Characteristics of the Bacterial Microbiota in the Upper Respiratory Tract of Children

At the phylum level, the basic bacterial structures in the adenoids, tonsils, oropharynx, and nostrils were generally similar: five main phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria form the majority of the microbiota. However, across these four sites, the microbiota composition differed. More specifically, the bacterial composition in the nostrils was unique. There, Firmicutes and Actinobacteria were the most abundant phyla, while Bacteroides and Fusobacteria were the least abundant. At the genus level, Staphylococcus, Dolosigranulum, Corynebacterium, and Moraxella were the most plentiful, while Fusobacteria was the least ample. Across all sites, Streptococcus displayed similar abundances. Fusobacteria exhibited higher abundances in the lymphoid tissues and oropharynx. Haemophilus and Neisseria were more plentiful in the tonsils and oropharynx. Notably, Klebsiella, which is normally localized to the gut, was abundant in the adenoids and tonsils.

The airway microbiota plays a crucial role in local immune function and dysbiosis of microbiota in upper respiratory tract infection, leads to disease development.

Determine precise origins of the localized pathogenic bacteria


  • 25 children with hyperplasia of adenoids and tonsils



  • Obstructive Sleep Apnea (OSA)
  • Recurrent tonsillitis
  • Uncomplicated childhood OSA
  • 7 months



  • Collection of Mucosal swabs from nostril or oropharynx, lymphoid tissues like adenoids
  • DNA was extracted for the 16S rRNA analysis
  • Identify diversity of localized pathogenic bacteria
  • Basic bacterial structures at phylum and genus level
  • The operational taxonomic units (OUT) and the Chao index revealed that adenoids and palatine tonsils had higher community richness than the oropharynx and nostrils.
  • The Shannon Diversity Index revealed that nostrils had lower microbial diversity than other sites.


Secondary outcome



At phylum level
  • The basic bacterial structures were similar, however compositions varied

At genus level
  • Streptococcus was found across all sites.
  • Fusobacteria were found in greater numbers in lymphoid tissues and oropharyn
  • Firmicutes and Actinobacteria were the most abundant
  • Bacteroides and Fusobacteria were least

  • Most abundant : Staphylococcus, Dolosigranulum, Corynebacterium, and Moraxella
  • Least abundant: Fusobacteria
  • Haemophilus and Neisseria - prevalent in tonsils and oropharynx
  • Klebsiella - prevalent in the adenoids and tonsils

Upper respiratory tract lymphoid tissues, normally considered immune organs, may serve as reservoirs for pathogenic bacteria

    1. Cao W, Sun Y, Zhao N, Song J, Zhang N, Liu L, Liu Q et al. Characteristics of the bacterial microbiota in the upper respiratory tract of children. European Archives of Oto-Rhino-Laryngology 2022 Feb;279(2):1081-9.

MAT-IN-2202924 V1.0 11/22