TABLE 2.

Overview of some of the most pioneering URT and OM microbiome studies

Focus or OM type	Sample type(s)	Disease-associated bacteriaa	Sequencing method	No. of subjects (country)	Age(s) (mos or as indicated), no. of subjects/group	Reference
Focus
Respiratory microbiota in healthy infants	Nasal swabs	Haemophilus, Streptococcus	454 sequencing, V5-V7 region	60 (The Netherlands)	1.5–24	41
	Nasal aspirates	Moraxella, Streptococcus, Haemophilus	Illumina MiSeq, V4 region	234 (Australia)	2–12	52
OM type
AOM	Nasal swabs	S. pneumoniae, Haemophilus, Rothia, Actinomyces	454 sequencing, V1-V2 region	108 (USA)	6–78	59
	Nasal swabs	Moraxellaceae, Streptococcaceae, Pasteurellaceae	454 sequencing, V3-V5 region	153 (Switzerland)	0–24	60
	Nasal swabs	S. pneumoniae, H. influenzae, M. catarrhalis	454 sequencing, V1-V2 region	240 (USA)	3–36	15
	MEF aspirates	S. pneumoniae, H. influenzae, M. catarrhalis, T. otitidis, S. auricularis	Illumina MiSeq, V4 region	79 (Finland)	5–42	61
	Nasal swabs	Moraxella, Haemophilus, Streptococcus	Illumina MiSeq, V4 region	139 (USA)	1–12	282
	MEF aspirates, middle ear aspirates, ear canal swabs, nasal swabs	Haemophilus, Turicella, Alloiococcus, Staphylococcus	Illumina MiSeq, V3-V4 region	196 (Australia)	0–60	64
OME	MEF aspirates, adenoid and tonsil tissue samples	Pseudomonadaceae, Streptococcaceae, Fusobacteriaceae, Pasteurellaceae	454 sequencing, V3-V4 region	1 (USA)	96	65
	MEF aspirates, adenoid swabs, nasal swabs	Alloiococcus, Haemophilus, Streptococcus, Moraxella	Illumina MiSeq, V1-V3 region	11 (Australia)	3–10 yrs	66
	MEF aspirates, adenoid swabs	Alloiococcus, Haemophilus, Moraxella, Staphylococcus, Streptococcus, Pseudomonas, Corynebacterium	Illumina MiSeq, V3-V4 region	18 (Australia)	1–16 yrs	67, 68
	Middle ear, adenoid, and tonsil swabs	Fusobacterium, Haemophilus, Neisseria, Porphyromonas	Illumina MiSeq, V3-V4 region	10 (New Zealand)	2–10 yrs	70
COM	Middle ear swabs, mastoid swabs	Haemophilus, Staphylococcus, Alloiococcus	Illumina MiSeq, V3-V4 region	46 (New Zealand)	6 mos–87 yrs	72
	MEF aspirates	Haemophilus, Moraxella, Turicella	Illumina MiSeq, V4 region	55 (USA)	0–24, 25 subjects; >24, 30 subjects	71

^aBacteria were significantly more abundant in this group, as indicated by the authors.