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Adaptive immunity induces mutualism between commensal eukaryotes

Abstract

Pathogenic fungi reside in the intestinal microbiota but rarely cause disease. Little is known about the interactions between fungi and the immune system that promote commensalism. Here we investigate the role of adaptive immunity in promoting mutual interactions between fungi and host. We find that potentially pathogenic Candida species induce and are targeted by intestinal immunoglobulin A (IgA) responses. Focused studies on Candida albicans reveal that the pathogenic hyphal morphotype, which is specialized for adhesion and invasion, is preferentially targeted and suppressed by intestinal IgA responses. IgA from mice and humans directly targets hyphal-enriched cell-surface adhesins. Although typically required for pathogenesis, C. albicans hyphae are less fit for gut colonization1,2 and we show that immune selection against hyphae improves the competitive fitness of C. albicans. C. albicans exacerbates intestinal colitis3 and we demonstrate that hyphae and an IgA-targeted adhesin exacerbate intestinal damage. Finally, using a clinically relevant vaccine to induce an adhesin-specific immune response protects mice from C. albicans-associated damage during colitis. Together, our findings show that adaptive immunity suppresses harmful fungal effectors, with benefits to both C. albicans and its host. Thus, IgA uniquely uncouples colonization from pathogenesis in commensal fungi to promote homeostasis.

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Fig. 1: Adaptive immune responses target and suppress C. albicans hyphae in the gut.
Fig. 2: IgA targets C. albicans adhesins.
Fig. 3: Adaptive immunity enhances the competitive fitness of C. albicans.
Fig. 4: Vaccination against C. albicans adhesin prevents damage during colitis.

Data availability

Raw C. albicans RNA-seq reads have been deposited at the NCBI Sequence Read Archive under the BioProject accession number PRJNA728116. All other data needed to evaluate the conclusions in the paper are available within the Article or its Supplementary InformationSource data are provided with this paper.

Code availability

All code used for processing and mapping RNA-seq reads is available at https://github.com/RoundLab/Ost_CandidaRNASeq.

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Acknowledgements

We thank A. Weis and J. Hill for their edits of this manuscript; R. Wheeler for providing the pENO1-iRFP and pENO1-Neon C. albicans constructs; L. Cowen for the pLC605 TetO construct; J. Berman for the YJM11522 C. albicans strain; A. Nobbs for the S. cerevisiae strains expressing C. albicans adhesins; D. Stillman for S. cerevisiae strains and reagents; and the ULAM GF Mouse Facility at the University of Michigan for the GF Rag1−/− mice. Proteomics mass spectrometry analysis was performed at the Mass Spectrometry and Proteomics Core Facility at the University of Utah. Mass spectrometry equipment was obtained through a Shared Instrumentation Grant 1 S10 OD018210 01A1. This work was supported by the Helen Hay Whitney Foundation (K.S.O.), a University of Utah NRSA Microbial Pathogenesis T32 Training Grant (K.S.O.), a CCFA Senior Research Award (J.L.R.), NIDDK R01DK124336 (J.L.R.), the Edward Mallinckrodt Jr. Foundation (J.L.R.), a NSF CAREER award (IOS-1253278) (J.L.R.), a Packard Fellowship in Science and Engineering (J.L.R.), a Burroughs Welcome Investigator in Pathogenesis Award (J.L.R), the American Asthma Foundation (J.L.R.), the Margolis Foundation (J.L.R.), an MS Society Center grant (J.L.R.), NIAID R01046223 (B.C.), an NIH New Innovator Award DP2GM111099-01 (R.M.O.), NHLBI R00HL102228-05 (R.M.O.), an American Cancer Society Research Grant (R.M.O.), a Kimmel Scholar Award (R.M.O.), R01AG047956 (R.M.O.) and NIAID R01AI141202 (A.S.I.). This work was supported by the University of Utah Flow Cytometry Facility in addition to the National Cancer Institute through award number 5P30CA042014-24. The support and resources from the Center for High Performance Computing at the University of Utah are gratefully acknowledged.

