We had previously described a forty-patient study defining the impact of a endotracheal tube (ETT) clearing device on biolumenal occlusion-secretion and its microbiota using traditional and non-traditional methods, emphasizing the endogenous oral flora.
Here, using metagonomics and taxonomic signature, it was our goal to 1) define the microbiome and mycobiome using “cluster analysis” to establish 2) oral contribution while projecting improved institutional oral healthcare of vented patients.
Method:
20 ETT were collected and within 2 hours the biolumenal secretions were removed using the clearing device. HOMIM (Forsyth Research Institute) examined complex oral microbial diversity in a single hybridization with 16s rRNA while 18s rDNA used a Multi-tag pyrosequencing (MTPS) technique (Fungal Center, Case Western Reserve). The stabilized occlusion/secretion (Pre) and residual biofilm (Post) were analyzed.
Phyla/Class/Order and Family taxonomic descriptions were defined by next generation sequencing based on diversity of 16S and 18S rRNA and rDNA genes.
Result:
A total of 101 bacterial species (range 8-38, mean 16) were detected in both Pre (87) and Post (88) samples. For 16S, these represented 7 Phyla (mean 3, range 1-4) Pre and Post with Fimicutes at 100%, Proteobacteria at 61%, Bacteroidetes 17% and Actinobacteria 3% most prevalent. 6/20 Pre and Post samples were markedly dissimilar. For 18S, total fungal species were 117 (range 2-45, mean 11) with Pre (73) and Post (72). Phyla taxonomic distinctions were limited (Basidiomycota and Ascomycota) given that 75% of ETT had Candida species (Phyla Basidiomycota). Class description yielded 13 (mean 3, range 1-7) with Saccharomycetes 100% and Ascomycetes 50%, most prevalent. Both the Phyla (16S) and Class (18S) were consistent with established oral microbiota.
Conclusion: Redefining the ETT biolumenal microbiota using metagenomics highlighted the unique taxonomic patterns and contribution of oral mycobiota, the resilience of the bacterial-fungal communities to clearing and their probable endogenous oral origin.