• Dietary fibers
• Dietary patterns
• Gut microbiota
• Intestinal inflammation
• Metagenomics

• Humans
• Inflammatory Bowel Diseases/microbiology
• Inflammatory Bowel Diseases/diet therapy
• Gastrointestinal Microbiome
• Dysbiosis/microbiology
• Nutritional Status
• Animals
• Diet

• causal inference
• de-confounding
• longitudinal microbiome analysis
• multi-omic integration
• unfolding

• Humans
• Algorithms
• Microbiota/genetics
• Longitudinal Studies
• Gastrointestinal Microbiome/genetics
• Metabolomics
• Computational Biology/methods
• Multiomics

• 1R15AI128714-01 HHS | NIH | OSC | Common Fund (NIH Common Fund)
• Dissertation Year Fellowship University Graduate School, Florida International University (UGS)

• Crohn’s disease
• Crohn’s disease exclusive diet
• FODMAP diet
• exclusive enteral nutrition
• inflammatory bowel disease
• mechanical stress
• microbiota
• nutritional therapy
• semi-vegetarian diet
• specific carbohydrate diet

• Crohn Disease/therapy
• Crohn Disease/diet therapy
• Enteral Nutrition/methods
• Humans
• Animals
• Nutrition Therapy/methods

• R01 DK124611 NIDDK NIH HHS
• W81XWH2010681 The United States Department of Defense

• Catheter-associated infections
• cost
• nosocomial infections
• pediatric intensive care unit
• traumatic brain injury

• Crohn's disease
• inflammatory bowel disease
• metabolome
• microbiome
• ulcerative colitis

• HaCat cells
• antimicrobial activity
• biocompatibility
• cell infection assays
• chitosan nanoparticles
• skin pathogens
• yellow everzol textile dyes

Inflammatory bowel disease (IBD) represents a chronic relapsing–remitting condition affecting the gastrointestinal system. The specific triggering IBD elements remain unknown: genetic variability, environmental factors, and alterations in the host immune system seem to be involved. An unbalanced diet and subsequent gut dysbiosis are risk factors, too. This review focuses on the description of the impact of pro- and anti-inflammatory food components on IBD, the role of different selected regimes (such as Crohn’s Disease Exclusion Diet, Immunoglobulin Exclusion Diet, Specific Carbohydrate Diet, LOFFLEX Diet, Low FODMAPs Diet, Mediterranean Diet) in the IBD management, and their effects on the gut microbiota (GM) composition and balance. The purpose is to investigate the potential positive action on IBD inflammation, which is associated with the exclusion or addition of certain foods or nutrients, to more consciously customize the nutritional intervention, taking also into account GM fluctuations during both disease flare-up and remission.

• diet
• food
• inflammation
• inflammatory bowel disease
• microbiome
• microbiota
• nutrition

Background: The gut microbial ecosystem is an important factor that regulates host health and the onset of chronic diseases, such as inflammatory bowel diseases, obesity, hyperlipidemia, and diabetes mellitus, which are important risk factors for atherosclerosis. However, the links among diet, microbiota composition, and atherosclerotic progression are unclear. Methods and results: Four-week-old mice (^-/- mice, C57Bl/6) were randomly divided into two groups, namely, supplementation with culture medium (control, CTR) and Bacteroides fragilis (BFS), and were fed a high-fat diet. The gut microbiota abundance in feces was evaluated using the 16S rDNA cloning library construction, sequencing, and bioinformatics analysis. The atherosclerotic lesion was estimated using Oil Red O staining. Levels of CD36, a scavenger receptor implicated in atherosclerosis, and F4/80, a macrophage marker in small intestine, were quantified by quantitative real-time PCR. Compared with the CTR group, the BFS group showed increased food intake, fasting blood glucose level, body weight, low-density lipoprotein level, and aortic atherosclerotic lesions. BFS dramatically reduced Lactobacillaceae (LAC) abundance and increased Desulfovibrionaceae (DSV) abundance. The mRNA expression levels of CD36 and F4/80 in small intestine and aorta tissue in the BFS group were significantly higher than those in the CTR group. Conclusions: gut microbiota dysbiosis was induced by BFS. It was characterized by reduced LAC and increased DSV abundance and led to the deterioration of glucose/lipid metabolic dysfunction and inflammatory response, which likely promoted aorta plaque formation and the progression of atherosclerosis.