Author information

Authors and Affiliations

Authors

Contributions

K.S.O. conceived the study, performed most experiments and helped to write the manuscript. T.R.O. helped with experimental design and fungal strain creation, and edited the manuscript. W.Z.S. analysed the RNA-seq data, helped with experimental design and edited the manuscript. T.C. helped with the immune profiling experiments and edited the manuscript. H.Z. helped to perform the C. albicans IgA screens and edited the manuscript. J.P. helped with fungal IgA-binding assays and edited the manuscript. R.B. managed the GF mouse experiments, helped with the immune profiling experiments and edited the manuscript. J.R.C., D.S. and N.W.P. provided the collection of human faecal samples, provided guidance on human antibody experiments and edited the manuscript. D.H.C. and K.A.C. guided the imaging flow cytometry experiments and edited the manuscript. E.H.-W. and B.C. created the S. cerevisiae strains expressing the C. glabrata adhesin-like proteins and edited the manuscript. K.E.H. edited the manuscript and provided the clinical C. glabrata strains. R.M.O. provided guidance on immunological experiments. S.M.N. provided C. albicans strains, provided guidance on fungal genetics experiments and edited the manuscript. A.S.I. and S.S. provided the NDV-3A vaccine and edited the manuscript. J.F.V. provided the human serum samples. J.L.R conceived the study, guided the experiments, analysed data and helped to write the manuscript.

Corresponding author

Correspondence to June L. Round.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks Gordon Brown and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Fig. 1 Human faecal and serum anti-fungal antibodies.

a, Human faecal antibody binding to cultured fungi and quantified by flow cytometry after staining with fluorescent secondary antibodies (n = 70). Staining intensity normalized to fungi stained with secondary antibodies but without human faecal wash. Box plots show minimum 25% quartile and maximum 75% quartile around the median and whiskers show range. b, IgA binding to cultured fungi from serial dilutions of human faecal wash (n = 30 healthy, n = 23 Crohn’s disease and n = 17 UC). Geometric mean with 95% CI c, d, Human serum antibody binding to cultured fungi. Serum diluted 1:75. (n = 12, n = 4 healthy and n = 8 Crohn’s disease). Mean ± s.d. e, Faecal ASCA IgA levels from undiluted faecal wash (n = 30 healthy, n = 18 Crohn’s disease and n = 14 UC). Median with 95% CI f, Serum ASCA IgA levels from human serum samples diluted 1:100 (n = 4 healthy and n = 8 Crohn’s disease). Median with 95% CI. P values calculated using two-way ANOVA with Tukey’s test (a), one-way ANOVA with Dunn’s test (c) or two-sided Mann–Whitney U-test (f, d).

Source data

Extended Data Fig. 2 IgA targets Candida species but not S. cerevisiae.

a, IgA-bound faecal fungi gating strategy. b, Peyer’s patch GC B cell and TFH cell gating strategy. c, Colon LP IgA plasma cell gating strategy (n = 4 mice per group 30 days after inoculation; representative of two experiments for b, c). d, IgA binding to faecal GFP+ S. cerevisiae and GFP+ C. albicans in monocolonized SW mice. e, Total IgA levels from monocolonized SW mice. f, Flow cytometry quantification of SW IgA binding to cultured S. cerevisiae and C. albicans (n = 4 C. albicans-colonized and n = 5 S. cerevisiae-colonized, one experiment for df). g, h, Serum antibody binding to cultured C. albicans or S. cerevisiae from SW (g) or B6 (h) GF or monocolonized mice. Antibody quantified by flow cytometry from serum diluted 1:25 (SW: GF n = 4, Sc-colonized n = 5, Ca-colonized n = 5; B6: GF n = 3, Sc n = 5, Ca-colonized n = 3). i, Lumen and tissue-associated fungal burden in monocolonized B6 mice 30 days after inoculation (n = 4 mice per group; one experiment; representative of two experiments). j, Whole-intestinal IgA four weeks after inoculation. k, Caecal wash IgA binding to cultured C. glabrata measured by flow cytometry. l, Peyer’s patch TFH cells four weeks after inoculation. m, Peyer’s patch GC B cells (n = 4 mice per group; one experiment for jm). n, IgA binding to cultured C. glabrata, S. cerevisiae and C. albicans from faecal wash from GF, C. albicans-monocolonized or C. glabrata-monocolonized intestinal wash (n = 2 C. albicans, n = 3 C. glabrata and n = 3 S. cerevisiae faecal washes) o, Percentage of IgA binding and binding intensity of faecal C. albicans during colonization of antibiotic-treated wild-type and Tcrb−/− mice (n = 6 Tcrb−/− and n =8 wild-type mice from two experiments). P values calculated using two-way ANOVA (d, o), with Sidak’s test (b, e, f, g, h, n), or two-sided unpaired t-test (j, k, l, m). Mean values ± s.d. for b, d–o.

Source data

Extended Data Fig. 3 An IgA response is not induced by 124 distinct S. cerevisiae strains.

a, IgA binding to the 20–24 strains from each pool was assessed by flow cytometry. Mice were gavaged weekly with the indicated pool for three weeks and caecal wash from mice was used as a source of IgA. C. albicans bound by IgA from C. albicans-monocolonized mice is shown in red. b, Total IgA in caecum contents quantified by ELISA. Mean values ± s.d. c, IgA binding to S. cerevisiae (pre-gated on CFW intermediate) populations from caecal material. (n = 3 mice per group representative of two experiments).

