Next Article in Journal
Single Amino Acids as Sole Nitrogen Source for the Production of Lipids and Coenzyme Q by Thraustochytrium sp. RT2316-16
Previous Article in Journal
The Impact of High-Temperature Stress on Gut Microbiota and Reproduction in Siberian Hamsters (Phodopus sungorus)
Previous Article in Special Issue
A Highly Homogeneous Airborne Fungal Community around a Copper Open Pit Mine Reveals the Poor Contribution Made by the Local Aerosolization of Particles
 
 
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves

1
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
2
National Laboratory for Health, Environment and Food, Department for Public Health Microbiology, Grablovičeva Ulica 44, SI-1000 Ljubljana, Slovenia
3
Department of Public Health, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
4
Karst Research Institute, Research Centre of the Slovenian Academy of Sciences and Arts, Titov Trg 2, SI-6230 Postojna, Slovenia
5
UNESCO Chair on Karst Education, University of Nova Gorica, SI-5271 Vipava, Slovenia
*
Author to whom correspondence should be addressed.
Microorganisms 2024, 12(7), 1427; https://doi.org/10.3390/microorganisms12071427 (registering DOI)
Submission received: 28 June 2024 / Revised: 10 July 2024 / Accepted: 12 July 2024 / Published: 14 July 2024
(This article belongs to the Special Issue Airborne Microbial Communities)

Abstract

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.
Keywords: MALDI-TOF MS; OmniLog ID System; microbial identification; metagenomics; speleotherapy; cave aerobiology; nitrocellulose filters MALDI-TOF MS; OmniLog ID System; microbial identification; metagenomics; speleotherapy; cave aerobiology; nitrocellulose filters

Share and Cite

MDPI and ACS Style

Tomazin, R.; Cerar Kišek, T.; Janko, T.; Triglav, T.; Strašek Smrdel, K.; Cvitković Špik, V.; Kukec, A.; Mulec, J.; Matos, T. Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves. Microorganisms 2024, 12, 1427. https://doi.org/10.3390/microorganisms12071427

AMA Style

Tomazin R, Cerar Kišek T, Janko T, Triglav T, Strašek Smrdel K, Cvitković Špik V, Kukec A, Mulec J, Matos T. Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves. Microorganisms. 2024; 12(7):1427. https://doi.org/10.3390/microorganisms12071427

Chicago/Turabian Style

Tomazin, Rok, Tjaša Cerar Kišek, Tea Janko, Tina Triglav, Katja Strašek Smrdel, Vesna Cvitković Špik, Andreja Kukec, Janez Mulec, and Tadeja Matos. 2024. "Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves" Microorganisms 12, no. 7: 1427. https://doi.org/10.3390/microorganisms12071427

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Article metric data becomes available approximately 24 hours after publication online.
Back to TopTop