Cited by 581T-cell and B-cell ImmunologyImmunotherapy and Immune ResponsesPsoriasis: Treatment and Pathogenesis

MAIT cells are imprinted by the microbiota in early life and promote tissue repair

Open access
Constantinides, Michael G., Link, Verena M., Tamoutounour, Samira, Wong, Andrea C., Perez-Chaparro, P. Juliana, Han, Seong-Ji, Chen, Y. Erin, Li, Kelin +15 more·2019·Science

Abstract

Commensals rule the MAITrix: Mucosal-associated invariant T (MAIT) cells play an important role in mucosal homeostasis. MAIT cells recognize microbial small molecules presented by the major histocompatibility complex class Ib molecule MR1. MAIT cells are absent in germ-free mice, and the mechanisms by which microbiota control MAIT cell development are unknown (see the Perspective by Oh and Unutmaz). Legoux et al. show that, in mice, development of MAIT cells within the thymus is governed by the bacterial product 5-(2-oxopropylideneamino)-6- d -ribitylaminouracil, which rapidly traffics from the mucosa to the thymus, where it is captured by MR1 and presented to developing MAIT cells. Constantinides et al. report that MAIT cell induction only occurs during a limited, early-life window and requires exposure to defined microbes that produce riboflavin derivatives. Continual interactions between MAIT cells and commensals in the skin modulates tissue repair functions. Together, these papers highlight how the microbiota can direct immune cell development and subsequent function at mucosal sites by secreting compounds that act like self-antigens. Science , this issue p. 494 , p. eaax6624 ; see also p. 419

AI snapshot

Written from the paper’s full text.

TL;DR

MAIT cells require a narrow early-life window of microbial exposure, especially riboflavin-synthesizing bacteria, to establish long-term tissue populations. In adult skin, these cells become a dominant IL-17A-producing, tissue-resident subset that responds to commensal antigens and cytokines and accelerates wound repair in mice.

Key findings

  • MAIT cells were enriched in mouse skin, reaching up to 40% of αβ T cells, and averaged about 2% of CD3+ lymphocytes in human skin; germ-free mice had reduced MAIT cells across thymus, spleen, gut, skin, lungs, and liver.
  • A defined five-species early-life community, or monocolonization with *Proteus mirabilis* alone, restored MAIT cell development in neonatal germ-free mice, whereas later-life exposure or adult conventionalization did not; topical 5-OP-RU also induced skin MAIT cells only when given early.
  • Cutaneous MAIT cells were mostly double-negative, produced IL-17A rather than IFNγ, expressed type-17 genes including *Rorc*, *Il22*, *Il1r1*, and *Il23r*, and showed a tissue-repair transcriptional signature; IL-23 receptor deficiency reduced MAIT cell numbers, IL-18 blockade limited their expansion after *S. epidermidis*, and IL-1 receptor deficiency reduced IL-17A production.
  • *S. epidermidis* lacking *ribD* failed to expand MAIT cells, while inducible MR1 deletion after development did not affect steady-state MAIT cells but prevented their response to *S. epidermidis*; in wounding experiments, MAIT-sufficient *Tcrd−/−* mice had longer epidermal tongues than MAIT-deficient *Mr1−/− Tcrd−/−* mice, and topical 5-OP-RU increased epidermal tongue length in wild-type mice.

Methods

  • Mouse immunology study using SPF, germ-free, gnotobiotic, knockout, transgenic, parabiosis, and wound-healing models; early-life colonization was performed by oral gavage or topical skin association, with 16S rRNA sequencing and bacterial whole-genome sequencing to characterize communities and riboflavin synthesis genes.
  • Immune populations were analyzed by flow cytometry, MR1 tetramer enrichment, confocal microscopy, RNA-sequencing, and single-cell RNA-sequencing; human skin specimens from elective surgery were digested and analyzed for MAIT cell frequency.
  • Statistical comparisons used two-tailed unpaired Student’s t-tests; RNA-seq differential expression used DESeq2 with GO enrichment via Metascape, and scRNA-seq used Cell Ranger, CITE-seq-Count, and Seurat.

