shortening, and fungal overgrowth in the intestines of DCX3CR1 mice without worsening the
disease in littermate controls (Fig. 3E and fig. S20,
A and B). Despite the increased disease susceptibility and augmented Candida burden,
DCX3CR1 mice failed to mount a systemic antifungal IgG antibody response (Fig. 3F and fig.
S20, C and D), which is consistent with the defective antifungal immunity that we observed
during the steady state. These results indicate that
CX3CR1+ MNPs play a crucial role in controlling
fungal microbiota during intestinal disease.
Having established a role for CX3CR1+ MNPs
in the control of gut fungi during intestinal disease,
and finding that CX3CR1+ MNPs have the poten-
tial to intake other species of mouse and human
commensal fungi (Fig. 4A), we explored whether
genetic variations of the human CX3CR1 gene
affect immunity to fungi in inflammatory bowel
disease (IBD). Defects in CX3CR1 have been shown
to increase susceptibility of mice and humans to
systemic candidiasis (19) but not to vulvovaginal
and oral candidiasis (27). By contrast, the role of
CX3CR1 in the initiation of antifungal responses in
the gut is unknown. We focused on polymorphisms
in the coding region of the CX3CR1 gene (fig. S21)
that have been previously associated with human
inflammatory diseases such as arteriosclerosis and
coronary artery disease (28, 29). Although none of
these polymorphisms were associated with a pre-
disposition to IBD (table S1), we identified a striking
association of CX3CR1 T280M (rs3732378) poly-
morphism specifically with IgG ASCA positivity
in a cohort of 503 CD patients [odds ratio (OR) =
0.59, logistic regression P = 3.73 × 10−03] (Fig. 4B).
By contrast, antibodies against bacterial and host
antigens previously shown to increase in IBD (7)
were not affected by this mutation (Fig. 4B and
table S2). Because ASCA antibodies are directed
against both S. cerevisiae and C. albicans (7), we next
assessed whether antifungal antibody responses
to common human commensals are also affected
by CX3CR1 T280M. Compared with nonaffected
individuals, patients homozygous for CX3CR1
T280M were severely impaired in their ability to
generate systemic IgG recognizing a variety of gut-
relevant fungi belonging to the phylum Ascomycota,
while producing normal antibody responses against
the bacterial antigen flagellin (Fig. 4, C and D, and
fig. S22), which is consistent with the hypothesis
that this mutation in CX3CR1 leads to impaired
responses to fungi in the gut.
We identified a specific subset of gut-resident
phagocytes—namely, the CX3CR1+ MNPs—that
are able to recognize and respond to the gut
mycobiota in a Syk-dependent manner. CX3CR1+
MNPs can influence adaptive immune responses
to gut fungi and control the mycobiota during
experimental colitis. In humans, we found that a
CX3CR1 polymorphism is strongly associated with
a decrease of antifungal antibody responses in CD
patients. CX3CR1 T280M is a common polymor-
phism [23.3% heterozygous and 4.4% homozygous
(30)] and has been previously associated with ex-
traintestinal inflammatory diseases (28, 29). Con-
ceivably, gut mycobiota and CX3CR1-dependent
immune responses might further contribute to
extraintestinal manifestations of inflammatory
diseases. In support of this notion, antifungal anti-
bodies are increased in patients with alcoholic
liver disease, spondyloarthritis, Graves’ disease,
and systemic lupus erythematosus (6–9). Altogether,
our findings provide evidence for the influence of
gut fungal communities on both local and systemic
immunity, which is mediated by the recognition of
intestinal fungi by CX3CR1+ MNPs.
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This work was funded by the U. S. National Institutes of Health
(grants DK113136, DK098310, and AI123819 to I.D.I; P01 DK046763
and U01 DK062413 to D. P.B. M.), Infect-ERA FUNCOMPATH
(PCIN-2014-052 to J.P), Ministerio de Economía y Competitividad
(BIO2015-6477-P to J.P.), Swiss National Science Foundation
(fellowship P2ZHP3_164850 to I.L), Kenneth Rainin Foundation
(Innovator and Breakthrough awards to I. D. I), and support from the Jill
Roberts Institute for Research in IBD. The data presented in this
study are tabulated in the main text and supplementary materials.
Microbiota sequencing data are deposited in National Center for
Biotechnology Information (NCBI) Sequence Read Archive (SRA;
www.ncbi.nlm.nih.gov/Traces/sra, run numbers SRP124782,
SRP124783, SRP124736, and SRP124742). RNA-seq data are deposited in
the NCBI Gene Expression Omnibus under accession no. GSE106594.
Materials and Methods
Figs. S1 to S22
Tables S1 and S2
22 June 2017; resubmitted 15 November 2017
Accepted 9 December 2017
236 12 JANUARY 2018 • VOL 359 ISSUE 6372 sciencemag.org SCIENCE
P. kudriavazevii S. cerevisiae A. versicolor A. amstelodami
20µm 20µm 20µm 20µm
SNP serology FA* FU OR L95 U95 P
anca 0.181 0.174 1.13 0.77 1.64 0.535
cbir 0.165 0.182 0.88 0.63 1.23 0.459
rs3732378 i2 0.159 0.202 0.69 0.48 0.98 0.041
igg.asca0.135 0.205 0.59 0.41 0.84 3.73E-3
AA GG AA GG
AA AG GG
AA AG GG
300 ns ns ns AA GG AA GG AA GG
Fig. 4. Polymorphisms in the coding region of the CX3CR1 gene are associated with decreased
antifungal IgG responses in CD patients. (A) Representative images of the intake of fungal species
(colored) by CX3CR1+ MNPs (gray) in the colon. (B) Association between the missense mutation rs3732378
and the systemic serologic markers anti-neutrophil cytoplasmic antibodies (anca), flagellin (cbir),
Pseudomonas fluorescens–associated sequence I-2 (i2), and antibodies to S. cerevisiae IgG ( igg.asca)
among 503 CD patients. FA, frequency affected; FU, frequency unaffected; L95 and U95, lower and upper
95th confidence interval. (C) IgG ASCA and antiflagellin (cbir) IgG responses were assessed in the sera from
rs3732378 homozygous (AA), heterozygous (AG), and control (GG) CD patients by means of ELISA. Dots
represent individual patients, and bars represent mean. (D) IgG responses against different commensal
fungi. C. albicans, Pichia kudrazevii, S. cerevisiae, Aspergillus amstellodamii, Wallemia sebi, and Malassezia
restricta were assessed. Dots represent individual patients, and bars represent mean. Statistical analysis:
*P < 0.05, **P < 0.01, ***P < 0.001; Mann-Whitney test in (D) and one-way ANOVA in (C).