Table 2.

Overview of investigations on microbiota and acute otitis media discussed in this review.

Title (Year of Publication) [Ref]	Study Design	N. of Subjects	Age	Site of Investigation	Main Findings
Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children (2011) [20]	Comparison of NP microbial communities in children with and without OM	108 (25 with AOM; 83 without AOM)	6–78 m	NP	Microbial communities with S. pneumoniae were significantly less diverse and less even Higher relative abundance of Corynebacterium and Dolosigranulum, in addition to Propionibacterium, Lactococcus, and Staphylococcus, was associated with a lower incidence of pneumococcal colonization and lower risk of AOM
Nasopharyngeal Microbiota in Infants with Acute Otitis Media (2012) [44]	Comparison of NP microbial communities in children with and without OM	163 (153 with AOM; 10 without AOM)	<2 y	NP	NP bacterial density was lower during an AOM episode in comparison to health Otopathogens predominated over commensal families during AOM
Upper Respiratory Tract Microbial Communities, Acute Otitis Media Pathogens, and Antibiotic Use in Healthy and Sick Children (2012) [19]	Comparison of NP microbial communities in healthy children vs. children with URTI with and without concurrent AOM	240 (73 healthy subjects; 95 subjects with URTI without concurrent AOM; 72 subjects with URTI with concurrent AOM)	6 m–3 y	NP	Lower diversity was associated with a higher colonization rate by S. pneumoniae, H. influenzae, and M. catarrhalis Biodiversity levels were significantly higher in healthy children than during disease Children with antibiotic use in the past 6 months and a higher abundance of Lactococcus and Propionibacterium had a lower risk of AOM Children with no antibiotic use in the past 6 months, a low abundance of Streptococcus and Haemophilus, and a high abundance of Corynebacterium and Dolosigranulum had a lower risk of AOM
Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media (2017) [45]	NP microbiota analysis of children followed from near birth for the first 12 months of life or until the occurrence of the first AOM episode. NP swabs collected monthly or during each URTI or AOM episode.	139 patients (971 samples)	<1 y	NP	Bacterial diversity was lower in culture-samples positive for S. pneumoniae and H. influenzae compared to cultured-negative samples Otopathogen colonization was related to higher incidence of URTI Higher abundance of otopathogens and lower abundance of Pseudomonas, Myroides, Yersinia, and Sphingomonas during URTI and AOM Higher otopathogen abundance during symptomatic viral infection but not during asymptomatic infection An unstable microbiota during URTI and the predominance of otopathogens was associated with a higher risk of transition from URTI to AOM
The Adenoid Microbiome in Recurrent Acute Otitis Media and Obstructive Sleep Apnea (2017) [58]	Comparison of adenoid microbiota in subjects undergoing surgery for RAOM or OSA	10 (5 AOM; 5 OSA)	2–11 y	Adenoid	H. influenzae, M. catarrhalis, S. pneumoniae, P. aeruginosa, and S. aureus were predominant in all samples Relative abundance of S. pneumoniae and M. catharralis was higher in the RAOM group The microbial profiles associated with RAOM were different from, but overlapped with OSA
Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media (2017) [59]	ME microbiota analysis during AOM episodes	79 subjects (90 samples)	5–42 m	ME	S. pneumoniae was detected in 31% of samples, H. influenzae in 27%, M. catarrhalis in 20%, Staphylococcus spp. in 23%, T. otitidis in 5.6%, A. otitidis in 3.3% S. pneumoniae was the dominant pathogen in 16% of samples, H. influenzae in 17%, M. catarrhalis in 5.6%
A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera (2018) [22]	Comparison of NP microbiota between children undergoing grommet insertion for RAOM (cases) vs. healthy children (controls); analysis of ME and EAC microbiota in cases	196 (93 cases; 103 controls)	<5 y	NP ME EAC	Significantly higher abundance of Corynebacterium and Dolosigranulum was detected in NP of controls in comparison to cases Paired NP and ME were not highly concordant: Alloiococcus, and Turicella were abundant in ME and EAC of cases and almost absent in NP of both groups Gemella and Neisseria were typical of the NP in cases prevalent in the middle ear
Comparative Analysis of Microbiome in Nasopharynx and Middle Ear in Young Children with Acute Otitis Media (2019) [60]	Comparison of NP microbiota 1 to 3 weeks prior to onset of AOM vs. at onset of AOM; comparison of NP and ME microbiome during AOM	6	6–24 m	NP ME	Significantly higher abundance of A. otitidis detected in MEF during AOM compared to NP in health and disease NP microbiome during health had a significantly higher diversity than during AOM
Age-Dependent Dissimilarity of the Nasopharyngeal and Middle Ear Microbiota in Children with Acute Otitis Media (2019) [61]	NP microbiota analysis during AOM; Paired NP and ME microbiota analysis in children with STMP	286 (42/286 MEF from STMP)	0–6 y	NP ME	Alpha and beta diversity levels were strictly related to age: older children had a higher richness and more personalized bacterial profiles NP and MEF microbiome were concordant when MEF was dominated by S. pyogenes, H. influenzae, or S. pneumoniae
Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children with Tympanostomy Tubes (2019) [67]	Paired analysis of NP and ME microbiota in children with otorrhea on tympanostomy tubes	94	<5 y	NP ME	Microbiota composition of NP and ME differed significantly, although paired NP and ME samples were more similar than unpaired samples P. aeruginosa, S. aureus, S. pyogenes, T. otitidis, K. pneumoniae, and Haemophilus spp. were correlated between NP and ME Moraxella spp., S. pneumoniae, and Corynebacterium/Dolosigranulum were predominant in NP than in MEF Turicella, P. aeruginosa, and S. aureus were strongly associated to ME Higher abundance of Corynebacterium and Dolosigranulum in NP related to better clinical outcomes

AOM: Acute otitis media. OSA: Obstructive Sleep Apnea. RAOM: Recurrent Acute Otitis media. EAC: External Auditory Canal. NP: Nasopharynx. STMP: Spontaneous Tympanic Membrane Perforation. ME: Middle Ear. MEF: Middle Ear Fluid. URTI: Upper Respiratory Tract Infection.