Comparison of culture-dependent and culture-independent methods for routine identification of airborne microorganisms in speleotherapeutic caves

Tomazin, Rok (author), Cerar Kišek, Tjaša (author), Janko, Tea (author), Triglav, Tina (author), Strašek Smrdel, Katja (author), Špik, Vesna (author), Kukec, Andreja (author), Mulec, Janez (author), Matos, Tadeja (author)

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.

• Language: English
• Keywords: MALDI-TOF MS, OmniLog ID System, microbial identification, metagenomics, speleotherapy, cave aerobiology, nitrocellulose filters
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2024
• Number of pages: 28 str.
• Numbering: Vol. 12, iss. 7, art.1427
• PID: 20.500.12556/RUL-179222
• UDC: 616.9:579
• ISSN on article: 2076-2607
• DOI: 10.3390/microorganisms12071427
• COBISS.SI-ID: 202944515
• Publication date in RUL: 09.02.2026

Record is a part of a journal

• Title: Microorganisms
• Shortened title: Microorganisms
• Publisher: MDPI
• ISSN: 2076-2607
• COBISS.SI-ID: 523277081

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: MALDI-TOF MS, sistem OmniLog ID, mikrobna identifikacija, metagenomika, speleoterapija, jamska aerobiologija, nitrocelulozni filtri

Projects

• Funder: ARRS - Slovenian Research Agency
• Project number: P6-0119
• Name: Raziskovanje krasa

• Funder: ARRS - Slovenian Research Agency
• Project number: P3-0083
• Name: Odnosi parazitskega obstajanja