Lactobacilli Have a Niche in the Human Nose

Although an increasing number of beneficial microbiome members are characterized for the human gut and vagina, beneficial microbes are underexplored for the human upper respiratory tract (URT). In this study, we demonstrate that taxa from the beneficial Lactobacillus genus complex are more prevalent in the healthy URT than in patients with chronic rhinosinusitis (CRS). Several URT-specific isolates are cultured, characterized, and further explored for their genetic and functional properties related to adaptation to the URT. Catalase genes are found in the identified lactobacilli, which is a unique feature within this mostly facultative anaerobic genus. Moreover, one of our isolated strains, Lactobacillus casei AMBR2, contains fimbriae that enable strong adherence to URT epithelium, inhibit the growth and virulence of several URT pathogens, and successfully colonize nasal epithelium of healthy volunteers. This study thus demonstrates that specific lactobacilli are adapted to the URT and could have a beneficial keystone function in this habitat. •Lactic acid bacteria are enriched in the healthy human nose and nasopharynx•Lactobacillus casei AMBR2 is functionally adapted to the upper respiratory tract•L. casei AMBR2 has antimicrobial and immunomodulatory properties•Live L. casei AMBR2 is safe for intranasal application in healthy humans De Boeck et al. show that lactobacilli are decreased in patients with chronic rhinosinusitis and enriched in healthy controls. They isolate one strain adapted to the nasopharyngeal mucosa that shows beneficial probiotic effects and safety in the form of a nasal spray in healthy volunteers.