Home entertainment Fungal symbiont transmitted by free-living mice promotes type 2 immunity

Fungal symbiont transmitted by free-living mice promotes type 2 immunity

23
0

  • Iliev, I. D. & Leonardi, I. Fungal dysbiosis: immunity and interactions at mucosal barriers. Nat. Rev. Immunol. 17, 635–646 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rosshart, S. P. et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science 365, eaaw4361 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dollive, S. et al. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS ONE 8, e71806 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Limon, J. J., Skalski, J. H. & Underhill, D. M. Commensal fungi in health and disease. Cell Host Microbe 22, 156–165 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Solomon, K. V. et al. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Science 351, 1192–1195 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Doron, I. et al. Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies. Cell 184, 1017–1031.e1014 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, X. V. et al. Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature 603, 672–678 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhai, B. et al. High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis. Nat. Med. 26, 59–64 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Koh, A. Y., Kohler, J. R., Coggshall, K. T., Van Rooijen, N. & Pier, G. B. Mucosal damage and neutropenia are required for Candida albicans dissemination. PLoS Pathog. 4, e35 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Limon, J. J. et al. Malassezia is associated with Crohn’s disease and exacerbates colitis in mouse models. Cell Host Microbe 25, 377–388 e376 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Ivanov, I. I. et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fiers, W. D., Gao, I. H. & Iliev, I. D. Gut mycobiota under scrutiny: fungal symbionts or environmental transients? Curr. Opin. Microbiol. 50, 79–86 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • van Uden, N. Zur Kenntnis von Torulopsis pintolopesii sp. nov. Mit Beobachtungen über die parasitäre Phase von Acladium castellanii Pinoy. Archiv für Mikrobiologie 17, 199–208 (1952).

    Article 
    CAS 

    Google Scholar 

  • Savage, D. C. & Dubos, R. J. Localization of indigenous yeast in the murine stomach. J. Bacteriol. 94, 1811–1816 (1967).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fan, D. et al. Activation of HIF-1α and LL-37 by commensal bacteria inhibits Candida albicans colonization. Nat. Med. 21, 808–814 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vylkova, S. et al. The fungal pathogen Candida albicans autoinduces hyphal morphogenesis by raising extracellular pH. mBio 2, e00055-00011 (2011).

    Article 

    Google Scholar 

  • Chen, H., Zhou, X., Ren, B. & Cheng, L. The regulation of hyphae growth in Candida albicans. Virulence 11, 337–348 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rahman, D., Mistry, M., Thavaraj, S., Challacombe, S. J. & Naglik, J. R. Murine model of concurrent oral and vaginal Candida albicans colonization to study epithelial host-pathogen interactions. Microbes Infect. 9, 615–622 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McDonough, L. D. et al. Candida albicans isolates 529L and CHN1 exhibit stable colonization of the murine gastrointestinal tract. mBio 12, e0287821 (2021).

    Article 
    PubMed 

    Google Scholar 

  • Liang, S. H. et al. Hemizygosity enables a mutational transition governing fungal virulence and commensalism. Cell Host Microbe 25, 418–431.e416 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tso, G. H. W. et al. Experimental evolution of a fungal pathogen into a gut symbiont. Science 362, 589–595 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Shao, T. Y. et al. Commensal Candida albicans positively calibrates systemic Th17 immunological responses. Cell Host Microbe 25, 404–417.e406 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hoffmann, C. et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE 8, e66019 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tropini, C., Earle, K. A., Huang, K. C. & Sonnenburg, J. L. The gut microbiome: connecting spatial organization to function. Cell Host Microbe 21, 433–442 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kurtzman, C. P. et al. Multigene phylogenetic analysis of pathogenic candida species in the Kazachstania (Arxiozyma) telluris complex and description of their ascosporic states as Kazachstania bovina sp. nov., K. heterogenica sp. nov., K. pintolopesii sp. nov., and K. slooffiae sp. nov. J. Clin. Microbiol. 43, 101–111 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ha, N. C. et al. Supramolecular assembly and acid resistance of Helicobacter pylori urease. Nat. Struct. Biol. 8, 505–509 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Lionakis, M. S., Drummond, R. A. & Hohl, T. M. Immune responses to human fungal pathogens and therapeutic prospects. Nat. Rev. Immunol. 23, 433–452 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Leonardi, I. et al. Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity. Cell 185, 831–846.e814 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Desai, M. S. et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339–1353.e1321 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Conti, H. R. et al. Th17 cells and IL-17 receptor signaling are essential for mucosal host defense against oral candidiasis. J. Exp. Med. 206, 299–311 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wlodarska, M. et al. Antibiotic treatment alters the colonic mucus layer and predisposes the host to exacerbated Citrobacter rodentium-induced colitis. Infect. Immun. 79, 1536–1545 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cayrol, C. et al. Environmental allergens induce allergic inflammation through proteolytic maturation of IL-33. Nat. Immunol. 19, 375–385 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Fei, L. et al. Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development. Nat. Genet. 54, 1051–1061 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Schmitz, J. et al. IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines. Immunity 23, 479–490 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Lefrancais, E. et al. Central domain of IL-33 is cleaved by mast cell proteases for potent activation of group-2 innate lymphoid cells. Proc. Natl Acad. Sci. USA 111, 15502–15507 (2014).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Brandt, E. B. et al. Mast cells are required for experimental oral allergen-induced diarrhea. J. Clin. Invest. 112, 1666–1677 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Galli, S. J. & Tsai, M. IgE and mast cells in allergic disease. Nat. Med. 18, 693–704 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Diesner, S. C. et al. Dose-dependent food allergy induction against ovalbumin under acid-suppression: a murine food allergy model. Immunol. Lett. 121, 45–51 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Anderson, R. M. & May, R. M. Coevolution of hosts and parasites. Parasitology 85, 411–426 (1982).

