Bifidobacterium longum subsp. nexus nov., a novel subspecies isolated from infant stool

Bifidobacterium species are well-established members of the human gut microbiome, particularly prominent during infancy, contributing to host health. Within this genus, Bifidobacterium longum ( BL. ) is a widespread species found in both infant and adult guts, known for its complexity and functional diversity among its known subspecies: BL. longum , BL. infantis and BL. suis . Here, using genomic and phylogenetic tools we propose a novel subspecies within the BL. species, Bifidobacterium longum subsp. nexus subspecies novel. We analyzed 435 BL. genomes using a polyphasic taxonomic approach comprising average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and pangenome analysis. We identified nine BL. strains, isolated from human infants and adults stool samples, as members of a distinct lineage within the BL. species. The type strain, LL6991, was isolated from the stool of a two-week-old Dutch infant in the Lifelines NEXT birth cohort. Phenotypically, BL. nexus exhibits a distinct morphological pattern, predominantly forming rod-shaped cells, often in chains with visible septa, contrasting with the Y-shaped morphology commonly observed for other BL. subspecies. Furthermore, BL. nexus demonstrates unique metabolic capabilities, including efficient utilization of fructose, and starch, carbohydrates not metabolized well by other tested BL. subspecies. This ability may be attributed to specific genes, such as a gene predicted to encode an extracellular amylopullulanase. This characterization expands the known diversity within the BL. species and provides insights into BL. nexus ’s unique adaptations and potential ecological roles within the human gut, especially in infants. Based on the consistent results from genotypic, phylogenetic, and phenotypic analyses, a novel subspecies with the name Bifidobacterium longum subsp. nexus , with type strain LL6991, is proposed.