Inflammatory Bowel Disease-Associated Gut Commensals Degrade Components of the Extracellular Matrix

Porras, Ana Maria; Zhou, Hao; Shi, Qiaojuan; Xiao, Xieyue; ,; Longman, Randy; Brito, Ilana Lauren

doi:10.1128/mbio.02201-22

Cited by 13 publications

(6 citation statements)

References 98 publications

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“…Regarding microbiota, IBD patients display reduced microbial diversity, decreased relative abundance of Firmicutes and an expansion of Proteobacteria and Bacteroidetes ( 14–16 ). Dysbiosis and relapse-related microbiomes have been identified ( 41 ), and the effects of many specific bacterial strains on IBD have been demonstrated in vivo ( 42 , 43 ). Notably, most studies have utilized a cross-sectional design, with samples collected at a single time point.…”

Section: Discussionmentioning

confidence: 99%

An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)

Kai,

Qingsong,

Kejia

et al. 2024

Database

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IBD, including ulcerative colitis and Crohn’s disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources. Valuable and comprehensive IBD-related data were collected from PubMed, Google, GMrepo, gutMega, gutMDisorder, Single Cell Portal and other sources. Then, the data were systematically sorted, and these resources were manually curated. We systematically sorted and cataloged more than 320 unique risk SNPs associated with IBD in the SNP section. We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related microbiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. We introduced two interactive single-cell data plug-in units that provided data visualization based on cells and genes. Finally, we listed 18 significant IBD web resources, such as the official European Crohn’s and Colitis Organisation and International Organization for the Study of IBD websites, IBD scoring tools, IBD genetic and multi-omics resources, IBD biobanks and other useful research resources. The IBDIRP website is the first integrated resource for global IBD researchers. This portal will help researchers by providing comprehensive knowledge and enabling them to reinforce the multidimensional impression of IBD. The IBDIRP website is accessible via www.ibdirp.com Database URL: www.ibdirp.com.

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Section: Discussionmentioning

confidence: 99%

An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)

Kai,

Qingsong,

Kejia

et al. 2024

Database

View full text Add to dashboard Cite

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“…Hyaluronan is known to be deposited in the extracellular matrix (ECM) at inflamed sites, and is ac3vely involved in the recruitment of immune cells (Petrey & de la MoCe, 2019). It was also previously shown that IBD-associated bacteria are able to degrade ECM components, including hyaluronan (Porras et al, 2022). How these dynamics influence IBD onset and progression needs to be inves3gated.…”

Section: Discussionmentioning

confidence: 99%

Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease

Rühlemann,

Waschina,

Wacker

et al. 2023

Preprint

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Inflammatory bowel disease (IBD) is associated with dysbiotic microbiomes. However, whether microbiomes of family members of IBD patients harbour microbial disease signatures of IBD is unknown. Here, we generate shotgun metagenomic data of an IBD family cohort and treatment-naive IBD cases, which we combine with published IBD metagenomes, to perform a meta-analysis of IBD-microbiome associations. Our study reveals microbial shifts that are specific to IBD or IBD subtypes (Crohn’s disease and ulcerative colitis). We find that IBD cohorts share signatures of association with disease irrespective of geography, and we report novel species-level identifications of microbial taxa that are universal markers of Crohn’s disease. We further demonstrate that the microbiome of healthy family members at high risk for IBD represent transitional states between the microbiome of unrelated healthy controls and IBD cases, and harbor diversity, compositional and ecological features that are also observed among IBD microbiomes. Overall, our study provides valuable insights into the intricate relationship between the gut microbiome and IBD, with implications for better predicting disease onset among individuals with high susceptibility for IBD.

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“…Consequently, fibre-deprived diets have been shown to lead to erosion of the mucus layer as bacteria shift their metabolism to mucus utilisation, which in turn facilitates gut microbes to get closer to the epithelium 3,4 . Compromised barrier integrity is an important feature of gastrointestinal diseases, such as inflammatory bowel disease (IBD) and colorectal cancer (CRC), in which gut microbial CAZymes involved in degradation of host extracellular matrix and mucins are enriched as shown by metagenomic analyses 7,8 , respectively. Given the central role of the gut microbiome as a mediator of dietary effects on host health, understanding how Western lifestyle shapes the CAZyme repertoire can yield important insights into disease processes.…”

Section: Introductionmentioning

confidence: 99%

Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman

Ducarmon,

Karcher,

Tytgat

et al. 2024

Preprint

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Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but bioinformatics tools for CAZyme profiling and interpretation of substrate preferences in microbial community data are lacking. To address this, we developed a CAZyme profiler (Cayman) and a hierarchical substrate annotation scheme. Leveraging these, we genomically survey CAZymes in human gut microbes (n=107,683 genomes), which suggests novel mucin-foraging species. In a subsequent meta-analysis of CAZyme repertoires in Western versus non-Western gut metagenomes (n=4,281) we find that non-Western metagenomes are richer in fibre-degrading CAZymes despite lower overall CAZyme richness. We additionally pinpoint the taxonomic drivers underlying these CAZyme community shifts. A second meta-analysis comparing colorectal cancer patients (CRC) to controls (n=1,998) shows that CRC metagenomes are deprived of dietary fibre-targeting, but enriched in glycosaminoglycan-targeting CAZymes. A genomic analysis of co-localizing CAZyme domains predicts novel substrates for CRC-enriched CAZymes. Cayman is broadly applicable across microbial communities and freely available fromhttps://github.com/zellerlab/cayman.

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Inflammatory Bowel Disease-Associated Gut Commensals Degrade Components of the Extracellular Matrix

Abstract: Healthy gut epithelial cells form a barrier that keeps bacteria and other substances from entering the blood or tissues of the body. Those cells sit on scaffolding that maintains the structure of the gut and informs our immune system about the integrity of this barrier.

Cited by 13 publications

References 98 publications

An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)

An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)

Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease

Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman

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