Gut microbiome influences immune development. We investigated the relationship between colostrum microbiome and allergic disease to 18 years in a birth cohort at high risk of allergy.

Mothers (n=189) from Melbourne Atopy Cohort Study provided colostrum. Microbial DNA extracted using Power Food DNA (MoBio), sequenced using V3-V4 regions of 16S rRNA gene (Illumina). Shannon index measured alpha diversity. Beta diversity measured by PCoA/ PERMANOVA. Clinical characteristics recorded over childhood by questionnaires on wheeze/asthma/eczema/hayfever and Skin Prick Tests for common food/aero-allergens at 1,2,12 and 18 yrs. Using all time points, 2 Latent Class Analyses were performed: 1 found 2 classes of clinical allergy: minimal/resolved (72%), persistent(28%), and the second found 3 sensitization classes: minimal(41%), late aero(46%), high food/aero (13%).

Colostrum had 273 Operational Taxonomic Units. Top 5 genera (rel. abund.) were Rothia (18%), Acinetobacter(6%), Staphylococcus (5%), Neisseria (3%) and Streptococcus (3%). Children with persistent clinical allergies consumed colostrum with higher median relative abundance of Veillonella, Rothia and Acinetobacter.  Increased ? diversity in top three quartiles of Shannon index was associated with reduced odds of late aero sensitization by 96%, 85%, and 93%, respectively compared to 1st quartile (least diverse) (eg Q4vsQ1 OR 0.071 95%CI 0.006, 0.889). No associations found for ? diversity.

Colostrum microbiome composition differed for children with clinical allergy and sensitization up to age 18 years. Reduced ? diversity was associated with increased risk of atopy /allergy. Strategies that protect or promote microbial diversity in colostrum may reduce allergy risk in breastfed children.