbiotic relationship established with the host. In numerous clinical indications or following treatments such as chemotherapies or immunotherapies, the intestinal microbiota may be markedly altered, often showing reduced diversity of dominant microorganisms. Recent studies looked...
Article
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Fecal microbiota transfer (FMT) consists in the administration of a fecal dilution from a healthy donor into the intestinal tract of a recipient to restore microbial diversity and confer a health benefit. FMT has been demonstrated to successfully treat recurrent Clostridium difficile infection but may also have therapeutic potential for other disea...
Article
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Paradoxically, loss of immunoglobulin A (IgA), one of the most abundant antibodies, does not irrevocably lead to severe infections in humans but rather is associated with relatively mild respiratory infections, atopy, and autoimmunity. IgA might therefore also play covert roles, not uniquely associated with control of pathogens. We show that human...
Article
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The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota–host association imposes itself. Ideally, a stable state of equilibrium, homeostasis, is maint...
Article
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Peptide-YY (PYY) and Glucagon-Like Peptide-1 (GLP-1) play important roles in the regulation of food intake and insulin secretion, and are of translational interest in the field of obesity and diabetes. PYY production is highest in enteroendocrine cells located in the distal intestine, mirroring the sites where high concentrations of short chain fat...
Article
Full-text available
Peptide-YY (PYY) and Glucagon-Like Peptide-1 (GLP-1) play important roles in the regulation of food intake and insulin secretion, and are of translational interest in the field of obesity and diabetes. PYY production is highest in enteroendocrine cells located in the distal intestine, mirroring the sites where high concentrations of short chain fat...
Article
Le transfert du microbiote fécal (TMF) est l’administration de la dilution des selles d’un donneur sain dans le tractus intestinal d’un receveur afin de restaurer sa diversité microbienne et apporter un bénéfice pour sa santé. Il a été démontré que le TMF peut traiter avec succès une infection récurrente à Clostridium difficile , mais peut égalemen...
Article
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Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation...
Article
Background & aims: Paneth cell dysfunction causes deficiencies in intestinal C-type lectins and antimicrobial peptides, which leads to dysbiosis of the intestinal microbiota, alters the mucosal barrier, and promotes development of inflammatory bowel diseases. We investigated whether transgenic expression of the human regenerating family member 3 a...
Preprint
Full-text available
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens. Yet, this question remains hypothetical because of the difficulty to identify ARDs from intestinal bacteria. Here, we developed and validated a new annotation method (called pairw...
Article
Full-text available
Introduction et but de l’étude L’anorexie mentale est une maladie psychiatrique avec des conséquences somatiques potentiellement graves. Les troubles fonctionnels intestinaux sont une des complications les plus fréquemment rapportées dans la littérature. Leur physiopathologie reste, cependant, peu connue. L’objectif de ce travail était d’étudier l’...