Limitations

  • The paper states that how microbiota-derived riboflavin intermediates before and after birth contribute to human MAIT cell maturation and long-term tissue imprinting remains to be addressed.
  • The functional wound-healing evidence is from murine punch-biopsy experiments, and MAIT cell function was tested in *Tcrd−/−* mice to reduce competition from γδ T cells, a setting the authors note is more relevant to human skin because human skin has fewer γδ T cells than mouse skin.
  • Evident from the text: human data are limited mainly to skin MAIT cell frequency, and the study relies heavily on specific mouse models, defined bacterial strains, and early-life colonization conditions, so direct human causal tests of MAIT cell function are not provided.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1126/science.aax6624

Cites

80 of 80 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 11 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    A defined five-species early-life microbial community given to neonatal GF mice at weeks 1, 2, and 3 induces MAIT cell development to the same extent as in SPF mice with high MAIT cell frequencies.

    “The colonization of neonatal GF mice with our early-life microbial community induced MAIT cell development to the same extent observed in SPF mice harboring high MAIT cell frequencies (Fig. 1I).”
    Quote in the paperSubstantial claim
  • Findingown data

    Monocolonization of neonatal GF mice with P. mirabilis, but not L. johnsonii, is sufficient to drive MAIT cell development.

    “Indeed, the monocolonization of neonatal GF mice with P. mirabilis, but not L. johnsonii, was sufficient to drive MAIT cell development (Fig. 1K).”
    Quote in the paperSubstantial claim
  • Findingown data

    Topical application of 5-OP-RU to the skin of adult GF mice fails to induce MAIT cells.

    “In agreement with our observation that adult microbial colonization was insufficient to promote MAIT cell development (Fig. 1I), topical application of 5-OP-RU to the skin of adult GF mice failed to induce MAIT cells (Fig. 1L).”
    Quote in the paperSubstantial claim
  • Findingown data

    Cutaneous MAIT cells display a markedly different transcriptional profile from MAIT cells in other tissues by single-cell RNA sequencing.

    “Cutaneous MAIT cells displayed a markedly different transcriptional profile (Figs. 2I–J & S2F–G).”
    Quote in the paperSubstantial claim
  • Findingown data

    Cutaneous MAIT cells express a transcriptional profile consistent with T cell activation, including leukocyte differentiation, migration, cell adhesion, cytokine production, and the ERK1/2 cascade.

    “Gene ontology (GO) enrichment analysis revealed that cutaneous MAIT cells express a transcriptional profile consistent with T cell activation, including leukocyte differentiation, migration and cell adhesion, cytokine production, and the ERK1/2 cascade, which is downstream of TCR signaling (Fig. 2C).”
    Quote in the paperNot a substantial claim
  • May combine two claims. 16
  • Classified as probably not a substantial claim. 7
  • May combine two claims.

    Findingown data

    Genetically identical SPF mice housed in different cages show wide variation in skin MAIT cell proportion, while mice in the same cage have similar frequencies.

    “Although MAIT cells were highly abundant within the skin, WT SPF mice housed in distinct cages showed striking variability in the proportion of MAIT cells among genetically identical animals, ranging from <5%−40% of αβ T cells (Fig. 1D–E). In contrast, animals in the same cage had similar frequencies of MAIT cells in the skin and other organs (Fig. 1E)”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    MAIT cells are highly enriched in mouse skin, where they can make up as much as 40% of αβ T cells.

    “This analysis revealed that MAIT cells were highly enriched in the skin (Fig. 1B–C), where they comprised up to 40% of αβ T cells (Fig. 1D–E).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Topical application of 5-OP-RU to the skin of GF mice beginning at one week of age significantly increases skin MAIT cell numbers without promoting other T cell subsets.

