Association Between Gut Microbiota Development and Allergy in Infants Born During Pandemic-Related Social Distancing Restrictions

To examine the effects of variations in microbial exposure and gut microbiota development in the first year of life on the prevalence of allergies at up to 24 months of age.The study included 360 infants recruited postnatally to the CORAL study (Impact of Coronavirus Pandemic on Allergic and autoimmune dysregulation in Infants Born During Lockdown). A longitudinal prospective study was conducted with term Irish infants born during the first 3 months of the COVID-19 pandemic. Exclusion criteria were prebirth polymerase chain reaction–proven SARS-CoV-2 infection in a parent or co-dwelling person, intravenous antibiotics in the neonatal period, multiple births, or major congenital anomaly.Fecal samples were sequenced from infants at 6 and 12 months of age using 16S sequencing. Published 16S data from pre-pandemic cohorts were used for microbiota comparisons. Online questionnaires were used to obtain information on home environment, infant health, allergic diseases, diet, and health care utilization. At 12 and 24 months of age, skin prick testing was performed (to peanut, egg, milk, house dust mite, grass pollen, and cat dander) and assessments were made regarding atopic dermatitis and food allergies.The amount of bifidobacteria was higher, and that of environmentally transmitted bacteria such as Clostridia was lower, in CORAL infants compared with previous cohorts. The abundance of multiple Clostridia taxa correlated with a microbial exposure index. A more plant-based food diet led to relative abundances of Bifidobacterium, Lactobacillus, Collinsella, and Bacteroides, similar to breastfeeding and vaginal birth. Bifidobacteria levels at 6 months of age and relative abundance of butyrate producers (like Clostridia) at 12 months of age were negatively correlated with atopic dermatitis and skin prick test positivity. However, the prevalence of allergen sensitization, atopic dermatitis, and food allergy was not increased over pre-pandemic levels.The gut microbiota in infants born during the early stage of the COVID-19 pandemic was different compared with pre-pandemic cohorts, and specific taxa were associated with risk of allergic diseases. However, the results do not support the hypothesis that this deviation in microbiota development resulted in increased allergic diseases. The data support the importance of increasing the relative abundance of beneficial maternally transmitted microbes along with plant-based dietary support to protect against allergic diseases.Several hypotheses have linked reduced microbial exposure to increased prevalence of allergies. During and following birth, infants acquire microbes from their mother (vertical transmission), and later, especially after the first 6 months, from the environment (horizontal transmission). Although reduced exposure to humans and environment outside of the immediate family during the COVID-19 restrictions altered infants’ gut microbiota development in this study, with a lower relative abundance of horizontally transmitted bacteria and a higher relative abundance of bifidobacteria, factors such as lack of breastfeeding and subsequent plant-based weaning food and frequent antibiotic use may be more contributory to the development of allergic diseases.