20.500.12556/RUL-179222 Comparison of culture-dependent and culture-independent methods for routine identification of airborne microorganisms in speleotherapeutic caves The effective identification of bacterial and fungal isolates is essential for microbiological monitoring in environments like speleotherapeutic caves. This study compares MALDI-TOF MS and the OmniLog ID System, two high-throughput culture-based identification methods. MALDI-TOF MS identified 80.0% of bacterial isolates to the species level, while the OmniLog ID System identified 92.9%. However, species-level matches between the methods were only 48.8%, revealing considerable discrepancies. For discrepant results, MALDI-TOF MS matched molecular identification at the genus level in 90.5% of cases, while the OmniLog ID System matched only in 28.6%, demonstrating MALDI-TOF MS’s superiority. The OmniLog ID System had difficulties identifying genera from the order Micrococcales. Fungal identification success with MALDI-TOF MS was 30.6% at the species level, potentially improvable with a customised spectral library, compared to the OmniLog ID System’s 16.7%. Metagenomic approaches detected around 100 times more microbial taxa than culture-based methods, highlighting human-associated microorganisms, especially Staphylococcus spp. In addition to Staphylococcus spp. and Micrococcus spp. as indicators of cave anthropisation, metagenomics revealed another indicator, Cutibacterium acnes. This study advocates a multi-method approach combining MALDI-TOF MS, the OmniLog ID System, culture-based, and metagenomic analyses for comprehensive microbial identification. Metagenomic sampling on nitrocellulose filters provided superior read quality and microbial representation over liquid sampling, making it preferable for cave air sample collection. MALDI-TOF MS OmniLog ID System microbial identification metagenomics speleotherapy cave aerobiology nitrocellulose filters MALDI-TOF MS sistem OmniLog ID mikrobna identifikacija metagenomika speleoterapija jamska aerobiologija nitrocelulozni filtri true false false Angleški jezik Slovenski jezik Članek v reviji 2026-02-09 07:11:19 2026-02-09 07:11:24 2026-02-10 07:06:11 0000-00-00 00:00:00 2024 0 0 28 str. iss. 7, art.1427 Vol. 12 2024 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 616.9:579 2076-2607 10.3390/microorganisms12071427 202944515 RAZ_Tomazin_Rok_2024.pdf RAZ_Tomazin_Rok_2024.pdf 1 1BDE10F723B77CFC0E8356CF6C7F1B39 ae22811dd579680d42f6a53177378637c31fe926b70e37cedbbdecd0864914db e73b9377-057e-11f1-a1ba-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=227521 https://www.mdpi.com/2076-2607/12/7/1427 1 092d4761-057e-11f1-a1ba-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=227519 Medicinska fakulteta 0 0 0