Source data

Extended Data Fig. 4 Fungal burden and GO term enrichment analysis of RNA-seq comparison of C. albicans in monocolonized wild-type and Rag1−/− mice.

a, Fungal burden in wild-type and Rag1−/− mice monocolonized with C. albicans four weeks after inoculation. Mean values ± s.d. b, c, Biological process (b) or molecular function (c) GO term enrichment in genes with q ≤ 0.05 and log2-transformed fold change ≥ 1 or ≤ −1. d, Volcano plot of the ratio of C. albicans transcripts in wild-type and Rag1−/− mice with active transmembrane transporter activity genes labelled in red (n = 5 wild type and 4 Rag1−/− mice for ad; one experiment). e, C. albicans morphology in colon contents from monocolonized wild-type or Rag1−/− mice four weeks after colonization. Mean values ± s.d. (n = 3 mice per group; one experiment). f, IgA binding to C. albicans in the faeces of antibiotic-treated wild-type and μMT−/− mice four weeks after inoculation. Mean values ± s.d. (n = 5 mice per group; one experiment). P values calculated using two-way ANOVA with Sidak’s multiple comparisons test (a, f) or two-sided unpaired t-test (e).

Source data

Extended Data Fig. 5 Filamentation and Ahr1 promote intestinal IgA responses.

a, Morphology of indicated C. albicans strains incubated for 4 h in RPMI with 10% FBS, YPD or YPD + 5 μg ml−1 aTC). TetO-NRG1 constitutively expresses NRG1 when untreated (TetOn), but aTC repressed NRG1 expression (TetOff). b, C. albicans in caecum contents stained with AF488 anti-Candida antibody. c, Intestinal fungal burden (mean values ± s.d.). d, Peyer’s patch TFH cells (ICOS+PD-1+CD4+CD3+ live cells) (mean values ± s.d.). e, Peyer’s patch GC B cells (GL-7+Fas+IgDCD19+ live cells) (mean values ± s.d.). f, Colon LP IgA+ plasma cells (IgA+CD138+CD45+CD3CD19 live cells) (mean values ± s.d.) quantified from mice monocolonized for four weeks (for cf, n = 4 mice per group; one experiment). g, Faecal AHR1 qPCR in aTC-treated mice monocolonized with wild-type or TetO-AHR1 (TetOff-AHR1) (wild type n = 3 and TetOff-ALS1 n = 5; one experiment). Mean values ± s.d. h, Fungal burden of wild-type- and TetOff-AHR1-monocolonized mice. i, IgA from wild-type- or TetOff-AHR1-monocolonized mice, j, k, Peyer’s patch TFH cells (j) and Peyer’s patch GC B cells (k) from mice monocolonized with wild type or TetOff-AHR1. l, qRT–PCR from the small intestinal contents of monocolonized mice (for hl, wild type n = 8 and TetOff-ALS1 n = 10 mice per group from two experiments). m, Intestinal IgA (from C. albicans-monocolonized mice) binding to strains that were cultured untreated or were treated with aTC. n, Human IgA binding to indicated strains cultured without aTC (wild type, ahr1∆/∆, ahr1∆/∆ TetOn-ALS1) or with 5 μg ml−1 aTC (ahr1∆/∆ TetOff-ALS1). IgA binding quantified by flow cytometry (healthy n = 13 and IBD n = 22; one experiment. Samples chosen had enough C. albicans-reactive IgA to bind at least 10% of cultured wild-type C. albicans). P values calculated using one-way ANOVA with Tukey’s test (cf), two-way ANOVA with Sidak’s test (i), two-sided unpaired t-test (j, k, l), two-sided Mann–Whitney U-test (g) or Friedman test with Dunn’s test (n).

Source data

Extended Data Fig. 6 C. albicans- and C. glabrata-induced IgA targets adhesins or adhesin-like proteins.

a, Anti-HA staining of the control S. cerevisiae expressing the Cwp1 scaffold control and the S. cerevisiae strains expressing HA-tagged C. albicans adhesins. b, Anti-HA and IgA binding to S. cerevisiae strains expressing HA-tagged C. glabrata adhesins after incubation in caecal wash from mice monocolonized with C. glabrata. SC104, SC106, SC97 and SC27 express adhesins not tagged by HA. HA and IgA binding quantified by flow cytometry.

Source data

Extended Data Fig. 7 Antibody induction by S. cerevisiae strains expressing Candida adhesins.

