Society: AGA

Background The gut microbiome is central to Crohn’s disease (CD) pathogenesis but the relative contribution of different environmental factors to disease compositional variation is unknown. We determined the impact of environmental factors and diet on microbiome variation in this international study.
Methods 480 stool samples from 240 CD patients and 240 healthy controls from regions of different epidemiologic stages: Australia (Compounding prevalence; AUS: 97 CD; 77 controls), Hong Kong (Acceleration in incidence; HK: 90 CD; 63 controls) and Mainland China (Emergence in incidence; MC: 53 CD;100 controls) were studied. Demographic, clinical and 3 food intake questionnaires (processed food intake in early life, recent (last 12 months) and current (last 3-days)) were obtained from all subjects. Fecal microbiota was assessed by shotgun metagenomic sequencing. Dysbiosis score was defined as the median Bray-Curtis dissimilarity to the reference control group. Adonis was performed to rank the effect of disease-associated parameters, clinical metadata, dietary intake and geography on overall microbial composition.
Results Microbiota diversity was significantly reduced in CD compared with controls in all three geographical cohorts (all p<0.05). Beta diversity analysis showed a significant disease-associated shift along principal components for active CD followed by inactive CD away from controls (p<0.001). Gut microbiome structure of HK subjects were intermediate between that of AUS and MC. CD patients in MC had the highest dysbiosis score compared with AUS and HK, but dissimilarity scores were no different between controls in AUS, HK and MC (Fig 1A). Geography had the greatest impact on microbiota variance followed by disease diagnosis and bowel resection history. Additionally, disease complications, feeding pattern and processed food exposure at early age were significantly correlated with microbiota variance. CD patients who consumed more processed food at early age had a higher dysbiosis score than those who did not (p<0.05). Amongst all diet types consumed, current fiber intake was the most dominant in contributing to microbiome variance. Other major dietary factors that correlated with microbiome variance belonged to fat (polyunsatuated fat, saturated fat, monounsaturated fat and cholesterol) and vitamins (Fig 1B). The proportion of dietary factor-associated species in CD was lower than that of controls, suggesting that gut microbiota in controls were more susceptible to the effects of diet.
Conclusion Geography especially regions transiting through different epidemiologic stages of disease is a dominant driver of gut microbiome variation, followed by Crohn’s disease diagnosis. The Crohn’s disease microbiota is also shaped and influenced by current dietary pattern and early life food additive intake.

This work is supported by Helmsley Charitable Trust

<b>Fig1. (A)</b> Distribution of stool dysbiosis scores in relation to presence of Crohn’s disease (median Bray-Curtis dissimilarity between a sample and healthy control samples). <b>(B) </b>Current dietary factors impact on microbiota variance. Adjusted permutational multivariate analysis was performed to rank the variances. *<i>p</i><0.05; **<i>p</i><0.01; ***<i>p</i><0.001.

Fig1. (A) Distribution of stool dysbiosis scores in relation to presence of Crohn’s disease (median Bray-Curtis dissimilarity between a sample and healthy control samples). (B) Current dietary factors impact on microbiota variance. Adjusted permutational multivariate analysis was performed to rank the variances. *p<0.05; **p<0.01; ***p<0.001.

Yinglei Miao

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