Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance

An Author Correction to this article was published on 06 September 2019

This article has been updated


Neonates at risk of childhood atopy and asthma exhibit perturbation of the gut microbiome, metabolic dysfunction and increased concentrations of 12,13-diHOME in their faeces. However, the mechanism, source and contribution of this lipid to allergic inflammation remain unknown. Here, we show that intra-abdominal treatment of mice with 12,13-diHOME increased pulmonary inflammation and decreased the number of regulatory T (Treg) cells in the lungs. Treatment of human dendritic cells with 12,13-diHOME altered expression of PPARγ-regulated genes and reduced anti-inflammatory cytokine secretion and the number of Treg cells in vitro. Shotgun metagenomic sequencing of neonatal faeces indicated that bacterial epoxide hydrolase (EH) genes are more abundant in the gut microbiome of neonates who develop atopy and/or asthma during childhood. Three of these bacterial EH genes (3EH) specifically produce 12,13-diHOME, and treatment of mice with bacterial strains expressing 3EH caused a decrease in the number of lung Treg cells in an allergen challenge model. In two small birth cohorts, an increase in the copy number of 3EH or the concentration of 12,13-diHOME in the faeces of neonates was found to be associated with an increased probability of developing atopy, eczema or asthma during childhood. Our data indicate that elevated 12,13-diHOME concentrations impede immune tolerance and may be produced by bacterial EHs in the neonatal gut, offering a mechanistic link between perturbation of the gut microbiome during early life and atopy and asthma during childhood.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Peritoneal treatment with 12,13-diHOME exacerbates lung inflammation in mice challenged with CRA.
Fig. 2: 12,13-diHOME acts through PPARγ on DCs to decrease the number of Tregs.
Fig. 3: Neonatal gut-microbiome-derived EH genes from B. bifidum and E. faecalis produce 12,13-diHOME and decrease the number of lung Treg cells in mice challenged with CRA.
Fig. 4: Increased concentrations of 12,13-diHOME and the 3EH genes in neonatal stool are associated with the development of childhood atopy, eczema and/or asthma in two US cohorts.

Data availability

Metagenomic data generated in this study are available in the EMBLI repository as PRJEB24006 (https://www.ebi.ac.uk/ena/). Further datasets and materials are available from the corresponding author on reasonable request.

Code availability

Datasets and R scripts used for statistical analysis and figures are available on GitHub (https://github.com/srlevan/).

Change history

  • 06 September 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


  1. 1.

    Havstad, S. et al. Atopic phenotypes identified with latent class analyses at age 2 years. J. Allergy Clin. Immunol. 134, 722–727 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  2. 2.

    Yamamoto-Hanada, K., Yang, L., Narita, M., Saito, H. & Ohya, Y. Influence of antibiotic use in early childhood on asthma and allergic diseases at age 5. Ann. Allergy Asthma Immunol. 119, 54–58 (2017).

    CAS  PubMed  Article  Google Scholar 

  3. 3.

    Chu, S. et al. Cesarean section without medical indication and risks of childhood allergic disorder, attenuated by breastfeeding. Sci. Rep. 7, 9762 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  4. 4.

    Silvers, K. M. et al. Breastfeeding protects against current asthma up to 6 years of age. J. Pediatr. 160, 991–996 (2012).

    Article  Google Scholar 

  5. 5.

    Fall, T. et al. Early exposure to dogs and farm animals and the risk of childhood asthma. JAMA Pediatr. 169, e153219 (2015).

    PubMed  Article  Google Scholar 

  6. 6.

    Genuneit, J. Exposure to farming environments in childhood and asthma and wheeze in rural populations: a systematic review with meta-analysis. Pediatr. Allergy Immunol. 23, 509–518 (2012).

    PubMed  Article  Google Scholar 

  7. 7.

    Gonzalez-Perez, G. et al. Maternal antibiotic treatment impacts development of the neonatal intestinal microbiome and antiviral immunity. J. Immunol. 196, 3768–3779 (2016).

