Objectives: Biofilm formation on tracheal tubing is a key risk factor for ventilator-associated pneumonia. The microbiology of endotracheal tubing has been reviewed systematically but the profile of tracheostomy tubing has not. Analysis of the tube-associated microbiome is not standardised, and sampling methods are varied. We seek to compare the microbiome of patients intubated by endotracheal or tracheostomy tubes and observe the impact of sampling by tracheal aspiration or direct culture. Methods: Eligible clinical microbiology studies were retrieved from PubMed, SCOPUS and Web of Knowledge from 2000-2024, and a data extraction performed to record tubing and sampling type, and the most prevalent genera. Genera were compared by Spearman’s rank correlation and pairwise analyses by Šidák’s multiple comparisons test. Results: Data from 49 studies identified 30 genera. Pseudomonas were the most prevalent in all conditions, followed by Klebsiella, Staphylococcus, and Acinetobacter. 25 studies performed tracheal aspiration, and 22, direct culture. 2 studies used both methods. Correlation was observed between endotracheal and tracheostomy tubes, and aspirates and direct cultures. (Spearman’s rho=0.69; 0.59) Pseudomonas were more prevalent in tracheostomy tubes. (p<0.0001) Coagulase positive Staphylococci were more common in tracheal aspirates, and coagulase-negative Staphylococci in direct culture. Conclusions: The microbial profiles of endotracheal and tracheostomy tubes are comparable, with Pseudomonas being the most common coloniser. Our analyses suggest that tracheal aspiration can effectively identify the constituents of biofilms without requiring tube removal, making it a valuable tool for clinical researchers to analyse or monitor biofilms before extubation or device failure using existing microbiology procedures.