High Abundance of Gut Bacteroides in Early Childhood correlates with Microbiome Stability and Resilience after Antibiotic Treatment and with Increased Risk for Childhood Infections

Background Early childhood events, up to the age of two, are critical for the development of the microbiome and balanced immunity later in life. We investigated whether susceptibility to infections and microbiome resilience after antibiotic treatment are associated with key taxa in the early childhood microbiota. Therefore, we performed longitudinal microbiota analysis from stool samples of children within the German LöwenKIDS intensified subcohort. According to the exposure to antibiotic treatment, sample groups were defined as never-treated controls, 45–225 days pre-treatment (pre45-225), 0–30 days pre-treatment (pre0-30), 0–30 days post-treatment (post0-30), or > 90 days post-treatment and age > 540 days (post > 90). Results 1176 stool samples of 162 children were included in our analysis, of which 49 children received antibiotics. Using generalized linear mixed models adjusted for age, we show that high abundance of Bacteroides was associated with receiving antibiotic treatment later, while low Bacteroides abundance before treatment was associated with low alpha diversity and increased beta diversity post treatment. Conclusions Our data suggest a key role of the genus Bacteroides for the susceptibility to infections requiring antibiotic treatment and for microbiome stability and resilience in early childhood.