• atherosclerotic
• dysbiosis
• gut microbiota
• metabolic syndrome

• Animals
• Aorta/metabolism
• Aortic Diseases/genetics
• Atherosclerosis/metabolism
• Bacteroides fragilis
• Diet, High-Fat/adverse effects
• Dietary Supplements
• Disease Models, Animal
• Dysbiosis/metabolism
• Ecosystem
• Gastrointestinal Microbiome/genetics
• Inflammation/metabolism
• Mice
• Mice, Inbred C57BL

Since the thyroid gland is one of the organs most affected by autoimmune processes, many patients with thyroiditis of Hashimoto (TH) seek medical advice on lifestyle variance and dietary modifications to improve and maintain their hyroid function. In this review, we aim to present and discuss some challenges associated with the nutritional management of TH, focusing on environmental and dietary deficits, inflammatory and toxic nutrients, cyanotoxins, etc. We discuss the relationships among different diets, chronic inflammation, and microbiota, and their impact on the development and exacerbation of TH in detail. We share some novel insights into the role of vitamin D and melatonin for preserving thyroid function during chronic inflammation in autoimmune predisposed subjects. A comprehensive overview is provided on anti-inflammatory nutrients and ecological diets, including foods for cleansing and detoxification, which represent strategies to prevent relapses and achieve overall improvement of life quality. In conclusion, data from biomedical and clinical studies provide evidence that an appropriate dietary and lighting regimen could significantly improve the function of the thyroid gland and reduce the reactivity of autoantibodies in TH. Compliance with nutritional guidelines may help TH patients to reduce the need for medicines.

• anti-inflammatory nutrients
• autoimmune Hashimoto’s thyroiditis
• detoxification
• ecological diet
• proinflammatory

• Autoantibodies
• Hashimoto Disease
• Humans
• Inflammation
• Thyroiditis

• Biomarker discovery
• Classification
• Feature selection
• Human gut microbiome
• Metagenomics

The integrity of the gastrointestinal tract structure and function is seriously compromised by two pathological conditions sharing, at least in part, several pathogenetic mechanisms: inflammatory bowel diseases (IBD) and coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. IBD and COVID-19 are marked by gut inflammation, intestinal barrier breakdown, resulting in mucosal hyperpermeability, gut bacterial overgrowth, and dysbiosis together with perturbations in microbial and human metabolic pathways originating changes in the blood and fecal metabolome. This review compared the most relevant metabolic and microbial alterations reported from the literature in patients with IBD with those in patients with COVID-19. In both diseases, gut dysbiosis is marked by the prevalence of pro-inflammatory bacterial species and the shortfall of anti-inflammatory species; most studies reported the decrease in Firmicutes, with a specific decrease in obligately anaerobic producers short-chain fatty acids (SCFAs), such as Faecalibacterium prausnitzii. In addition, Escherichia coli overgrowth has been observed in IBD and COVID-19, while Akkermansia muciniphila is depleted in IBD and overexpressed in COVID-19. In patients with COVID-19, gut dysbiosis continues after the clearance of the viral RNA from the upper respiratory tract and the resolution of clinical symptoms. Finally, we presented and discussed the impact of gut dysbiosis, inflammation, oxidative stress, and increased energy demand on metabolic pathways involving key metabolites, such as tryptophan, phenylalanine, histidine, glutamine, succinate, citrate, and lipids.

