Gut microbiota bacterial depletions and altered metabolic activity at 3 months are implicated in childhood atopy and asthma1. We hypothesized that compositionally distinct human neonatal gut microbiota (NGM) exist, and are differentially related to relative risk (RR) of childhood atopy and asthma. Using stool samples (n = 298; aged 1–11 months) from a US birth cohort and 16S rRNA sequencing, neonates (median age, 35 d) were divisible into three microbiota composition states (NGM1–3). Each incurred a substantially different RR for multisensitized atopy at age 2 years and doctor-diagnosed asthma at age 4 years. The highest risk group, labeled NGM3, showed lower relative abundance of certain bacteria (for example, Bifidobacterium, Akkermansia and Faecalibacterium), higher relative abundance of particular fungi (Candida and Rhodotorula) and a distinct fecal metabolome enriched for pro-inflammatory metabolites. Ex vivo culture of human adult peripheral T cells with sterile fecal water from NGM3 subjects increased the proportion of CD4+ cells producing interleukin (IL)-4 and reduced the relative abundance of CD4+CD25+FOXP3+ cells. 12,13-DiHOME, enriched in NGM3 versus lower-risk NGM states, recapitulated the effect of NGM3 fecal water on relative CD4+CD25+FOXP3+ cell abundance. These findings suggest that neonatal gut microbiome dysbiosis might promote CD4+ T cell dysfunction associated with childhood atopy.

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This study was supported by the US National Institutes of Health and National Institute of Allergy and Infectious Diseases P01 AI089473-01 (C.C.J., D.R.O., H.A.B., N.W.L., S.V.L., G.W., and E.M.Z.) and the Alfred P. Sloan Foundation 2013-6-03 (S.V.L.). We thank C. Arrieta and B. Finlay for graciously sharing sequencing data from the CHILD study.

Author information

Author notes

    • Christine C Johnson
    •  & Susan V Lynch

    These authors co-directed this work.


  1. Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA.

    • Kei E Fujimura
    • , Din L Lin
    • , Sophia Levan
    • , Douglas Fadrosh
    • , Ariane R Panzer
    • , Brandon LaMere
    • , Elze Rackaityte
    •  & Susan V Lynch
  2. Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA.

    • Alexandra R Sitarik
    • , Suzanne Havstad
    • , Ganesa Wegienka
    • , Albert M Levin
    •  & Christine C Johnson
  3. Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA.

    • Nicholas W Lukacs
  4. Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA.

    • Homer A Boushey
  5. Section of Allergy–Immunology, Augusta University, Augusta, Georgia, USA. .

    • Dennis R Ownby
  6. Department of Internal Medicine, Division of Allergy and Immunology, Henry Ford Health System, Detroit, Michigan, USA.

    • Edward M Zoratti


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S.V.L., C.C.J., D.R.O., H.A.B., N.W.L., G.W., and E.M.Z., designed research; C.C.J., D.R.O., K.E.F., D.F., B.L., D.L.L., S.L., A.R.P., E.R., and G.W., performed research; A.R.S., S.H., and A.M.L. contributed new analytic tools; K.E.F., A.R.S., S.H., S.L., A.M.L., and S.V.L. analyzed data; and K.E.F. and S.V.L. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Christine C Johnson or Susan V Lynch.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–9 and Supplementary Tables 1–2, 8–10; Supplementary Note

Excel files

  1. 1.

    Supplementary Table 3

    Association between early life factors and IGMs

  2. 2.

    Supplementary Table 4

    Association between early life factors and NGMs

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    Supplementary Table 5

    Factors tested for possible confounding effect on the risk of developing PM atopy for NGM

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    Supplementary Table 6

    Bacterial taxa exhibiting significantly increased relative abundance in low-risk NGM1 versus the high-risk NGM3 neonatal gut microbiota

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    Supplementary Table 7

    Bacterial taxa exhibiting significantly increased relative abundance in low-risk NGM2 versus the high-risk NGM3 neonatal gut microbiota

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    Supplementary Table 11

    Metabolites significantly enriched in low-risk NGM1 versus high-risk NGM3 neonatal gut microbiota.

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    Supplementary Table 12

    Metabolites significantly enriched in low-risk NGM2 versus high-risk NGM3 neonatal gut microbiota

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