​Medsebojni vpliv mikrobiote človeka in aerobioma kraških jam

Tomazin, Rok (author), Matos, Tadeja (mentor), Mulec, Janez (comentor)

V disertaciji smo raziskovali antropogene vplive na populacije mikroorganizmov v zraku v slovenskih turističnih jamah in speleoterapevtski jami, s poudarkom na ekoloških posledicah jamskega turizma in speleoterapije. Aerosoli v jamah zagotavljajo vpogled v atmosferske razmere in spremembe, ki jih povzroča človek. Študija je vključevala vzorčenje zraka v Postojnski jami, Škocjanskih jamah in v Bolnišnični jami Sežana pred in po prisotnosti ljudi, da bi ocenili vpliv na mikrobne združbe v zraku. Uporabljene so bile metode, kot so gojenje na gojiščih, pretočna citometrija, detekcija ß-D-glukana in metagenomski pristop. Prisotnost ljudi (turistov in bolnikov) je v 91,7 % primerov povzročila povečanje koncentracije mikroorganizmov v zraku, medtem ko ravni ß-D-glukana in CO2 niso pokazale takšnega trenda in so bile bolj pod vplivom sezonskih variacij. V nobeni jami nismo zaznali primarno patogenih mikroorganizmov, zaznali smo le oportunistične vrste, kot so Aspergillus spp., Paecilomyces spp. in Alternaria spp. med glivami ter Staphylococcus spp. in Pseudomonas spp. med bakterijami. Študija je poudarila učinkovitost naravnega in umetnega prezračevanja pri zmanjševanju mikrobne obremenitve. MALDI-TOF MS je pokazal večjo natančnost pri identifikaciji mikrobov, zlasti na ravni rodu, v primerjavi s sistemom OmniLog ID in identificiral mikrobe, povezane s človekom, kot kazalce antropizacije jam. Prevladovali so prokariontski debla Actinomycetota, Bacillota in Pseudomonadota, kar so potrdile tako metode, ki temeljijo na kulturi, kot tudi metagenomski pristopi. Metagenomski pristop je razkril večjo vrstno raznolikost in zaznal približno 100-krat več taksonov kot konvencionalne metode, kar poudarja pomembnost uporabe več metod za celovito analizo. Kot zanesljive indikatorje antropizacije jam smo prepoznali: Micrococcus luteus, Kocuria rosea, Staphylococcus hominis, Staphylococcus capitis, Staphylococcus epidermidis, kompleks Streptococcus mitis in Moraxella spp. Metagenomski pristop je poleg omenjenih bakterijskih vrst v vzorcih zraka identificiral tudi bakterijo Cutibacterium acnes, ki predstavlja del stalne mikrobiote na koži ljudi in jo je težko vzgojiti v standardnih laboratorijskih pogojih.

• Language: Slovenian
• Keywords: jamska aerobiologija, biokontaminacija, antropizacija jam, kraške jame, speleoterapija, identifikacija mikroorganizmov
• Work type: Doctoral dissertation
• Organization: MF - Faculty of Medicine
• Year: 2024
• PID: 20.500.12556/RUL-165127
• Publication date in RUL: 23.11.2024

Secondary language

• Language: English
• Title: Interaction of human microbiota and aerobiome in karst caves

Abstract

This dissertation investigates the anthropogenic influences on the airborne microbial populations in Slovenian show caves and a speleotherapeutic cave, emphasizing the ecological implications of cave tourism and speleotherapy. Aerosols in caves provide insights into atmospheric conditions and human-induced changes. As part of the study, air samples were taken from Postojnska jama, Škocjanske jame and Bolnišnična jama Sežana before and after the presence of humans to assess the impact on airborne microbial communities. Methods such as culture-dependent techniques, flow cytometry, β-D-glucan detection and shotgun metagenomics were used. Results showed that human activity increased airborne microbial concentrations in ⡤ 91.7% of cases, with seasonal variation in β-D-glucan and CO2 concentrations. No primary pathogens were detected in either cave, only opportunistic species such as Aspergillus spp., Paecilomyces spp. and Alternaria spp. among the fungi and Staphylococcus spp. and Pseudomonas spp. among the bacteria. The study emphasises the effectiveness of natural and artificial ventilation in reducing the microbial load. MALDI-TOF MS showed higher accuracy in the microbial identification, especially at the genus level, compared to the OmniLog ID system and identified human-associated microbes as indicators of cave anthropisation. The predominant prokaryotic phyla identified were Actinomycetota, Bacillota and Pseudomonadota, which was confirmed by both culture-based and metagenomics-based approaches. The metagenomics-based approach revealed greater species diversity and detected about 100 times more taxa than conventional culture-based methods, emphasising the importance of using multiple methods for a comprehensive analysis. Micrococcus luteus, Kocuria rosea, Staphylococcus hominis, Staphylococcus capitis, Staphylococcus epidermidis, Streptococcus mitis complex and Moraxella spp. were identified as reliable indicators of cave anthropisation. The metagenomics-based approach also identified Cutibacterium acnes, a core member of the human skin microbiota that is difficult to cultivate under standard laboratory conditions, as an additional indicator organism.

• Keywords: cave aerobiology, biocontamination, cave anthropisation, karst caves, speleotherapy, microorganism identification