    “Topical application of 5-OP-RU was sufficient to induce a significant increase in the number of MAIT cells within the skin (Fig. 1L), without promoting the accumulation of other T cell subsets (Fig. S1J).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    MAIT cells are enriched in human skin compared with peripheral blood, averaging about 2% of CD3+ lymphocytes.

    “Furthermore, MAIT cells were also enriched in human skin compared to the reported ~1% in peripheral blood (20), averaging ~2% of CD3+ lymphocytes (Fig. 1F).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Following stimulation, skin MAIT cells robustly produce IL-17A but not IFNγ.

    “Following stimulation, skin MAIT cells robustly produced IL-17A, but not IFNγ (Fig. 2A)”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Topical association with S. epidermidis expands the cutaneous double-negative MAIT cell population and increases their IL-17A production.

    “we observed that in both cases, topical association expanded the cutaneous DN MAIT cell population and increased their production of IL-17A (Figs. 3A–D & S3B–D).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Association with the S. epidermidis ΔribD mutant fails to induce a MAIT cell response, while CD8+ and γδ T cell responses are conserved.

    “association with the S. epidermidis ΔribD mutant failed to induce a MAIT cell response (Fig. 4C), even though the CD8+ and γδ T cell responses were conserved (Fig. S4B–C).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Early-life exposure to commensals that produce defined metabolites, or to microbially derived metabolites alone, is required for MAIT cell development and for their presence later in life.

    “Thus, early-life exposure to commensals that produce defined metabolites, or to microbially derived metabolites alone, is required for MAIT cell development and their presence later in life.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Homeostatic IL-23 contributes to MAIT cell development and/or accumulation within tissues.

    “supporting the idea that homeostatic IL-23 contributes to MAIT cell development and/or accumulation within tissues.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Microbial exposure in early life is required for the development of tissue MAIT cells, but not for thymic developmental stages.

    “indicating that microbial exposure in early life is required for the development of tissue MAIT cells, but not the thymic developmental stages.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    In the reported mouse experiments, mice were matched for age and sex and were between 6 and 12 weeks old unless stated otherwise.

    “Unless otherwise noted, age- and sex-matched mice between 6 and 12 weeks of age were used for each experiment.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Dead cells were excluded from flow cytometric analyses using DAPI for live samples and LIVE/DEAD or Ghost Dye Violet 510 for fixed samples.

    “Dead cells were excluded from live samples using 4′, 6-diamidino-2-phenylindol (DAPI; Sigma-Aldrich), whereas either LIVE/DEAD Fixable Blue Dead Cell Stain Kit (Invitrogen Life Technologies) or Ghost Dye Violet 510 (Tonbo Biosciences) was used in fixed samples.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    For single-cell RNA-sequencing analysis, only singlets were retained, leaving 585 cells.

    “HTO were read in and assigned to the single cells and only singlets were used for further analysis leaving 585 cells.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationown data

    MAIT cells are induced during a specific early-life window in response to riboflavin-synthesizing commensals, and this permanently imprints the abundance of this subset in tissues.

    “Notably, we show that MAIT cells are induced during a specific early-life window in response to riboflavin-synthesizing commensals, a phenomenon that permanently imprints the abundance of this subset in tissues.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    The S. epidermidis ribD deletion mutants used were verified by colony PCR and sequencing.

    “Successful knockouts were confirmed by colony PCR and sequencing.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Flow cytometric staining was performed in the presence of purified anti-mouse CD16/32 and purified rat gamma globulin.

    “All staining was performed in the presence of purified anti-mouse CD16/32 and purified rat gamma globulin (Jackson ImmunoResearch).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationown data

    γδ T cells restrict the MAIT cell population at steady state and constrain their response to commensals.