    Article 
    PubMed 

    Google Scholar 

  • Florsheim, E. B., Sullivan, Z. A., Khoury-Hanold, W. & Medzhitov, R. Food allergy as a biological food quality control system. Cell 184, 1440–1454 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Camberis, M., Le Gros, G. & Urban, J. Jr. Animal model of Nippostrongylus brasiliensis and Heligmosomoides polygyrus. Curr. Protoc. Immunol. https://doi.org/10.1002/0471142735.im1912s55 (2003).

  • Hube, B. From commensal to pathogen: stage- and tissue-specific gene expression of Candida albicans. Curr. Opin. Microbiol. 7, 336–341 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Heckman, D. S. et al. Molecular evidence for the early colonization of land by fungi and plants. Science 293, 1129–1133 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Hardison, S. E. & Brown, G. D. C-type lectin receptors orchestrate antifungal immunity. Nat. Immunol. 13, 817–822 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S. & Medzhitov, R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118, 229–241 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Trompette, A. et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat. Med. 20, 159–166 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Leidy, J. On the existence of entophyta in healthy animals, as a natural condition. Proc. Acad. Natl. Sci. Phila. 4, 225–233 (1849).

    Google Scholar 

  • Sekeresova Kralova, J. et al. Competitive fungal commensalism mitigates candidiasis pathology. J. Exp. Med. 221, e20231686 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tan, T. G. et al. Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice. Proc. Natl Acad. Sci. USA 113, E8141–E8150 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Alexander, M. et al. Human gut bacterial metabolism drives Th17 activation and colitis. Cell Host Microbe 30, 17–30.e19 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ladinsky, M. S. et al. Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis. Science 363, eaat4042 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Atarashi, K. et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell 163, 367–380 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Perdue, K. A. et al. Naturally occurring murine norovirus infection in a large research institution. J. Am. Assoc. Lab. Anim. Sci. 46, 39–45 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • Beura, L. K. et al. Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature 532, 512–516 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yeung, F. et al. Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. Cell Host Microbe 27, 809–822.e806 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rutlin, M. et al. The Villin1 gene promoter drives cre recombinase expression in extraintestinal tissues. Cell. Mol. Gastroenterol. Hepatol. 10, 864–867.e865 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Doron, I. et al. Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease. Nat. Microbiol. 6, 1493–1504 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Christensen, W. B. Urea decomposition as a means of differentiating proteus and paracolon cultures from each other and from Salmonella and Shigella types. J. Bacteriol. 52, 461–466 (1946).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Han, H. et al. IL-33 promotes gastrointestinal allergy in a TSLP-independent manner. Mucosal Immunol. 11, 394–403 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Esterhazy, D. et al. Compartmentalized gut lymph node drainage dictates adaptive immune responses. Nature 569, 126–130 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Leonardi, I. et al. CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi. Science 359, 232–236 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Ewels, P. A. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 38, 276–278 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Straub, D. et al. Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (gene) amplicon sequencing pipeline. Front. Microbiol. 11, 550420 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).

    Article 

    Google Scholar 

  • Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Leonardi, I. et al. Fungal trans-kingdom dynamics linked to responsiveness to fecal microbiota transplantation (FMT) therapy in ulcerative colitis. Cell Host Microbe 27, 823–829 e823 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinformatics 14, 178–192 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Medaka, O. Sequence correction provided by ONT Research. GitHub https://github.com/nanoporetech/medaka (2018).

  • Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).

  • Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M. & Stanke, M. BRAKER1: unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32, 767–769 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Rawlings, N. D., Waller, M., Barrett, A. J. & Bateman, A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 42, D503–D509 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Fuentes, D. et al. PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. Nucleic Acids Res. 50, D1062–D1068 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Demir, M. et al. The fecal mycobiome in non-alcoholic fatty liver disease. J. Hepatol. 76, 788–799 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Hartmann, P. et al. Dynamic changes of the fungal microbiome in alcohol use disorder. Front. Physiol. 12, 699253 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nash, A. K. et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome 5, 153 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Xu, J. et al. Alterations of fungal microbiota in patients with cholecystectomy. Front. Microbiol. 13, 831947 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Abarenkov, K. et al. The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered. Nucleic Acids Res. 52, D791–D797 (2024).

    Article 
    PubMed 

    Google Scholar 

  • Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S. & Ralser, M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat. Methods 17, 41–44 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333–339 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pan, X. et al. Identifying a confused cell identity for esophageal squamous cell carcinoma. Signal Transduct. Target. Ther. 7, 122 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Alquicira-Hernandez, J. & Powell, J. E. Nebulosa recovers single-cell gene expression signals by kernel density estimation. Bioinformatics 37, 2485–2487 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • source

    LEAVE A REPLY

    Please enter your comment!
    Please enter your name here