University of Groningen
The gut microbiome in intestinal diseases
Imhann, Floris
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Imhann, F. (2019). The gut microbiome in intestinal diseases: and the infrastructure to investigate it.
Rijksuniversiteit Groningen.
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CHAPTER 10
Letter to the Editor
SLC39A8 missense variant
is associated with Crohn’s
disease but not with the gut
microbiota composition
An adapted full article version was published in PLoS ONE 2019
Collij V1,2, Imhann F1,2*, Vich Vila A1,2*, Fu J3, Dijkstra G1, Festen EAM1,2, Barbieri R1,2, Daly MJ4,
Xavier RJ4,5, Wijmenga C2, Zhernakova A2, Weersma RK1
*shared second authors
1 University of Groningen, University Medical Center Groningen,
Department of Gastroenterology and Hepatology, Groningen, the Netherlands
2 University of Groningen, University Medical Center Groningen,
Department of Genetics, Groningen, the Netherlands
3 University of Groningen, University Medical Center Groningen,
Department of Pediatrics, Groningen, the Netherlands
4 Broad Institute of Harvard and MIT, Boston, USA 5 Massachusetts General Hospital, Boston, USA
Letter to the editor
Recently, three independent studies have been published in Nature Genetics investigating the interaction between the host genome and the gut microbiota
composition in the general population.1–3 The results of these studies showed very little
overlap, probably due to the complexity and variability of the gut microbiota. Genome-microbiota associations should therefore be regarded with caution, and replication of
gene-microbiota associations is certainly warranted.4
In September 2016 we published a case-control study in Gut in which we investigated the effects of the host genetic risk of inflammatory bowel disease (IBD) on the gut
microbiota.5 We defined a genetic risk score (GRS) composed of 11 variants in
IBD-related genes (NOD2, ATG16L1, IRGM, CARD9 and FUT2) proven to be IBD-related to gut microbiota alterations. The GRS was associated with unfavourable pro-inflammatory
changes in the gut microbiota in healthy individuals.5 Shortly thereafter, Li et al reported
in Gastroenterology the identification of a novel exonic missense variant in the SLC39A8 gene (alanine 391 threonine, rs13107325) associated with Crohn’s disease (CD) using the genotypes of 10,523 patients with IBD and 5,726 controls. Li et al further reported an association of the SLC39A8 [Thr]391 risk variant with the gut microbiota composition
using 338 mucosal lavage samples of 171 patients with CD and controls.6
Here, we aimed to replicate the Li et al’s association between the SLC39A8 [Thr]391 risk allele and the gut microbiota using 16S rRNA gut microbiota data from stool samples and whole exome sequencing (WES) data from 558 individuals: 168 patients with CD and 390 healthy controls. The 16S rRNA gut microbiota was obtained and processed
as previously described.5 WES data was generated using sample preparation (Illumina
Nextera), hybrid capture (Illumina Rapid Capture Enrichment 37Mb target), and sequencing (Illumina, HiSeq machines, 150bp paired reads).
We found the SLC39A8 [Thr]391 risk allele in 21 of the 168 patients with CD (12.5%) and in 27 of the 390 healthy controls (6.9%). In agreement with Li et al, patients with CD were more often carriers than healthy controls (OR=1.92; P=0.03, Wilcoxon-Mann-Whitney test). However, we could not identify any statistically significant differences between SLC39A8 [Thr]391 risk allele carriers and non-carriers in the first five principal coordinates found in principal coordinate analyses of the gut microbiota composition in patients with CD, healthy controls or both groups combined as depicted in Figure 1 (Wilcoxon-Mann-Whitney test). Nor could we identify any statistically significant
associations between the SLC39A8 [Thr]391 risk allele and the individual microbial taxa in patients with CD, healthy controls or both groups combined, and this was true for both the univariate analysis and the multivariate analysis using age, sex, body mass index, read-depth, proton pump inhibitor use, antibiotics and IBD medication
(mesalazines, steroids, thiopurines, methotrexate and TNF-α inhibitors) as covariates
In summary, we could confirm that the [Thr]391 risk allele is associated with CD. However, even in a sample size three times larger than Li et al’s original cohort, we could not identify any statistically significant association between the exonic missense variant in SLC39A8 and the gut microbiota composition in either patients with CD, healthy controls, or both groups combined.
−0.2 −0.1 0.0 0.1 0.2 −0.2 0.0 0.2 PC1 PC2 −0.2 −0.1 0.0 0.1 0.2 0.3 −0.4 −0.2 0.0 0.2 PC1 PC2 −0.2 −0.1 0.0 0.1 0.2 −0.2 0.0 0.2 PC1 PC2
A
B
C
Figure 1. Principal coordinate analysis of gut microbiota composition generated using 16S rRNA sequencing of stool samples.
Declarations
Funding
RKW and JF are supported by VIDI grants (016.136.308 and 864.13.013) from the Netherlands Organization for Scientific Research (NWO). Sequencing of the control cohort was funded by a Top Institute Food and Nutrition grant GH001 to CW. CW is further supported by an ERC advanced grant (ERC-671274) and a Spinoza award (NWO SPI 92-266). AZ holds a Rosalind Franklin fellowship (University of Groningen) and an ERC Starting Grant (ERC-715772). JF and AZ are also supported by a CardioVasculair Onderzoek Nederland grant (CVON 2012-03)
Competing interests
The authors have no conflicts of interest to declare with this work.
Author contributions
VC, FI, AVV and RB gathered and prepared the data. VC and AVV analysed the data. VC and FI wrote the manuscript. RKW designed the study. AVV, JF, GD, EAMF, RB, MJD, RJX, CW, AZ and RKW critically reviewed the manuscript.
Supplementary documents
The adapted full article version of this manuscript including supplementary
documents is available online: https://journals.plos.org/plosone/article?id=10.1371/
References
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4. Benson, A. K. The gut microbiome -
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5. Imhann, F. et al. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory
bowel disease. Gut 67, 108–119 (2016).
6. Li, D. et al. A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn’s Disease and Human Gut Microbiome
Composition. Gastroenterology 151,
Segmented filamentous bacteria (SFBs) embedded in the epithelium of a mouse Peyer's patch. Peyer's patches are regions of lymphoid tissue in the intestine of all mammals. These bacteria attach firmly to the brush border of the
