Gut microbiome in chronic rheumatic and inflammatory bowel diseases: Similarities and differences

AbstractBackground & AimsInflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts.MethodsUsing the IL-10 gene-deficient (IL-10 KO) murine model where early life dysbiosis from antibiotic (cefoperozone, CPZ) treated dams vertically-transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to eventual clinical outcomes.ResultsCompared to controls, offspring acquiring maternal CPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership both in bacteriome and mycobiome that were associated with alterations in specific functional subsystems. Furthermore, among IL-10 KO offspring from CPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome.ConclusionsOur findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD.SynopsisCurrently, predictive markers for the development and course of inflammatory bowel diseases (IBD) are not available. This study supports the notion that gut microbiome metagenomic profiles could be developed into a useful tool to assess risk and manage human IBD.

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FUT2 deficiency may influence the pathogenesis of inflammatory bowel diseases through gut microbiome

The FASEB Journal ◽

10.1096/fasebj.2020.34.s1.02866 ◽

2020 ◽

Vol 34 (S1) ◽

pp. 1-1

Author(s):

Sijing Cheng ◽

Jun Hu ◽

Xianrui Wu ◽

Na Jiao ◽

Yichen Li ◽

...

Keyword(s):

Inflammatory Bowel Diseases ◽

Gut Microbiome ◽

Bowel Diseases ◽

Inflammatory Bowel

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Effects of a Novel Probiotic Combination on Pathogenic Bacterial-Fungal Polymicrobial Biofilms

mBio ◽

10.1128/mbio.00338-19 ◽

2019 ◽

Vol 10 (2) ◽

Cited By ~ 14

Author(s):

Christopher L. Hager ◽

Nancy Isham ◽

Kory P. Schrom ◽

Jyotsna Chandra ◽

Thomas McCormick ◽

...

Keyword(s):

Inflammatory Bowel Diseases ◽

Gut Microbiome ◽

Biofilm Formation ◽

Bacterial Species ◽

Bacterial Flora ◽

Confocal Scanning Laser Microscopy ◽

Antibiofilm Activity ◽

Content Type ◽

Bowel Diseases ◽

Inflammatory Bowel

ABSTRACTDysbiosis of the gut microbiome has been implicated in inflammatory bowel diseases. We have shown that levels ofCandida tropicalis, along with those ofEscherichia coliandSerratia marcescens, are significantly elevated in Crohn’s disease (CD) patients. Here, we evaluated the ability of a novel probiotic to prevent and treat polymicrobial biofilms (PMB) formed byC. tropicaliswithE. coliandS. marcescens. SinceCandida albicanshas been reported to be elevated in CD patients, we investigated the interactions ofC. albicanswith these bacterial species in biofilm formation. We determined whether the interaction betweenCandidaspp. and bacteria is specific by usingTrichosporon inkinandSaccharomyces fibuligeraas comparators. Additionally, the effects of probiotics onC. albicansgermination and biofilm formation were determined. To determine the ability of the probiotic to prevent or treat mature biofilms, probiotic filtrate was added to the PMB at early (prevention) and mature (treatment) phases. Biofilm thickness and architecture were assessed by confocal scanning laser microscopy. The effects of the probiotic on germination were evaluated in the presence of serum. Exposure ofC. tropicalisPMB to probiotic filtrate reduced biofilm matrix, decreased thickness, and inhibited hyphal formation. We showed thatC. albicansorC. tropicalisformed significantly thicker PMB than control biofilms, indicating that this interaction isCandidaspecific. Treatment with probiotic filtrate inhibitedC. albicansgermination and prevented/treatedC. albicansPMB. The designed probiotic may have utility in the management of biofilm-associated gastrointestinal diseases such as Crohn’s and colorectal cancer.IMPORTANCEThe effects of diversity of the gut microbiome on inflammation have centered mainly on bacterial flora. Recent research has implicated fungal species and their interactions with other organisms in the inflammatory process. New ways to restore microbial balance in the gut are being explored. Our goal was to identify beneficial probiotic strains that would antagonize these fungal and bacterial pathogens that are elevated in the inflamed gut, and which also have antibiofilm activity. Fungus-bacterium correlation analysis allowed us to identify candidate probiotic species that can antagonize microbial pathogens, which we subsequently incorporated into a novel probiotic formulation. Amylase, which is known to have some antibiofilm activity, was also added to the probiotic mixture. This novel probiotic may have utility for the management of inflammatory bowel diseases by disrupting polymicrobial biofilm formation.

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605 THE IMPACT OF FUT2 LOSS-OF-FUNCTION MUTATION ON THE PATHOGENESIS OF INFLAMMATORY BOWEL DISEASES MEDIATED BY THE GUT MICROBIOME

Gastroenterology ◽

10.1016/s0016-5085(21)01037-4 ◽

2021 ◽

Vol 160 (6) ◽

pp. S-119

Author(s):

Sijing Cheng ◽

Jun Hu ◽

Xianrui Wu ◽

Na Jiao ◽

Yichen Li ◽

...