    CAS  PubMed  Article  Google Scholar 

  8. 8.

    Dominguez-Bello, M. G. et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl Acad. Sci. USA 107, 11971–11975 (2010).

    PubMed  Article  Google Scholar 

  9. 9.

    Fujimura, K. E. et al. House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc. Natl Acad. Sci. USA 111, 805–810 (2014).

    CAS  PubMed  Article  Google Scholar 

  10. 10.

    Arrieta, M.-C. et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci. Transl. Med. 7, 307ra152 (2015).

    PubMed  Article  CAS  Google Scholar 

  11. 11.

    Fujimura, K. E. et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat. Med. 22, 1187–1191 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. 12.

    Durack, J. et al. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nat. Commun. 9, 707 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  13. 13.

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

    CAS  PubMed  Article  Google Scholar 

  14. 14.

    Fonseca, W. et al. Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation. Mucosal Immunol. 10, 1569–1580 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15.

    Hartl, D. et al. Quantitative and functional impairment of pulmonary CD4+ CD25hi regulatory T cells in pediatric asthma. J. Allergy Clin. Immunol. 119, 1258–1266 (2007).

    CAS  PubMed  Article  Google Scholar 

  16. 16.

    Lundström, S. L. et al. Allergic asthmatics show divergent lipid mediator profiles from healthy controls both at baseline and following birch pollen provocation. PLoS ONE 7, e33780 (2012).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  17. 17.

    Lynes, M. D. et al. The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue. Nat. Med. 37, 631–637 (2017).

    Article  CAS  Google Scholar 

  18. 18.

    Stanford, K. I. et al. 12,13-diHOME: an exercise-induced lipokine that increases skeletal muscle fatty acid uptake. Cell Metab. 27, 1111–1120 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  19. 19.

    Zimmer, B. et al. The oxidized linoleic acid metabolite 12,13-DiHOME mediates thermal hyperalgesia during inflammatory pain. Biochim. Biophys. Acta 1863, 669–678 (2018).

    CAS  Article  Google Scholar 

  20. 20.

    Gouveia-Figueira, S., Späth, J., Zivkovic, A. M. & Nording, M. L. Profiling the oxylipin and endocannabinoid metabolome by UPLC-ESI-MS/MS in human plasma to monitor postprandial inflammation. PLoS ONE 10, e0132042 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  21. 21.

    Byndloss, M. X. et al. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 357, 570–575 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22.

    Khare, A., Chakraborty, K., Raundhal, M., Ray, P. & Ray, A. Cutting edge: dual function of PPARγ in CD11c+ cells ensures immune tolerance in the airways. J. Immunol. 195, 431–435 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. 23.

    Wahli, W. & Michalik, L. PPARs at the crossroads of lipid signaling and inflammation. Trends Endocrinol. Metab. 23, 351–363 (2012).

    CAS  PubMed  Article  Google Scholar 

  24. 24.

    Iyer, S. S. & Cheng, G. Role of interleukin 10 transcriptional regulation in inflammation and autoimmune disease. Crit. Rev. Immunol. 32, 23–63 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  25. 25.

    Szatmari, I. et al. PPAR regulates the function of human dendritic cells primarily by altering lipid metabolism. Blood 110, 3271–3280 (2007).

    CAS  PubMed  Article  Google Scholar 

  26. 26.

    Choo, J. et al. A novel peroxisome proliferator-activated receptor (PPAR)γ agonist 2-hydroxyethyl 5-chloro-4,5-didehydrojasmonate exerts anti-inflammatory effects in colitis. J. Biol. Chem. 290, 25609–25619 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  27. 27.

    Woerly, G. et al. Peroxisome proliferator-activated receptors α and γ down-regulate allergic inflammation and eosinophil activation. J. Exp. Med. 198, 411–421 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  28. 28.

    Nobs, S. P. et al. PPARγ in dendritic cells and T cells drives pathogenic type-2 effector responses in lung inflammation. J. Exp. Med. 8, 3015 (2017).