• COVID-19
• Crohn’s disease
• SARS-CoV-2
• inflammatory bowel disease
• metabolomics
• microbiomics
• ulcerative colitis

• Akkermansia muciniphila
• Bacteroides fragilis
• Faecalibacterium prausnitzii
• Gut microbiota
• cancer
• immunotherapy
• next-generation probiotics

• Diet
• Inflammatory bowel disease
• Microbiome
• Pathogenia

Inflammatory bowel disease (IBD) is a chronic, autoimmune disorder of the gastrointestinal tract with numerous genetic and environmental risk factors. Patients with Crohn’s disease (CD) or ulcerative colitis (UC) often demonstrate marked disruptions of their gut microbiome. The intestinal microbiota is strongly influenced by diet. The association between the increasing incidence of IBD worldwide and increased consumption of a westernized diet suggests host nutrition may influence the progression or treatment of IBD via the microbiome. Several nutritional therapies have been studied for the treatment of CD and UC. While their mechanisms of action are only partially understood, existing studies do suggest that diet-driven changes in microbial composition and function underlie the diverse mechanisms of nutritional therapy. Despite existing therapies for IBD focusing heavily on immune suppression, nutrition is an important treatment option due to its superior safety profile, potentially low cost, and benefits for growth and development. These benefits are increasingly important to patients. In this review, we will describe the clinical efficacy of the different nutritional therapies that have been described for the treatment of CD and UC. We will also describe the effects of each nutritional therapy on the gut microbiome and summarize the strength of the literature with recommendations for the practicing clinician.

• CD
• CD-TREAT
• CDED
• EEN
• FODMAP
• IBD
• Mediterranean
• PEN
• SCD
• UC
• UCED
• diet
• microbiome
• nutrition

• Child
• Diet
• Disease Management
• Disease Susceptibility
• Enteral Nutrition/methods
• Gastrointestinal Microbiome
• Humans
• Inflammatory Bowel Diseases/diagnosis
• Inflammatory Bowel Diseases/diet therapy
• Inflammatory Bowel Diseases/etiology
• Nutrition Therapy/methods
• Randomized Controlled Trials as Topic
• Risk Factors
• Treatment Outcome

Inflammatory bowel diseases (IBD) are chronic medical disorders characterized by recurrent gastrointestinal inflammation. While the etiology of IBD is still unknown, the pathogenesis of the disease results from perturbations in both gut microbiota and the host immune system. Gut microbiota dysbiosis in IBD is characterized by depleted diversity, reduced abundance of short chain fatty acids (SCFAs) producers and enriched proinflammatory microbes such as adherent/invasive E. coli and H₂S producers. This dysbiosis may contribute to the inflammation through affecting either the immune system or a metabolic pathway. The immune responses to gut microbiota in IBD are extensively discussed. In this review, we highlight the main metabolic pathways that regulate the host-microbiota interaction. We also discuss the reported findings indicating that the microbial dysbiosis during IBD has a potential metabolic impact on colonocytes and this may underlie the disease progression. Moreover, we present the host metabolic defectiveness that adds to the impact of symbiont dysbiosis on the disease progression. This will raise the possibility that gut microbiota dysbiosis associated with IBD results in functional perturbations of host-microbiota interactions, and consequently modulates the disease development. Finally, we shed light on the possible therapeutic approaches of IBD through targeting gut microbiome.

• IBD
• SCFAs (short chain fatty acids)
• dysbiosis
• gut microbiota
• metabolome

• Crohn's disease
• Enteral nutrition
• Gut microbiota
• Inflammatory bowel disease
• Metabolomics
• Microbiome
• Short-chain fatty acids
• Ulcerative colitis

Chronic inflammation plays a central role in the pathophysiology of various non-communicable diseases. Dietary interventions can reduce inflammation, in part due to their effect on the gut microbiome. This systematic review aims to determine the effect of dietary interventions, specifically fiber intake, on chronic inflammatory diseases and the microbiome. It aims to form hypotheses on the potential mediating effects of the microbiome on disease outcomes after dietary changes. Included were clinical trials which performed a dietary intervention with a whole diet change or fiber supplement (>5 g/day) and investigated the gut microbiome in patients diagnosed with chronic inflammatory diseases such as cardiovascular disease (CVD), type 2 diabetes (T2DM), and autoimmune diseases (e.g., rheumatoid arthritis (RA), inflammatory bowel disease (IBD)). The 30 articles which met the inclusion criteria had an overall moderate to high risk of bias and were too heterogeneous to perform a meta-analysis. Dietary interventions were stratified based on fiber intake: low fiber, high fiber, and supplemental fiber. Overall, but most pronounced in patients with T2DM, high-fiber plant-based dietary interventions were consistently more effective at reducing disease-specific outcomes and pathogenic bacteria, as well as increasing microbiome alpha diversity and short-chain fatty acid (SCFA)-producing bacteria, compared to other diets and fiber supplements.

