Correction to: The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1

Imhann, Floris; Velde, K. Joeri van der; Barbieri, Ruggero; Alberts, Rudi; Voskuil, Michiel; Vila, Arnau Vich; Collij, Valerie; Spekhorst, Lieke M.; Sloot, Kimberley W. J. van der; Peters, Vera; Dullemen, Hendrik M. van; Visschedijk, Marijn C.; Festen, Eleonora A. M.; Swertz, Morris A.; Dijkstra, Gerard; Weersma, Rinse K.

doi:10.1186/s12876-019-0938-8

Cited by 11 publications

(9 citation statements)

References 1 publication

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“…Indeed, intestinal microbiota are increasingly recognized for their potential as IBD biomarkers and treatment targets, yet in-depth knowledge of how differences in microbe-host interactions shape CD location subtypes is lacking [ 8 , 9 ]. This is largely due to limitations such as small patient cohorts, limited metadata, reliance on patient-reported indices in place of endoscopic measurements, and a lack of comprehensive host-gut microbe profiling [ 10 – 13 ].…”

Section: Introductionmentioning

confidence: 99%

Location-specific signatures of Crohn’s disease at a multi-omics scale

et al. 2022

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Background Crohn’s disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum or colon) or a combination of locations (ileocolonic). To date, a comprehensive understanding of how isolated CD subtypes influence molecular profiles remains outstanding. To address this, we sought to define CD location signatures by leveraging a large cross-sectional feature set captured from the stool of over 200 IBD patients and healthy controls using metaproteomics, shotgun metagenomics, 16S rRNA sequencing, metabolomic profiling, and host genetics paired with clinical endoscopic assessments. Results Neither metagenomic nor host genetics alone distinguished CD location subtypes. In contrast, ileal and colonic CD were distinguished using mass spectrometry-based methods (metabolomics or metaproteomics) or a combined multi-omic feature set. This multi-omic feature set revealed colonic CD was strongly associated with neutrophil-related proteins. Additionally, colonic CD displayed a disease-severity-related association with Bacteroides vulgatus. Colonic CD and ulcerative colitis profiles harbored strikingly similar feature enrichments compared to ileal CD, including neutrophil-related protein enrichments. Compared to colonic CD, ileal CD profiles displayed increased primary and secondary bile acid levels and concomitant shifts in taxa with noted sensitivities such as Faecalibacterium prausnitzii or affinities for bile acid-rich environments, including Gammaproteobacteria and Blautia sp. Having shown robust molecular and microbial distinctions tied to CD locations, we leveraged these profiles to generate location-specific disease severity biomarkers that surpass the performance of Calprotectin. Conclusions When compared using multi-omics features, colonic- and ileal-isolated CD subtypes display striking differences that suggest separate location-specific pathologies. Colonic CD’s strong similarity to ulcerative colitis, including neutrophil and Bacteroides vulgatus involvement, is also evidence of a shared pathology for colonic-isolated IBD subtypes, while ileal CD maintains a unique, bile acid-driven profile. More broadly, this study demonstrates the power of multi-omics approaches for IBD biomarker discovery and elucidating the underlying biology.

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Section: Introductionmentioning

confidence: 99%

Location-specific signatures of Crohn’s disease at a multi-omics scale

et al. 2022

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“…To study the small intestinal microbiota and its potential implications in IBD, two independent Dutch cohorts were used: 1] the 1000IBD cohort 14 established in the IBD centre at the University Medical Center Groningen [UMCG], The Netherlands; and 2] Lifelines DEEP, 15 a general population cohort from the northern provinces of The Netherlands.…”

Section: Methodsmentioning

confidence: 99%

“…All faecal samples were collected according to the same protocol, which has been previously described. 14 , 15 Furthermore, all samples were collected during the same time period, handled by the same group of technicians, and processed using the same protocols and machines. In short, all participants were asked to collect and freeze [at -20 o C] their faecal samples at home, within 15 min of faeces production.…”