GF SW mice were monocolonized with the indicated strains or left GF. Colonized mice were gavaged three times per week with cultured strains. The control S. cerevisiae expresses the CWP1 cell surface scaffold but not an adhesin. a, Weekly faecal IgA levels normalized by faecal weight. b, c, Intestinal IgA (b) and IgG (c) levels at day 28 normalized by material weight. d, Colon lamina propria IgG1 plasma cells (live IgG1+IgACD138+CD19CD3CD45+ live cells). e, Colon lamina propria IgA plasma cells (live IgA+IgG1CD138+CD19CD3CD45+ live cells) (for ae, GF n = 6, control Sc n = 4, Sc + Als1 n = 5, Sc + Als3 n = 5, Sc + Hwp1 n = 4, Sc + CAGL0B00154g n = 5 mice per group; one experiment). P values calculated using one-way ANOVA with Tukey’s test (d, e) or two-way ANOVA with Tukey’s test (ac). All data are mean ± s.d.

Source data

Extended Data Fig. 8 Immune-enhanced fitness diminishes after 14 days.

Competitive index (CI) of C. albicans conditioned for four weeks in indicated GF recipient mice. B6-conditioned C. albicans was iRFP+ and Rag1−/−-conditioned C. albicans was Neon+. CI normalized to the CI when strains were competed in wild-type and Rag1−/− mice directly from culture (competition mice, n = 3 B6 and n = 4 Rag1−/− mice from one experiment). P values calculated using two-way ANOVA with Sidak’s test. Data are mean ± s.d.

Source data

Extended Data Fig. 9 AHR1 exacerbates DSS colitis.

a, Schematic of DSS colitis experiments. b, Histology images and scores for mice treated with no C. albicans or with TetO-AHR1 with and without aTC (no-Ca UT, no-Ca aTC and TetOn-AHR1 UT n = 7 mice per group, TetOff-AHR1 aTC n = 8 mice per group from two independent experiments). Data are mean ± s.d. c, DSS histology images for mice treated with no C. albicans or with wild-type C. albicans, ahr1∆/∆ C. albicans, TetOn-ALS1 ahr1∆/∆ C. albicans and TetOff-ALS1 ahr1∆/∆ C. albicans (aTC-treated). P values calculated using two-way ANOVA with Tukey’s test (b).

Source data

Extended Data Fig. 10 NDV-3A induces an intestinal anti-Als3 antibody response.

a, model of monocolonization and DSS experiment in vaccinated mice. b, c, ELISA quantification of Als3-specific IgA (b) and IgG (c) from the faeces of GF mice one week after boost with alum of NDV-3A vaccine. d, e, Faecal (d) and intestinal (e) lumen CFU of C. albicans in monocolonized alum or NDV-3A vaccinated mice. Intestinal CFU quantified 12 days after colonization. f, Imaging flow cytometry images of IgA+ C. albicans from caecum of NDV-3A vaccinated mice. g, Percentage of hyphae quantified using an AF488 anti-Candida antibody to visualize morphology from indicated intestinal region 12 days after monocolonization. h, HWP1 and HYR1 transcripts quantified by qRT–PCR from colon C. albicans 12 days after monocolonization. (for bh, n = 5 mice per group; one experiment). i, j, ELISA quantification of Als3-specific IgA (i) and IgG (j) in the faeces of conventionally colonized mice used for the DSS experiment. k, C. albicans CFU in colon contents after DSS treatment (for ik, n = 10 mice per group, one experiment). l, Example H&E-stained histology images from the NDV-3A DSS experiment. P values calculated using two-way ANOVA with Sidak’s test (b, c, i, j). All data are mean ± s.d. Silhouettes in a were created using BioRender.

Source data

Supplementary information

Supplementary Information

This file contains Supplementary Figure 1.

Reporting Summary

Supplementary Table 1

RNAseq differential gene expression analysis.

Supplementary Table 2

IgA binding screen of Noble and Homann knock-out collections.

Supplementary Table 3

IgA targeted hyphae vs. yeast cell wall proteomics analysis.

Supplementary Table 4

Fungal strains used in this study.

Supplementary Table 5

S. cerevisiae strains expressing C. albicans or C. glabrata adhesins or adhesin-like domains.

Supplementary Table 6

Primers used for this study.

Supplementary Table 7

Plasmids used in this study.

Supplementary Table 8

Flow cytometry antibodies used in this study.

Supplementary Table 9

Human fecal and serum metadata.

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Ost, K.S., O’Meara, T.R., Stephens, W.Z. et al. Adaptive immunity induces mutualism between commensal eukaryotes. Nature 596, 114–118 (2021). https://doi.org/10.1038/s41586-021-03722-w

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