• chronic inflammation
• diet
• fiber
• inflammatory disease
• microbiome

• Autoimmune Diseases/diet therapy
• Bacteria/classification
• Chronic Disease
• Diet
• Gastrointestinal Microbiome
• Humans
• Inflammation/diet therapy

• 555003210 ZonMw

Gastrointestinal symptoms in Crohn’s disease (CD) are common and affect the quality of life of patients; consequently, a growing number of studies have been published on diet interventions in this group. The role of the gut microbiota in the pathogenesis and the progression of inflammatory bowel diseases (IBD), including CD, has been widely discussed. Mainly, a decreased abundance of Firmicutes, species of the Bifidobacterium genus, and the Faecalibacterium prausnitzii species as well as a reduced general diversity have been described. In this review article, we summarize available data on the influence of reduction diets on the microbiome of patients with CD. One of the most frequently used elimination diets in CD patients is the low-FODMAP (Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols) diet. Although many papers show it may reduce abdominal pain, diarrhea, or bloating, it also reduces the intake of prebiotic substances, which can negatively affect the gut microbiota composition, decreasing the abundance of Bifidobacterium species and Faecalibacterium prausnitzii. Other elimination diets used by IBD patients, such as lactose-free or gluten-free diets, have also been shown to disturb the microbial diversity. On the other hand, CDED (Crohn’s disease exclusion diet) with partial enteral nutrition not only induces the remission of CD but also has a positive influence on the microbiota. The impact of diet interventions on the microbiota and, potentially, on the future course of the disease should be considered when nutritional guidelines for IBD patients are designed. Dietetic recommendations should be based not only on the regulation of the symptoms but also on the long-term development of the disease.

• Crohn’s disease
• elimination diets
• microbiome

• Bacteroides
• IBD
• array
• fucose
• microbiota
• oligosaccharide

• UL1 TR000454 NCATS NIH HHS

Inflammatory bowel disease (IBD) is a chronic relapsing–remitting systemic disease of the gastrointestinal tract, characterized by an inflammatory process that requires lifelong treatment. The underlying causes of IBD are still unclear, as this heterogeneous disorder results from a complex interplay between genetic variability, the host immune system and environmental factors. The current knowledge recognizes diet as a risk factor for the development of IBD and attributes a substantial pathogenic role to the intestinal dysbiosis inducing an aberrant mucosal immune response in genetically predisposed individuals. This review focused on the clinical evidence available that considers the impact of some nutrients on IBD onset and the role of different diets in the management of IBD and their effects on the gut microbiota composition. The effects of the Specific Carbohydrate Diet, low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet, gluten free diet, anti-inflammatory diet and Mediterranean diet are investigated with regard to their impact on microbiota and on the evolution of the disease. At present, no clear indications toward a specific diet are available but the assessment of dysbiosis prior to the recommendation of a specific diet should become a standard clinical approach in order to achieve a personalized therapy.