    Article  CAS  Google Scholar 

  29. 29.

    Green, D. et al. Central activation of TRPV1 and TRPA1 by novel endogenous agonists contributes to mechanical allodynia and thermal hyperalgesia after burn injury. Mol. Pain 12, 1–9 (2016).

    CAS  Article  Google Scholar 

  30. 30.

    Wang, Q. et al. [TRPV1 UTR-3 polymorphism and susceptibility of childhood asthma of the Han nationality in Beijing]. Wei Sheng Yan Jiu 38, 516–521 (2009).

    CAS  PubMed  Google Scholar 

  31. 31.

    Baker, K. et al. Role of the ion channel, transient receptor potential cation channel subfamily V member 1 (TRPV1), in allergic asthma. Respir. Res. 17, 67 (2016).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  32. 32.

    Ha, J., Dobretsov, M., Kurten, R. C., Grant, D. F. & Stimers, J. R. Effect of linoleic acid metabolites on Na+/K+ pump current in N20.1 oligodendrocytes: role of membrane fluidity. Toxicol. Appl. Pharmacol. 182, 76–83 (2002).

    CAS  PubMed  Article  Google Scholar 

  33. 33.

    Morisseau, C. Role of epoxide hydrolases in lipid metabolism. Biochimie 95, 91–95 (2013).

    CAS  PubMed  Article  Google Scholar 

  34. 34.

    Biswal, B. K. et al. The molecular structure of epoxide hydrolase B from Mycobacterium tuberculosis and its complex with a urea-based inhibitor. J. Mol. Biol. 381, 897–912 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. 35.

    Decker, M., Arand, M. & Cronin, A. Mammalian epoxide hydrolases in xenobiotic metabolism and signalling. Arch. Toxicol. 83, 297–318 (2009).

    CAS  PubMed  Article  Google Scholar 

  36. 36.

    Kaminski, J. et al. High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput. Biol. 11, e1004557 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  37. 37.

    Cedrone, F., Bhatnagar, T. & Baratti, J. C. Colorimetric assays for quantitative analysis and screening of epoxide hydrolase activity. Biotechnol. Lett. 27, 1921–1927 (2005).

    CAS  PubMed  Article  Google Scholar 

  38. 38.

    Wegienka, G. et al. Combined effects of prenatal medication use and delivery type are associated with eczema at age 2 years. Clin. Exp. Allergy 45, 660–668 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. 39.

    Havstad, S. et al. Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood. J. Allergy Clin. Immunol. 128, 880–885 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. 40.

    Burke, H. et al. Prenatal and passive smoke exposure and incidence of asthma and wheeze: systematic review and meta-analysis. Pediatrics 129, 735–744 (2012).

    PubMed  Article  Google Scholar 

  41. 41.

    Bao, Y. et al. Risk factors in preschool children for predicting asthma during the preschool age and the early school age: a systematic review and meta-analysis. Curr. Allergy Asthma Rep. 17, 85 (2017).

    PubMed  Article  Google Scholar 

  42. 42.

    Cabana, M. D. et al. Early probiotic supplementation for eczema and asthma prevention: a randomized controlled trial. Pediatrics 140, e20163000 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  43. 43.

    Gratton, J. et al. Optimized sample handling strategy for metabolic profiling of human feces. Anal. Chem. 88, 4661–4668 (2016).

    CAS  PubMed  Article  Google Scholar 

  44. 44.

    Tedjo, D. I. et al. The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects. PLoS ONE 10, e0126685 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  45. 45.

    Ye, F. et al. The dipeptide H-Trp-Glu-OH shows highly antagonistic activity against PPARγ: bioassay with molecular modeling simulation. Chembiochem 7, 74–82 (2005).

    Article  CAS  Google Scholar 

  46. 46.

    Laukens, D., Brinkman, B. M., Raes, J., De Vos, M. & Vandenabeele, P. Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design. FEMS Microbiol. Rev. 40, 117–132 (2016).

