Methods: Data from 298 infants enrolled in the Wayne County Health Environment Allergy and Asthma Longitudinal Study (WHEALS) birth cohort were analyzed. Using infant stool samples collected over the first 6 months of life (N=130), gut microbiome was profiled by 16S rRNA sequencing. Allergic-like response to pets at age 4 was defined as parental report of any coughing, wheezing, tightness, shortness of breath, runny nose, sneezing, or itchy eyes around pets. Compositional differences in the microbiome were evaluated using permutational multivariate analysis of variance. Tests of differential operational taxonomic unit (OTU) abundance were performed using zero-inflated negative binomial regression with false discovery rate adjustment (significance threshold q-value<0.05).
Results: Babies currently breastfed at 1 month were at decreased risk of developing allergic-like response to pets (p-value=0.028). Both breastfeeding and allergic-like response to pets were significantly related to compositional variation in gut microbiome (p-value<0.001, p-value=0.023, respectively). Of the 109 OTUs significantly associated with both breastfeeding and allergic-like response to pets, 77 (71%) were negatively associated with breastfeeding but positively associated with allergic-like response to pets. This subset of risk-increasing bacteria suppressed by breastfeeding were predominantly members of the family Lachnospiraceae [51 (66%)].
Conclusions: Breastfeeding in infancy may protect against gut enrichment of specific Lachnospiraceae bacteria which are associated with allergic-like response to pets in early childhood.