Case-Control Microbiome Study of Chronic Otitis Media with Effusion in Children Points at Streptococcus salivarius as a Pathobiont-Inhibiting Species

Jennifer Jörissen, Marianne F L van den Broek, Ilke De Boeck, Wannes Van Beeck, Stijn Wittouck, An Boudewyns, Paul Van de Heyning, Vedat Topsakal, Vincent Van Rompaey, Ine Wouters, Liesbet Van Heirstraeten, Pierre Van Damme, Surbi Malhotra-Kumar, Heidi Theeten, Olivier M Vanderveken, Sarah Lebeer

Research output: Contribution to journalArticle


Chronic otitis media with effusion (OME) has been associated with a shift in microbiome composition and microbial interaction in the upper respiratory tract (URT). While most studies have focused on potential pathogens, this study aimed to find bacteria that could be protective against OME through a case-control microbiome study and characterization of isolates from healthy subjects. The URT and ear microbiome profiles of 70 chronic OME patients and 53 controls were compared by 16S rRNA amplicon sequencing. Haemophilus influenzae was the most frequent classic middle ear pathobiont. However, other taxa, especially Alloiococcus otitis, were also frequently detected in the ear canal of OME patients. Streptococci of the salivarius group and Acinetobacter lwoffii were more abundant in the nasopharynx of healthy controls than in OME patients. In addition to the microbiome analysis, 142 taxa were isolated from healthy individuals, and 79 isolates of 13 different Streptococcus species were tested for their pathobiont-inhibiting potential. Of these, Streptococcus salivarius isolates showed a superior capacity to inhibit the growth of H. influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, A. otitis, and Corynebacterium otitidisS. salivarius strains thus show potential as a probiotic for prevention or treatment of OME based on their overrepresentation in the healthy nasopharynx and their ability to inhibit the growth of respiratory pathobionts. (This study has been registered at under registration no. NCT03109496.)IMPORTANCE The majority of probiotics marketed today target gastrointestinal health. This study searched for bacteria native to the human upper respiratory tract, with a beneficial potential for respiratory and middle ear health. Comparison of the microbiomes of children with chronic otitis media with effusion (OME) and of healthy controls identified Streptococcus salivarius as a health-associated and prevalent inhabitant of the human nasopharynx. However, beneficial potential should be assessed at strain level. Here, we also isolated specific S. salivarius strains from the healthy individuals in our study. These isolates showed a beneficial safety profile and efficacy potential to inhibit OME pathogens in vitro These properties will now have to be evaluated and confirmed in human clinical studies.

Original languageEnglish
Article numbere00056-21
Number of pages17
Issue number2
Publication statusPublished - 20 Apr 2021

Bibliographical note

Copyright © 2021 Jörissen et al.


  • 16S rRNA
  • Streptococcus salivarius
  • ear canal
  • microbiome
  • middle ear
  • otitis media
  • otitis media with effusion
  • pediatric
  • probiotics
  • upper respiratory tract

Fingerprint Dive into the research topics of 'Case-Control Microbiome Study of Chronic Otitis Media with Effusion in Children Points at Streptococcus salivarius as a Pathobiont-Inhibiting Species'. Together they form a unique fingerprint.

Cite this