• diet
• gut microbiota
• inflammatory bowel disease
• microbiome
• nutrition

• Inflammatory bowel disease
• crohn’s disease
• diet
• gut microbiome
• plant-based diet
• short chain fatty acids
• ulcerative colitis
• vegetarian diet

Inflammatory bowel disease (IBD) is a chronic complex inflammatory gut pathological condition, examples of which include Crohn’s disease (CD) and ulcerative colitis (UC), which is associated with significant morbidity. Although the etiology of IBD is unknown, gut microbiota alteration (dysbiosis) is considered a novel factor involved in the pathogenesis of IBD. The gut microbiota acts as a metabolic organ and contributes to human health by performing various physiological functions; deviation in the gut flora composition is involved in various disease pathologies, including IBD. This review aims to summarize the current knowledge of gut microbiota alteration in IBD and how this contributes to intestinal inflammation, as well as explore the potential role of gut microbiota-based treatment approaches for the prevention and treatment of IBD. The current literature has clearly demonstrated a perturbation of the gut microbiota in IBD patients and mice colitis models, but a clear causal link of cause and effect has not yet been presented. In addition, gut microbiota-based therapeutic approaches have also shown good evidence of their effects in the amelioration of colitis in animal models (mice) and IBD patients, which indicates that gut flora might be a new promising therapeutic target for the treatment of IBD. However, insufficient data and confusing results from previous studies have led to a failure to define a core microbiome associated with IBD and the hidden mechanism of pathogenesis, which suggests that well-designed randomized control trials and mouse models are required for further research. In addition, a better understanding of this ecosystem will also determine the role of prebiotics and probiotics as therapeutic agents in the management of IBD.

• fecal microbiota transplantation (FMT)
• gut microbiota
• inflammatory bowel disease
• pathogenesis
• prebiotics
• probiotics
• synbiotics

• Diet
• carbohydrate
• inflammatory bowel disease
• microbiome
• nutrient

• Diet
• Dietary practices
• Guidelines
• Inflammatory bowel disease

• Asia
• Consensus
• Diet
• Dietary Fats
• Dietary Proteins/administration & dosage
• Energy Intake
• Humans
• Inflammatory Bowel Diseases/complications
• Inflammatory Bowel Diseases/diet therapy
• Inflammatory Bowel Diseases/etiology
• Inflammatory Bowel Diseases/surgery
• Malnutrition/diagnosis
• Malnutrition/etiology
• Nutrition Assessment
• Postoperative Period

• . Abbott India Ltd

• Antiretrovirals
• HIV
• Male partner
• Non-disclosure
• PMTCT

• Crohn’s disease
• Diet
• inflammatory bowel disease
• nutrition
• ulcerative colitis

Diet has been speculated to be a factor in the pathogenesis of inflammatory bowel disease and may be an important factor in managing disease symptoms. Patients manipulate their diet in attempt to control symptoms, often leading to the adoption of inappropriately restrictive diets, which places them at risk for nutritional complications. Health professionals struggle to provide evidence-based nutrition guidance to patients due to an overall lack of uniformity or clarity amongst research studies. Well-designed diet studies are urgently needed to create an enhanced understanding of the role diet plays in the management of inflammatory bowel disease. The aim of this review is to summarize the current data available on dietary management of inflammatory bowel disease and to demonstrate that dietary modulation may be an important consideration in managing disease. By addressing the relevance of diet in inflammatory bowel disease, health professionals are able to better support patients and collaborate with dietitians to improve nutrition therapy.

• Crohn’s disease
• diet
• diet therapy
• inflammatory bowel disease
• nutrition
• nutrition therapy
• ulcerative colitis

• Databases, Factual
• Diet
• Evidence-Based Medicine
• Humans
• Inflammatory Bowel Diseases/diet therapy
• Meta-Analysis as Topic
• Nutritional Support
• Observational Studies as Topic
• Randomized Controlled Trials as Topic
• Recommended Dietary Allowances

• Crohn’s disease
• barrier function
• inflammatory bowel disease
• leaky gut
• microbiome

• GWAS
• biologic therapy
• micro-RNA
• microbiota
• stem cell therapy

• CAM
• Complementary and alternative medicine
• Crohn's disease
• Dietary therapy
• IBD
• Inflammatory bowel disease
• Low complex carbohydrate
• Nutritional therapy
• Pediatrics
• Specific carbohydrate diet
• Ulcerative colitis

• cats
• dermatophytes
• dogs
• humans
• zoonotic infections