Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease

1. G. Hoarau^a, 
2. P. K. Mukherjee^b, 
3. C. Gower-Rousseau^c, 
4. C. Hager^b, 
5. J. Chandra^b,
6. M. A. Retuerto^b, 
7. C. Neut^a, 
8. S. Vermeire^d, 
9. J. Clemente^e,^f, 
10. J. F. Colombel^c,^g, 
11. H. Fujioka^h,
12. D. Poulain^a, 
13. B. Sendid^a, 
14. M. A. Ghannoum^b

+Author Affiliations

1. aInserm U995-Team 2, Université Lille 2, Faculté de Médecine H. Warembourg, Pôle Recherche, CHRU de Lille, Lille, France
2. bCenter for Medical Mycology, University Hospitals Case Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
3. cEpimad Registry, Epidemiology Unit and LIRIC Inserm 995, Lille University and Hospital, Lille, France
4. dDepartment of Gastroenterology, University Hospital Leuven, Leuven, Belgium
5. eDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
6. fImmunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
7. gDepartment of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8. hEM Core Facility, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA

1. Address correspondence to B. Sendid, bsendid@univ-lille2.fr, or M. A. Ghannoum,Mahmoud.Ghannoum@case.edu.

1. G.H. and P.K.M. contributed equally to the study.
2. Editor Robert A. Bonomo, Louis Stokes Veterans Affairs Medical Center

 

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ABSTRACT

Crohn’s disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities. In the current study, we used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their nondiseased first-degree relatives (NCDR) in 9 familial clusters living in northern France-Belgium and in healthy individuals from 4 families living in the same area (non-CD unrelated [NCDU]).

Principal component, diversity, and abundance analyses were conducted, and CD-associated inter- and intrakingdom microbial correlations were determined. Significant microbial interactions were identified and validated using single- and mixed-species biofilms. CD and NCDR groups clustered together in the mycobiome but not in the bacteriome. Microbiotas of familial (CD and NCDR) samples were distinct from those of nonfamilial (NCDU) samples. The abundance of Serratia marcescens and Escherichia coli was elevated in CD patients, while that of beneficial bacteria was decreased. The abundance of the fungus Candida tropicalis was significantly higher in CD than in NCDR (P = 0.003) samples and positively correlated with levels of anti-Saccharomyces cerevisiae antibodies (ASCA). The abundance of C. tropicaliswas positively correlated with S. marcescens and E. coli, suggesting that these organisms interact in the gut. The mass and thickness of triple-species (C. tropicalis plus S. marcescens plus E. coli) biofilm were significantly greater than those of single- and double-species biofilms. C. tropicalis biofilms comprised blastospores, while double- and triple-species biofilms were enriched in hyphae. S. marcescens used fimbriae to coaggregate or attach with C. tropicalis/E. coli, while E. coli was closely apposed with C. tropicalis. Specific interkingdom microbial interactions may be key determinants in CD.

IMPORTANCE Here, we characterized the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in multiplex families with CD and healthy relatives and defined the microbial interactions leading to dysbiosis in CD. We identified fungal (Candida tropicalis) and bacterial (Serratia marcescens and Escherichia coli) species that are associated with CD dysbiosis. Additionally, we found that the level of anti-Saccharomyces cerevisiaeantibodies (ASCA; a known CD biomarker) was associated with the abundance ofC. tropicalis. We also identified positive interkingdom correlations between C. tropicalis,E. coli, and S. marcescens in CD patients and validated these correlations using in vitrobiofilms. These results provide insight into the roles of bacteria and fungi in CD and may lead to the development of novel treatment approaches and diagnostic assays.

This Articledoi: 10.1128/mBio.01250-1620 September 2016 mBio vol. 7no. 5 e01250-16

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