    “Therefore, γδ T cells restrict the MAIT cell population at steady-state and constrain their response to commensals.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    In single-cell RNA-sequencing analysis, cells were filtered to retain those with 900-3,000 gene counts, no more than 5% mitochondrial contamination, and no more than 10,000 RNA counts, leaving 5,678 cells.

    “Cells with less than 900 or more than 3,000 gene counts, more than 5% mitochondrial contamination, or more than 10,000 RNA counts were filtered out, leaving 5,678 cells for downstream analysis.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Interpretationnone given

    A central strategy by which the immune system interacts with the microbiota may be recognition of canonical microbially derived antigens by unconventional T cells, including MAIT cells, and this dialogue may play a dominant role in controlling host physiology.

    “In conclusion, our work proposes that a central strategy utilized by the immune system to interact with the microbiota may be via the recognition of canonical microbially derived antigens by unconventional T cells, including MAIT cells, a dialogue that may play a dominant role in the control of host physiology.”
    Quote in the paperNot a substantial claim
19 of 19
  • The paper relies on this without support.

    Human T cells develop in utero.

    “In contrast to mice, human T cells develop in utero supporting the hypothesis that such early MAIT cell imprinting may occur prior to birth.”
1 of 1

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The development and maturation of MAIT cells are dependent on microbiota, as demonstrated by reduced numbers of MAIT cells in GF mice, which can be restored through microbial colonization.

    “The development and maturation of MAIT cells are dependent on microbiota, as demonstrated by reduced numbers of MAIT cells in GF mice, which can be restored through microbial colonization.”

Cites

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Authors
Constantinides, M. G., Link, V. M., Tamoutounour, S., Wong, A. C., Perez-Chaparro, P. J., Han, S.-J., Chen, Y. E., Li, K., Farhat, S., Weckel, A., Krishnamurthy, S. R., Vujkovic-Cvijin, I., Linehan, J. L., Bouladoux, N., Merrill, E. D., Roy, S., Cua, D. J., Adams, E. J., Bhandoola, A., Scharschmidt, T. C., Aubé, J., Fischbach, M. A., & Belkaid, Y.
Affiliations
  • National Institutes of Health (US)
  • University of Pennsylvania (US)
  • NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
  • Stanford University (US)
  • University of North Carolina at Chapel Hill (US)
  • University of California, San Francisco (US)
  • University of Chicago (US)
  • Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
Corresponding author
Belkaid, Yasmine
Venue
Science
Published
2019-10-25
Volume
366
Issue
6464
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W2981494076
Cited by
567
References
81
Citations by year
2026: 57 · 2025: 93 · 2024: 82 · 2023: 81 · 2022: 92 · 2021: 76 · 2020: 80 · 2019: 4
FWCI
25.13
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • National Institutes of Health (R01-DK110174, DP1-DK113598, U19-AI111143)
  • Howard Hughes Medical Institute
  • National Institute of General Medical Sciences
  • Chan Zuckerberg Biohub
  • Cancer Research Institute
  • European Molecular Biology Organization
  • Division of Intramural Research, National Institute of Allergy and Infectious Diseases (ZIA-AI001115, ZIA-AI001132)
Topics
  • Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
  • Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
  • Life Sciences › Immunology and Microbiology › Immunology › Psoriasis: Treatment and Pathogenesis
Keywords
mucosal-associated invariant T cells, gut microbiota, MR1, riboflavin derivatives, thymus development, commensal bacteria, tissue repair, skin, mucosal immunity, microbial metabolites, germ-free mice
MeSH terms
Mucosal-Associated Invariant T Cells, Animals, Bacteria, Germ-Free Life, Humans, Interleukin-1, Mice, Inbred BALB C, Mice, Inbred C57BL, Riboflavin, Skin, Specific Pathogen-Free Organisms, Wound Healing, Histocompatibility Antigens Class I, Minor Histocompatibility Antigens, Mice, Knockout, Interleukin-17, Interleukin-18, Mice, Interleukin-23, Microbiota

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