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Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.

Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K - Am. J. Gastroenterol. (2015)

Bottom Line: OTUs that correlated positively or negatively with calprotectin decreased during EEN.The abundance of genes involved in biotin (P=0.005) and thiamine biosynthesis decreased (P=0.017), whereas those involved in spermidine/putrescine biosynthesis (P=0.031), or the shikimate pathway (P=0.058), increased during EEN.Disease improvement following treatment with EEN is associated with extensive modulation of the gut microbiome.

View Article: PubMed Central - PubMed

Affiliation: Warwick Medical School, University of Warwick, Warwick, UK.

ABSTRACT

Objectives: Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into the microbial origins of Crohn's disease (CD).

Methods: Fecal samples (n=117) were collected from 23 CD and 21 healthy children. From CD children fecal samples were collected before, during EEN, and when patients returned to their habitual diets. Microbiota composition and functional capacity were characterized using sequencing of the 16S rRNA gene and shotgun metagenomics.

Results: Microbial diversity was lower in CD than controls before EEN (P=0.006); differences were observed in 36 genera, 141 operational taxonomic units (OTUs), and 44 oligotypes. During EEN, the microbial diversity of CD children further decreased, and the community structure became even more dissimilar than that of controls. Every 10 days on EEN, 0.6 genus diversity equivalents were lost; 34 genera decreased and one increased during EEN. Fecal calprotectin correlated with 35 OTUs, 14 of which accounted for 78% of its variation. OTUs that correlated positively or negatively with calprotectin decreased during EEN. The microbiota of CD patients had a broader functional capacity than healthy controls, but diversity decreased with EEN. Genes involved in membrane transport, sulfur reduction, and nutrient biosynthesis differed between patients and controls. The abundance of genes involved in biotin (P=0.005) and thiamine biosynthesis decreased (P=0.017), whereas those involved in spermidine/putrescine biosynthesis (P=0.031), or the shikimate pathway (P=0.058), increased during EEN.

Conclusions: Disease improvement following treatment with EEN is associated with extensive modulation of the gut microbiome.

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Related in: MedlinePlus

KEGG module Shannon diversity for each EEN sample time and participant (a) and log relative abundance of modules that significantly changed during EEN (b). (a) Diversity was not impacted during EEN (P=0.260), but there was a difference between H and CD before EEN (P=0.05). (b): M00123, biotin biosynthesis, P=0.005; M00127, thiamine biosynthesis, P=0.0166; M00299, spermidine/putrescine transport system, P=0.0307; M00022, shikimate pathway, P=0.058. P-values are based on linear regressions of KEGG module log relative abundance against days on EEN with subject-dependent intercepts for 11 children with at least two shotgun metagenome samples. Benjamini–Hochberg false discovery rate was used to adjust significance values for multiple comparisons. All modules with a mean abundance >1.0 × 10−9 were tested; only those with adjusted P-value <0.1 are shown. A full color version of this figure is available at the American Journal of Gastroenterology journal online. CD, Crohn's disease; EEN, exclusive enteral nutrition; KEGG, Kyoto Encyclopedia of Genes and Genomes.
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fig4: KEGG module Shannon diversity for each EEN sample time and participant (a) and log relative abundance of modules that significantly changed during EEN (b). (a) Diversity was not impacted during EEN (P=0.260), but there was a difference between H and CD before EEN (P=0.05). (b): M00123, biotin biosynthesis, P=0.005; M00127, thiamine biosynthesis, P=0.0166; M00299, spermidine/putrescine transport system, P=0.0307; M00022, shikimate pathway, P=0.058. P-values are based on linear regressions of KEGG module log relative abundance against days on EEN with subject-dependent intercepts for 11 children with at least two shotgun metagenome samples. Benjamini–Hochberg false discovery rate was used to adjust significance values for multiple comparisons. All modules with a mean abundance >1.0 × 10−9 were tested; only those with adjusted P-value <0.1 are shown. A full color version of this figure is available at the American Journal of Gastroenterology journal online. CD, Crohn's disease; EEN, exclusive enteral nutrition; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Mentions: When reads were assigned to metabolic KEGG modules with HUMAnN, a significantly larger mean Shannon diversity, in richness equivalents, was observed in CD children compared with controls (CD vs. Controls: 48.1 vs. 43.2; P=0.05 Figure 4). Healthy and CD children differed at the level of KEGG modules, with marginal significance explaining 9.4% of the variation (P=0.059; Supplementary Figure S3). Several KEGG modules and orthologs (Supplementary Table S11) were different between the two groups, but their significance became marginal (P<0.100) when adjusted for multiple testing (Table 3). Modules more abundant in samples from CD patients included ubiquinone and lipopolysaccharide biosynthesis and the twin-arginine translocation (Tat) system, whereas key processes such as fatty acid biosynthesis, initiation, and sulfur reduction were overrepresented in controls (Table 3).


Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.

Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K - Am. J. Gastroenterol. (2015)

KEGG module Shannon diversity for each EEN sample time and participant (a) and log relative abundance of modules that significantly changed during EEN (b). (a) Diversity was not impacted during EEN (P=0.260), but there was a difference between H and CD before EEN (P=0.05). (b): M00123, biotin biosynthesis, P=0.005; M00127, thiamine biosynthesis, P=0.0166; M00299, spermidine/putrescine transport system, P=0.0307; M00022, shikimate pathway, P=0.058. P-values are based on linear regressions of KEGG module log relative abundance against days on EEN with subject-dependent intercepts for 11 children with at least two shotgun metagenome samples. Benjamini–Hochberg false discovery rate was used to adjust significance values for multiple comparisons. All modules with a mean abundance >1.0 × 10−9 were tested; only those with adjusted P-value <0.1 are shown. A full color version of this figure is available at the American Journal of Gastroenterology journal online. CD, Crohn's disease; EEN, exclusive enteral nutrition; KEGG, Kyoto Encyclopedia of Genes and Genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4697132&req=5

fig4: KEGG module Shannon diversity for each EEN sample time and participant (a) and log relative abundance of modules that significantly changed during EEN (b). (a) Diversity was not impacted during EEN (P=0.260), but there was a difference between H and CD before EEN (P=0.05). (b): M00123, biotin biosynthesis, P=0.005; M00127, thiamine biosynthesis, P=0.0166; M00299, spermidine/putrescine transport system, P=0.0307; M00022, shikimate pathway, P=0.058. P-values are based on linear regressions of KEGG module log relative abundance against days on EEN with subject-dependent intercepts for 11 children with at least two shotgun metagenome samples. Benjamini–Hochberg false discovery rate was used to adjust significance values for multiple comparisons. All modules with a mean abundance >1.0 × 10−9 were tested; only those with adjusted P-value <0.1 are shown. A full color version of this figure is available at the American Journal of Gastroenterology journal online. CD, Crohn's disease; EEN, exclusive enteral nutrition; KEGG, Kyoto Encyclopedia of Genes and Genomes.
Mentions: When reads were assigned to metabolic KEGG modules with HUMAnN, a significantly larger mean Shannon diversity, in richness equivalents, was observed in CD children compared with controls (CD vs. Controls: 48.1 vs. 43.2; P=0.05 Figure 4). Healthy and CD children differed at the level of KEGG modules, with marginal significance explaining 9.4% of the variation (P=0.059; Supplementary Figure S3). Several KEGG modules and orthologs (Supplementary Table S11) were different between the two groups, but their significance became marginal (P<0.100) when adjusted for multiple testing (Table 3). Modules more abundant in samples from CD patients included ubiquinone and lipopolysaccharide biosynthesis and the twin-arginine translocation (Tat) system, whereas key processes such as fatty acid biosynthesis, initiation, and sulfur reduction were overrepresented in controls (Table 3).

Bottom Line: OTUs that correlated positively or negatively with calprotectin decreased during EEN.The abundance of genes involved in biotin (P=0.005) and thiamine biosynthesis decreased (P=0.017), whereas those involved in spermidine/putrescine biosynthesis (P=0.031), or the shikimate pathway (P=0.058), increased during EEN.Disease improvement following treatment with EEN is associated with extensive modulation of the gut microbiome.

View Article: PubMed Central - PubMed

Affiliation: Warwick Medical School, University of Warwick, Warwick, UK.

ABSTRACT

Objectives: Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into the microbial origins of Crohn's disease (CD).

Methods: Fecal samples (n=117) were collected from 23 CD and 21 healthy children. From CD children fecal samples were collected before, during EEN, and when patients returned to their habitual diets. Microbiota composition and functional capacity were characterized using sequencing of the 16S rRNA gene and shotgun metagenomics.

Results: Microbial diversity was lower in CD than controls before EEN (P=0.006); differences were observed in 36 genera, 141 operational taxonomic units (OTUs), and 44 oligotypes. During EEN, the microbial diversity of CD children further decreased, and the community structure became even more dissimilar than that of controls. Every 10 days on EEN, 0.6 genus diversity equivalents were lost; 34 genera decreased and one increased during EEN. Fecal calprotectin correlated with 35 OTUs, 14 of which accounted for 78% of its variation. OTUs that correlated positively or negatively with calprotectin decreased during EEN. The microbiota of CD patients had a broader functional capacity than healthy controls, but diversity decreased with EEN. Genes involved in membrane transport, sulfur reduction, and nutrient biosynthesis differed between patients and controls. The abundance of genes involved in biotin (P=0.005) and thiamine biosynthesis decreased (P=0.017), whereas those involved in spermidine/putrescine biosynthesis (P=0.031), or the shikimate pathway (P=0.058), increased during EEN.

Conclusions: Disease improvement following treatment with EEN is associated with extensive modulation of the gut microbiome.

Show MeSH
Related in: MedlinePlus