Cerumen microbial community shifts between healthy and otitis affected dogs

Abstract

Otitis externa is a common multifactorial disease in dogs, characterized by broad and complex modifications of the ear microbiota. The goal of our study was to describe the ear cerumen microbiota of healthy dogs, within the same animal and between different animals, and to compare the cerumen microbiota of otitis affected dogs with that of healthy animals. The present study included 26 healthy dogs, 16 animals affected by bilateral otitis externa and 4 animals affected by monolateral otitis externa. For each animal cerumen samples from the right and left ear were separately collected with sterile swabs, and processed for DNA extraction and PCR amplification of the 16S rRNA gene. Amplicon libraries were sequenced using an Ion Torrent Personal Genome Machine (PGM), and taxonomical assignment and clustering were performed using QIIME 2 software. Our results indicate that the bacterial community of the cerumen in healthy dogs was characterized by extensive variability, with the most abundant phyla represented by Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Fusobacteria. The analysis of both alpha and beta diversity between pairs of left and right ear samples from the same dog within the group of affected animals displayed higher differences than between paired samples across healthy dogs. Moreover we observed reduced bacterial richness in the affected group as compared with controls and increased variability in population structure within otitis affected animals, often associated with the proliferation of a single bacterial taxon over the others. Moreover, Staphylococcus and Pseudomonas resulted to be the bacterial genera responsible for most distances between the two groups, in association with differences in the bacterial community structure. The cerumen microbiota in healthy dogs exhibits a complex bacterial population which undergoes significant modifications in otitis affected animals.

External Ear Canal Evaluation in Dogs with Chronic Suppurative Otitis Externa: Comparison of Direct Cytology, Bacterial Culture and 16S Amplicon Profiling

“…This observation highlights that, at least for the detection of P. aeruginosa, bacterial culture appears to be a sensitive method. The presence of P. aeruginosa in canine otitis externa with/without otitis media has been reported in several studies [5,7,[10][11][12]14,15,26,[28][29][30][31][32][33]. A prevalence from 7.2% to 35.5% of P. aeruginosa was recorded in bacterial culture [5,7,26,28,30,31,33].…”

“…This discrepancy could be explained by the presence of uncultured bacteria or the emergence of the fastest-growing bacteria. Recent studies using 16S amplicon profiling have shown that the bacterial population observed in canine otitis externa is more complex than expected based on the bacterial culture technique [ 10 , 11 , 12 , 13 , 14 , 15 ].…”

Different Non-Structural Carbohydrates/Crude Proteins (NCS/CP) Ratios in Diet Shape the Gastrointestinal Microbiota of Water Buffalo

“…All the features found in negative controls (Supplementary Table S1) were either absent or present in a negligible number of analyzed samples. Based on this evidence and the best practices for analyzing microbiomes [27][28][29], and in consideration of similar studies in the literature [36,37], we decided to filter out low abundance ASVs by removing all the features with a minimum frequency <150. Following taxonomic analysis, the analysis of the composition of microbiomes (ANCOM) implemented through the QIIME2 ANCOM plugin was carried out to evaluate the presence of statistical differences of population abundance between groups.…”

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial‐resistant Pseudomonas aeruginosa in dogs and cats

“…Isolates were cultured from the ear (6.1%), eye (4.4%), genitalia and rectum (both 3.1%) (Park et al, 2020). Microbiome studies in healthy dogs and those with otitis reported that Pseudomonadaceae were present in both groups, but the relative abundance differed with a higher abundance detected in dogs with otitis (Borriello et al, 2020). However, other studies have found very little evidence of Pseudomonas spp.…”