Strain-Level Differences of <i>Bifidobacterium breve</i> in the Gut Microbiome between Infants with and without Atopic Dermatitis: Insights from Genome Analysis and Immune Assays

<i>Bifidobacterium breve</i> is recognized as a probiotic with immune-enhancing properties. However, our previous studies revealed that this species is present at a higher relative abundance in the gut microbiome of infants with atopic dermatitis (AD). The potential functions of <i>B. breve</i> in the gut microbiome may vary at the strain level between infants with and without AD (non-AD). In this study, <i>B. breve</i> strains were isolated from the feces of infants with and without AD and analyzed whole genome sequencing and immune assay to identify strain level differences between AD and non-AD groups. Three <i>B. breve</i> strains were isolated from the feces of infants with AD (MHL_0001), in remission (MHL_0043), and non-AD infants (MHL_0062). The genomes of these isolates were compared to available complete genomes of <i>B. breve</i> strains. While the three isolates exhibited high overall genome similarity, differences in the sequence homology of immune related genes were observed between the AD strain (MHL_0001) and non-AD strain (MHL_0062). Immune assays further revealed marked differences in the anti-inflammatory effects between MHL_0001 and MHL_0062. These findings suggest that probiotic bacteria such as <i>B. breve</i> may adapt within the gut in response to host immune and physiological conditions. Moreover, the presence of <i>B. breve</i> in the gut microbiome does not necessarily guarantee beneficial effects for the host. Therefore, strain-level analysis is crucial to accurately determine the functional roles and impact of probiotic bacteria.