    CAS  PubMed  Article  Google Scholar 

  47. 47.

    Aichbhaumik, N. et al. Prenatal exposure to household pets influences fetal immunoglobulin E production. Clin. Exp. Allergy 38, 1787–1794 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Cabana, M. D., McKean, M., Wong, A. R., Chao, C. & Caughey, A. B. Examining the hygiene hypothesis: the Trial of Infant Probiotic Supplementation. Paediatr. Perinat. Epidemiol. 21, 23–28 (2007).

    PubMed  Article  Google Scholar 

  49. 49.

    DeAngelis, K. M. et al. Selective progressive response of soil microbial community to wild oat roots. ISME J. 3, 168–178 (2009).

    CAS  PubMed  Article  Google Scholar 

  50. 50.

    Han, M. et al. A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses. Microbiome 6, 43 (2018).

    PubMed  PubMed Central  Article  Google Scholar 

  51. 51.

    Rounge, T. B. et al. Evaluating gut microbiota profiles from archived fecal samples. BMC Gastroenterol. 18, 171 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  52. 52.

    Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).

    CAS  Article  Google Scholar 

  53. 53.

    Suzek, B. E. et al. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926–932 (2015).

    CAS  PubMed  Article  Google Scholar 

  54. 54.

    Tang, L. et al. A high‐throughput adrenaline test for the exploration of the catalytic potential of halohydrin dehalogenases in epoxide ring‐opening reactions. Biotechnol. Appl. Biochem. 62, 451–457 (2015).

    CAS  PubMed  Article  Google Scholar 

  55. 55.

    Maldonado, G. & Greenland, S. Simulation study of confounder-selection strategies. Am. J. Epidemiol. 138, 923–936 (1993).

    CAS  PubMed  Article  Google Scholar 

  56. 56.

    Henke, BradR. et al. N-(2-Benzoylphenyl)-l-tyrosine PPARγ agonists. 1. Discovery of a novel series of potent antihyperglycemic and antihyperlipidemic agents. J. Med. Chem. 41, 5020–5036 (1998).

    CAS  PubMed  Article  Google Scholar 

Download references


We thank the WHEALS and TIPS study participants; A. Iavarone and the mass spectrometry facility and genomic sequencing laboratory at QB3 Berkeley (http://qb3.berkeley.edu/), O. Rosenberg, B. Vogelstein and B. Spiegelman for plasmid donations and N. Lukacs for assessment of the manuscript. This research was funded by NIH/NIAID award AI089473.

Author information




S.R.L. designed the study, performed immune assays, animal models, metagenomic analysis, biochemical assays, mass spectrometry and statistical analyses, and developed the manuscript. K.A.S. assisted with animal models, performed all microscopy analysis and contributed to the manuscript. D.L.L. assisted with animal models and human immune assays. A.R.P. assisted with animal models and manuscript editing. K.E.F. and K.M. assisted with metagenomic and statistical analysis. E.F. assisted with microscopy. D.R.O., E.M.Z. and C.C.J. provided WHEALS cohort samples and data. M.M. and M.D.C. provided TIPS cohort samples and data. H.A.B. contributed to manuscript development. S.V.L. designed and supervised the study and developed the manuscript.

Corresponding author

Correspondence to Susan V. Lynch.

Ethics declarations

Competing interests

S.V.L. is co-founder of Siolta Therapeutics Inc., and serves as both a consultant and a member of its Board of Directors. Furthermore, the Regents of the University of California, UCSF have filed a provisional patent application (Application number 62/637,175) on behalf of S.V.L. and S.R.L. relating to the methods and compositions of EH genes.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–4 and Supplementary Tables 1–14.

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Levan, S.R., Stamnes, K.A., Lin, D.L. et al. Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance. Nat Microbiol 4, 1851–1861 (2019). https://doi.org/10.1038/s41564-019-0498-2

Download citation

Further reading


Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing