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Human leukocyte antigen-dependent colonization of Lactobacillus in the early-life gut

Meghan A Berryman1, Eric W Triplett1, Johnny Ludvigsson2

  • 1Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States.

Frontiers in Microbiomes
|March 19, 2026
PubMed

Insights

Lactobacillus colonization in infants is influenced by breastfeeding and human leukocyte antigen (HLA) genetics. Even with breastfeeding, many infants do not host Lactobacillus, highlighting the role of HLA type in gut microbiome development.

Area of Science:

  • Microbiome research
  • Pediatric health
  • Immunogenetics

Background:

  • Lactobacillus plays a role in the human gut microbiome.
  • Factors influencing Lactobacillus colonization in infants are not fully understood.

Purpose of the Study:

  • To investigate the prevalence and determinants of Lactobacillus colonization in a pediatric population.
  • To explore the relationship between breastfeeding, age, and Lactobacillus colonization.
  • To examine the influence of human leukocyte antigen (HLA) genetics on Lactobacillus colonization.

Main Methods:

  • Analysis of stool microbial composition from 1,602 children (0.3-37.2 months) in the All Babies in Southeast Sweden study.
  • Correlation of Lactobacillus prevalence and abundance with age, breastfeeding status, and HLA genotype.

Main Results:

  • Lactobacillus colonized only 32% of the pediatric cohort, with decreasing prevalence and abundance over time.
  • Active breastfeeding was a key factor, but 45.6% of breastfed infants remained uncolonized.
  • HLA genotype significantly impacted colonization; specific HLA types were associated with higher or lower Lactobacillus presence.

Conclusions:

  • Lactobacillus colonization in infants is multifactorial, influenced by both breastfeeding and host genetics.
  • HLA genetics are a significant determinant of Lactobacillus colonization, independent of breastfeeding status.
  • Consideration of HLA genetics is recommended for the development of Lactobacillus-based probiotics.

Keywords:
ABISDR15-DQ6DR5-DQ7Lactobacillusceliac diseasemicrobiomeprobiotictype 1 diabetes

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