Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells

Roy, Urmi; Galvez, Eric; Iljazović, Aida; Lesker, Till Robin; Błażejewski, Adrian J.; Pils, Marina C.; Heise, Ulrike; Huber, Samuel; Flavell, Richard A.; Strowig, Till

doi:10.1016/j.celrep.2017.09.097

Cited by 120 publications

(99 citation statements)

References 48 publications

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“…Also, the FMD treatment in the current study lasts 4 days and is repeated multiple times, compared to the single, water-only fasting lasting between 36–48 hours in previous studies. Notably, Paraprevotellaceae, associated with water-only fasting but not FMD treatment, has been previously regarded as pro-inflammatory in the context of IBD, with one study finding it to be especially enriched in mice with severe colitis (Roy et al, 2017). Another study also found Paraprevotellaceae abundance increased in rats with increased pro-inflammatory cytokines, such as IL-13, in colonic tissue (Shatzkes et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology

et al. 2019

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SUMMARY Dietary interventions are potentially effective therapies for inflammatory bowel diseases (IBDs). We tested the effect of 4-day fasting-mimicking diet (FMD) cycles on a chronic dextran sodium sulfate (DSS)-induced murine model resulting in symptoms and pathology associated with IBD. These FMD cycles reduced intestinal inflammation, increased stem cell number, stimulated protective gut microbiota, and reversed intestinal pathology caused by DSS, whereas water-only fasting increased regenerative and reduced inflammatory markers without reversing pathology. Transplants of Lactobacillus or fecal microbiota from DSS- and FMD-treated mice reversed DSS-induced colon shortening, reduced inflammation, and increased colonic stem cells. In a clinical trial, three FMD cycles reduced markers associated with systemic inflammation. The effect of FMD cycles on microbiota composition, immune cell profile, intestinal stem cell levels and the reversal of pathology associated with IBD in mice, and the anti-inflammatory effects demonstrated in a clinical trial show promise for FMD cycles to ameliorate IBD-associated inflammation in humans.

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Section: Discussionmentioning

confidence: 99%

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology

et al. 2019

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“…We also provide a multi-sample mouse gut data set for software developers to benchmark against. For 64 16S rRNA samples from the mouse gut [17], we simulated 5 Gb of Illumina and PacBio reads each. The mice were obtained from 12 different vendors and the samples characterized by 16S V4 amplicon sequencing (OTU mapping file in the supplement).…”

Section: Simulating Environment-specific Data Setsmentioning

confidence: 99%

“…We demonstrate the usability and utility of CAMISIM with several applications. We generated complex, multi-replicate benchmark data sets from taxonomic profiles of human and mouse gut microbiomes [1,17]. We also simulated thousands of small "minimally challenging metagenomes" to characterize the effect of varying sequencing coverage, evolutionary divergence of genomes, and sequencing error profiles on the popular MEGAHIT [18] and metaSPAdes [19] assemblers.…”

Section: Introductionmentioning

confidence: 99%

CAMISIM: Simulating metagenomes and microbial communities

Fritz

Hofmann

Majda

et al. 2018

Preprint

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Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. Here, we describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series and differential abundance studies, includes real and simulated strain-level diversity, and generates second and third generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT and metaSPAdes, on several thousand small data sets generated with CAMISIM. CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with truth standards for method evaluation. All data sets and the software are freely available at: https://github.com/CAMI-challenge/CAMISIM

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“…Previous studies have also reported on the link between neutrophils and the gut microbiome [18][19][20][21]. A study by Li et al isolated peripheral neutrophils from participants with the aim of identifying and characterising neutrophil-associated microbiomes [22].…”

Section: Cells; T Cells: T Lymphocytes; B Cells: Bmentioning

confidence: 99%

Correlation-based network analysis for biomarkers in obesity

Chen

West

Zhang

et al. 2018

2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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Background: Obesity is associated with chronic activation of the immune system and an altered gut microbiome, leading to increased risk of chronic disease development. As yet, no biomarkers have been found to distinguish individuals at greater risk of obesity-related disease. The aim of this study was to explore a correlationbased network approach to find existing patterns of immunemicrobiome interactions in obesity.Results: The current study performed correlation-based network analysis on five different datasets obtained from 11 obese and 12 healthy weight men: anthropometric measures, metabolic measures, immune cell abundance, serum cytokine concentration, and gut microbial composition. The obese cohort had a denser network (total number of edges, n = 237) compared to the healthy network (n = 190). Within the obese network, immune cell abundance was found to be correlated to biomarkers from all four other datasets while in the healthy network, immune cell abundance was only correlated with serum cytokine concentration and gut microbial composition. Neutrophils within the obese immune cell abundance group were correlated with the most number of other biomarkers. Two different types of neutrophil measurements were taken, an abundance measure from immune cell gene expression and a whole blood count, with correlations to 10 and 6 other biomarkers, respectively. From the combined number of 16 biomarkers, 4 biomarkers were correlated between the two measurements: Anaerostipes abundance, Blautia abundance, Escherichia/Shigella abundance and Flavonifractor abundance. Conclusion: The obesity-related dysregulation of immune biomarkers was suggested by the high connectivity of immune cells in the obese network compared to the healthy network.Our study also revealed the importance of integrated analysis to uncover immune-microbiome interactions in obesity that are likely to have been missed in univariate analysis.

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Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells

Cited by 120 publications

References 48 publications

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology

CAMISIM: Simulating metagenomes and microbial communities

Correlation-based network analysis for biomarkers in obesity

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