Keyword(s):

Inflammatory Bowel Diseases ◽

Gut Microbiome ◽

Loss Of Function ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

The Impact

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Diet, Gut Microbiome and Epigenetics: Emerging Links with Inflammatory Bowel Diseases and Prospects for Management and Prevention

10.20944/preprints201707.0039.v1 ◽

2017 ◽

Author(s):

Krasimira Aleksandrova ◽

Beatriz Romero ◽

Vicent Hernandez

Keyword(s):

Inflammatory Bowel Diseases ◽

Gut Microbiome ◽

Current Knowledge ◽

Health Concern ◽

Dietary Recommendations ◽

Nutritional Interventions ◽

Exclusive Enteral Nutrition ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Anti Inflammatory

Inflammatory bowel diseases (IBD) represent a growing public health concern due to increasing incidence worldwide. The current notion on the pathogenesis of IBD is that genetically susceptible individuals develop intolerance to dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental triggers. Among the environmental factors associated to IBD, diet plays an important role in modulating the gut microbiome, influencing epigenetic changes and, therefore, could be applied as a therapeutic tool to improve the disease course. Nevertheless, the current dietary recommendations for disease prevention and management are scarce and of weak evidence. This review summarizes the current knowledge on the complex interactions among diet, microbiome and epigenetics in IBD. Whereas over-abundance of calories and some macronutrients increases gut inflammation, several micronutrients have the potential to modulate it. Immunonutrition has emerged as a new concept putting forward the importance of vitamins such as vitamins A, C, E, D, folic acid and beta-carotene and trace elements such as zinc, selenium, manganese and iron. However, when assessed in clinical trials, specific micronutrients exerted a limited benefit. Beyond nutrients, anti-inflammatory dietary patterns as a complex intervention approach have become popular over the recent years. Hence, exclusive enteral nutrition in pediatric Crohn’s disease is the only nutritional intervention currently recommended as a first-line therapy. Other nutritional interventions or specific diets including the Specific Carbohydrate Diet, the low fermentable oligosaccharides, disaccharides, monosaccharides, and polyol diet and most recently the Mediterranean diet have shown strong anti-inflammatory properties and provide a promise for improving disease symptoms. Definitely, more work is required to evaluate the role of individual food compounds and complex nutritional interventions with potential to decrease inflammation as means for prevention and management of IBD.

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Diet, Gut Microbiome and Epigenetics: Emerging Links with Inflammatory Bowel Diseases and Prospects for Management and Prevention

Nutrients ◽

10.3390/nu9090962 ◽

2017 ◽

Vol 9 (9) ◽

pp. 962 ◽

Cited By ~ 48

Author(s):

Krasimira Aleksandrova ◽

Beatriz Romero-Mosquera ◽

Vicent Hernandez

Keyword(s):

Inflammatory Bowel Diseases ◽

Gut Microbiome ◽

Bowel Diseases ◽

Inflammatory Bowel

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Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00360.2020 ◽

2021 ◽

Author(s):

Ishan Manandhar ◽

Ahmad Alimadadi ◽

Sachin Aryal ◽

Patricia B. Munroe ◽

Bina Joe ◽

...

Keyword(s):

Machine Learning ◽

Inflammatory Bowel Diseases ◽

Gut Microbiome ◽

Supervised Machine Learning ◽

Metagenomic Data ◽

Predictive Diagnostics ◽

Operational Taxonomic Units ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Microbiome Data

Despite the availability of various diagnostic tests for inflammatory bowel diseases (IBD), misdiagnosis of IBD occurs frequently, and thus there is a clinical need to further improve the diagnosis of IBD. As gut dysbiosis is reported in IBD patients, we hypothesized that supervised machine learning (ML) could be used to analyze gut microbiome data for predictive diagnostics of IBD. To test our hypothesis, fecal 16S metagenomic data of 729 IBD and 700 non-IBD subjects from the American Gut Project were analyzed using five different ML algorithms. Fifty differential bacterial taxa were identified (LEfSe: LDA > 3) between the IBD and non-IBD groups, and ML classifications trained with these taxonomic features using random forest (RF) achieved a testing AUC of ~0.80. Next, we tested if operational taxonomic units (OTUs), instead of bacterial taxa, could be used as ML features for diagnostic classification of IBD. Top 500 high-variance OTUs were used for ML training and an improved testing AUC of ~0.82 (RF) was achieved. Lastly, we tested if supervised ML could be used for differentiating Crohn's disease (CD) and ulcerative colitis (UC). Using 331 CD and 141 UC samples, 117 differential bacterial taxa (LEfSe: LDA > 3) were identified, and the RF model trained with differential taxonomic features or high-variance OTU features achieved a testing AUC > 0.90. In summary, our study demonstrates the promising potential of artificial intelligence via supervised ML modeling for predictive diagnostics of IBD using gut microbiome data.

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