Crohn’s disease patients with the ATG16L1T300A allele are
unable to modify their mucosal microbiota profile upon
inflammation.
Anouk Regeling1#, Mehdi Sadaghian1,2#, Marcus C. de Goffau2, Klaas Nico Faber1, Hermie J.M. Harmsen2* Gerard
Dijkstra1*.
1Department
of Gastroenterology and Hepatology, and 2Department of Medical Microbiology, University of
Groningen, University Medical Center Groningen, Groningen, The Netherlands.
M.sadaghian@umcg.nl
Tel. +31-50-3615169
# Both first authors contributed equally
* Both last authors contributed equally
Introduction and Objectives: Crohn’s disease (CD) is a chronic inflammatory disorder of the
intestine that is caused by a complex interplay between genetic, microbiota and environmental
factors. Specific variants of the NOD2, ATG16L1 and IRGM genes are associated with CD and
functional studies suggest a crucial role of their gene products in innate immunity processes,
including autophagy and phagocytosis The human gut microbiota includes variety of beneficial
bacteria that balance potentially pathogenic bacteria, such as Bacteroides and Escherichia coli.
Alternation in the microbial composition (dysbiosis) could be a trigger to continuous inflammation
of intestinal tract. Aim: Here, we investigate whether ATG16L1 may affect mucosal clearance of
specific bacteria from the gut of CD patients and whether this is affected by inflammation.
Materials and Methods: A total number of 42 paired biopsies from inflamed and non-inflamed
regions of the ileum were obtained from 11 CD patients homozygous for the ATG16L1 mutant
allele (ATG16L1T300A and 10 CD patients homozygous for the ATG16L1 wild type allele
(ATG16L1T300).
DNA was extracted from the biopsy samples and the sequence of the amplified V1–V3 hyper
variable regions of the 16S rRNA gene was determined by 454 pyrosequencing. The obtained
data was analyzed using web-based pipelines in combination with the ARB database.
Results: From the 42 samples approximately 500,000 reads were obtained with an average of
12,000 reads/sample ranging from 5820 to 18479. No significant differences were detected in
relative abundance of bacterial species between non-inflamed mucosa of patients with the mutant
or the wild type ATG16L1 locus. Also, inflamed mucosa from ATG16L1 mutant patients showed a
microbiome profile that was comparable to non-inflamed mucosa. However, inflamed biopsies
from wild type ATG16L1 patients showed relatively less Bacteroides genus and more
Lachnospira family related sequences than the first three groups.
Conclusion: This study suggests that ATG16L1 is required to modify the microbiome profile
under inflammatory conditions. Unlike wild type patients, patients with the ATG16L1T300A allele
do not seem to be able to reduce the number of potentially pathogenic Bacteroides during
inflammation, in favor of the Lachnospira that may have more beneficial characteristics, such as
butyrate formation.