Section: Methodsmentioning

confidence: 99%

The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease

Ruigrok

Collij

Sureda

et al. 2021

Journal of Crohn's and Colitis

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Background and Aims The human gastrointestinal tract harbours distinct microbial communities essential for health. Little is known about small intestinal communities, despite the small intestine playing a fundamental role in nutrient absorption and host-microbe immune homeostasis. We aimed to explore the small intestine microbial composition and metabolic potential, in the context of inflammatory bowel disease (IBD). Methods Metagenomes derived from faecal samples and extensive phenotypes were collected from 57 individuals with an ileostomy or ileoanal pouch, and compared with 1178 general population and 478 IBD faecal metagenomes. Microbiome features were identified using MetaPhAn2 and HUMAnN2, and association analyses were performed using multivariate linear regression. Results Small intestinal samples had a significantly lower bacterial diversity, compared with the general population and, to a lesser extent, IBD samples. Comparing bacterial composition, small intestinal samples clustered furthest from general population samples and closest to IBD samples with intestinal resections. Veillonella atypica, Streptococcus salivarius and Actinomyces graevenitzii were among the species significantly enriched in the small intestine. Predicted metabolic pathways in the small intestine are predominantly involved in simple carbohydrate and energy metabolism, but also suggest a higher proinflammatory potential. Conclusion We described the bacterial composition and metabolic potential of the small intestinal microbiota. The colonic microbiome of IBD patients, particularly with intestinal resections, showed resemblance to that of the small intestine. Moreover, several features characterising the small intestinal microbiome have been previously associated with IBD. These results highlight the importance of studying the small intestinal microbiota to gain new insight into disease pathogenesis.

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“…5 Although the pathogenesis of UC is unclear, it is considered to be closely associated with many factors such as diet, environmental factors, and metabolism, and, in particular, intestinal immune dysfunction, gastrointestinal mucosal damage, and intestinal flora disorders mediated by intestinal infection. 6 At present, anti-inflammatory and immunomodulatory agents are the mainstays for the treatment of UC, supplemented by biological agents, such as infliximab, adalimumab and golimumab. 7 It has been demonstrated that the combination of biological and immunomodulatory therapy is superior to the monotherapy at reducing the risk of IBD-related complications.…”

Section: Introductionmentioning

confidence: 99%

Exopolysaccharide from Lactobacillus rhamnosusZFM231 alleviates DSS‐induced colitis in mice by regulating gut microbiota

et al. 2022

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BACKGROUND The exopolysaccharides (EPS) produced by Lactobacillus and other probiotics are associated with many benefits, such as immune regulation, antioxidant properties, antitumor effect, and regulation of intestinal microbe homeostasis. In the present study, the modulatory effect of EPS produced by Lactobacillus rhamnosus ZFM231 on the intestinal flora of mice with inflammatory bowel disease induced by dextran sulfate solution was investigated. RESULTS Results indicated that weight loss, colonic length, the disease activity index score and colonic tissue damage in mice were significantly improved by EPS treatment. Compared with the model group, in the EPS‐treated group, the diversity of and the composition of gut microbiota at both phylum and genus levels were found to recover to the levels of normal group, indicating the effective modulation on gut microbiota by EPS; short‐chain fatty acids, including acetic acid, propionic acid and butyric acid produced by intestinal microbial metabolism, increased significantly; the level of anti‐inflammatory factor transforning growth factor‐β significantly increased and the level of pro‐inflammatory factor tumor necrosis factor‐α significantly decreased in the colonic cells of EPS‐treated mice. CONCLUSION It is clear that EPS produced by L. rhamnosus ZFM231 could find application in functional foods with the property of anti‐ulcerative colitis. The experimental results provide new insights into the probiotic effect of EPS. © 2022 Society of Chemical Industry.

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Correction to: The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1

Cited by 11 publications

References 1 publication

Location-specific signatures of Crohn’s disease at a multi-omics scale

Location-specific signatures of Crohn’s disease at a multi-omics scale

The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease

Exopolysaccharide from Lactobacillus rhamnosusZFM231 alleviates DSS‐induced colitis in mice by regulating gut microbiota

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