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

Abstract

Bifidobacterium breve 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 B. breve in the gut microbiome may vary at the strain level between infants with and without AD (non-AD). In this study, B. breve 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 B. breve 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 B. breve 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 B. breve may adapt within the gut in response to host immune and physiological conditions. Moreover, the presence of B. breve 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. Copyright © 2025 by the authors. Licensee KMB. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.