Recurrent aphthous stomatitis (RAS) is the most common disease of the oral mucosa, and it has been recently associated with bacterial and fungal dysbiosis. To study this link further, we investigated microbial shifts during RAS manifestation at an ulcer site, in its surroundings, and at an unaffected site, compared with healed mucosa in RAS patients and healthy controls. We sampled microbes from five distinct sites in the oral cavity. The one site with the most pronounced differences in microbial alpha and beta diversity between RAS patients and healthy controls was the lower labial mucosa. Detailed analysis of this particular oral site revealed strict association of the genus Selenomonas with healed mucosa of RAS patients, whereas the class Clostridia and genera Lachnoanaerobaculum, Cardiobacterium, Leptotrichia, and Fusobacterium were associated with the presence of an active ulcer. Furthermore, active ulcers were dominated by Malassezia, which were negatively correlated with Streptococcus and Haemophilus and positively correlated with Porphyromonas species. In addition, RAS patients showed increased serum levels of IgG against Mogibacterium timidum compared with healthy controls. Our study demonstrates that the composition of bacteria and fungi colonizing healthy oral mucosa is changed in active RAS ulcers, and that this alteration persists to some extent even after the ulcer is healed.

1st Faculty of Medicine Charles University 121 08 Prague Czech Republic

Clinic of Dentistry Faculty of Medicine Masaryk University 625 00 Brno Czech Republic

Clinic of Dentistry St Anne's Faculty Hospital 656 91 Brno Czech Republic

Department of Zoology Faculty of Science Charles University 128 00 Prague Czech Republic

Faculty of Science Charles University 128 00 Prague Czech Republic

Institute of Animal Physiology and Genetics of the CAS v v i 142 20 Prague Czech Republic

Institute of Dental Medicine Department of Oral Medicine General University Hospital Prague 128 00 Prague Czech Republic

Institute of Experimental Medicine of the CAS v v i 142 20 Prague Czech Republic

Institute of Immunology and Microbiology 1st Faculty of Medicine Charles University and General University Hospital Prague 128 00 Prague Czech Republic

Institute of Microbiology of the CAS v v i 142 20 Prague Czech Republic

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