Is next generation sequencing an alternative to cultivation-based methods for investigating fungal diversity in indoor a
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ORIGINAL PAPER
Is next generation sequencing an alternative to cultivationbased methods for investigating fungal diversity in indoor air samples? ¨ kten Suzan O Ahmet Asan
. Burhan S¸en . Fatma Kaynak Onurdag˘ . Mustafa Kolukirik .
Received: 20 February 2019 / Accepted: 7 April 2020 Ó Springer Nature B.V. 2020
Abstract The direct effect of fungi on human health makes the fungal diversity in the air an important and necessary subject for examination.Studies that determine fungal diversity generally depends on culture methods. Developed culture-independent methods eliminate many disadvantages of existing culturedependent methods. In our study, duplicate air samples were collected on 5 different days at a Microbiology Research Laboratory to compare these methods. Samples were collected in 3 different groups: (A) culture method and ITS-targeted Sanger DNA sequencing with 100 L samples, (B) culture method and ITStargeted Sanger DNA sequencing with 1000 L samples, (C) filter method and next generation sequencing with 1000 L air sample. The Groups A, B and C defines culture, isolation and SANGER DNA-based methods, culture and next generation sequencing methods and directly next generation sequencing methods, respectively. Method-A failed to represent ¨ kten (&) F. Kaynak Onurdag˘ S. O Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Trakya University, 22030 Edirne, Turkey e-mail: [email protected] B. S¸ en A. Asan Department of Biology, Faculty of Science, Trakya University, Edirne, Turkey M. Kolukirik ENGY Environmental and Energy Technologies Biotechnology Research and Development Limited Company, Istanbul, Turkey
real fungal diversity. Method-B did represent the diversity but did not truly represent relative abundance of the species. Method-C can be completed in 2 days whereas Method-A and B can be completed in 2 weeks and 1 week, respectively. In conclusion, we recommend direct DNA isolation which is followed by ITS-targeted NGS in order to study fungal diversity in indoor air environments. Keywords
Fungal diversity Indoor air NGS ITS
1 Introduction Today, people spend about 90% of their time in indoor places (Klepeis et al. 2001). The presence of fungi in the air has a potential health risk for humans living in indoor environments. Particularly, it is known that fungal spores in the atmosphere may lead to many respiratory system diseases and various allergic diseases such as asthma and rhinitis (Rabito et al. 2008; Quansah et al. 2012; Dannemiller et al. 2014). Since the quality of indoor air is of great importance for general public health, many research studies have been carried out in this area (Bonetta et al. 2010). The various studies in this area are generally based on culture-dependent methods (Adams et al. 2013). These methods provide advantages such as analyzing the examined species for physiological state and obtaining qualitative and quantitative data (Buttner et al. 1997).
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Aerobiologia
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