Early gut mycobiota and mother-offspring transfer

Microbiome. 2017 Aug 24;5(1):107. doi: 10.1186/s40168-017-0319-x.


Background: The fungi in the gastrointestinal tract, the gut mycobiota, are now recognised as a significant part of the gut microbiota, and they may be important to human health. In contrast to the adult gut mycobiota, the establishment of the early gut mycobiota has never been described, and there is little knowledge about the fungal transfer from mother to offspring.

Methods: In a prospective cohort, we followed 298 pairs of healthy mothers and offspring from 36 weeks of gestation until 2 years of age (1516 samples) and explored the gut mycobiota in maternal and offspring samples. Half of the pregnant mothers were randomised into drinking probiotic milk during and after pregnancy. The probiotic bacteria included Lactobacillus rhamnosus GG (LGG), Bifidobacterium animalis subsp. lactis Bb-12 and Lactobacillus acidophilus La-5. We quantified the fungal abundance of all the samples using qPCR of the fungal internal transcribed spacer (ITS)1 segment, and we sequenced the 18S rRNA gene ITS1 region of 90 high-quantity samples using the MiSeq platform (Illumina).

Results: The gut mycobiota was detected in most of the mothers and the majority of the offspring. The offspring showed increased odds of having detectable faecal fungal DNA if the mother had detectable fungal DNA as well (OR = 1.54, p = 0.04). The fungal alpha diversity in the offspring gut increased from its lowest at 10 days after birth, which was the earliest sampling point. The fungal diversity and fungal species showed a succession towards the maternal mycobiota as the child aged, with Debaryomyces hansenii being the most abundant species during breast-feeding and Saccharomyces cerevisiae as the most abundant after weaning. Probiotic consumption increased the gut mycobiota abundance in pregnant mothers (p = 0.01).

Conclusion: This study provides the first insight into the early fungal establishment and the succession of fungal species in the gut mycobiota. The results support the idea that the fungal host phenotype is transferred from mother to offspring.

Trial registration: Clinicaltrials.gov NCT00159523.

Keywords: Fungi; Gut microbiota; Infant; Infant health; Mycobiota; Newborn; Probiotics.

Publication types

  • Randomized Controlled Trial

MeSH terms

  • Adult
  • Breast Feeding
  • Child, Preschool
  • Cohort Studies
  • DNA, Ribosomal Spacer
  • Debaryomyces / genetics
  • Debaryomyces / isolation & purification
  • Feces / microbiology*
  • Female
  • Fungi / classification
  • Fungi / genetics*
  • Fungi / isolation & purification
  • Gastrointestinal Microbiome*
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Infant
  • Infant, Newborn
  • Male
  • Mothers
  • Mycobiome*
  • Pregnancy
  • Probiotics / administration & dosage*
  • Prospective Studies
  • RNA, Ribosomal, 16S
  • RNA, Ribosomal, 18S
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / isolation & purification
  • Time Factors


  • DNA, Ribosomal Spacer
  • RNA, Ribosomal, 16S
  • RNA, Ribosomal, 18S

Associated data

  • ClinicalTrials.gov/NCT00159523