show Abstracthide AbstractImmunoglobulin A (IgA) is crucial for host-microbial homeostasis in the mammalian intestine. We identified intestinal Lactobacillus sp. to be differently targeted by host IgA in undernourished mice compared to healthy controls. Altered IgA recognition was a direct result of bacterial adaptations to host diet. Here we deposit whole genome sequencing data of Lactobacillus johnsonnii isolates from healthy or undernourished mice which display high or low IgA-binding abilities, respectively.