Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities

Abstract Culture-independent DNA sequencing of fungal internal transcribed spacer 2 (ITS2) region was compared to a culture-dependent morphological identification technique to characterize house dust-borne fungal communities. The abundant genera were Aspergillus, Wallemia, Cladosporium, and Penicill...

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Autores principales:	Naohide Shinohara, Cheolwoon Woo, Naomichi Yamamoto, Kazuhiro Hashimoto, Hiroko Yoshida-Ohuchi, Yuji Kawakami
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d2d4024f820344429d3ecf2af9b62a40
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spelling	oai:doaj.org-article:d2d4024f820344429d3ecf2af9b62a402021-12-02T13:24:25ZComparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities10.1038/s41598-021-81996-w2045-2322https://doaj.org/article/d2d4024f820344429d3ecf2af9b62a402021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-81996-whttps://doaj.org/toc/2045-2322Abstract Culture-independent DNA sequencing of fungal internal transcribed spacer 2 (ITS2) region was compared to a culture-dependent morphological identification technique to characterize house dust-borne fungal communities. The abundant genera were Aspergillus, Wallemia, Cladosporium, and Penicillium. Statistically significant between-method correlations were observed for Wallemia and Cladosporium (Spearman’s ρ = 0.75 and 0.72, respectively; p < 0.001). Penicillium tended to be detected with much higher (averaged 26-times) relative abundances by the culture-based method than by the DNA-based method, although statistically significant inter-method correlation was observed with Spearman’s ρ = 0.61 (p = 0.002). Large DNA sequencing-based relative abundances observed for Alternaria and Aureobasidium were likely due to multicellularity of their spores with large number of per-spore ITS2 copies. The failure of the culture-based method in detectiing Toxicocladosporium, Verrucocladosporium, and Sterigmatomyces was likely due to their fastidiousness growth on our nutrient medium. Comparing between the two different techniques clarified the causes of biases in identifying environmental fungal communities, which should be amended and/or taken into consideration when the methods are used for future fungal ecological studies.Naohide ShinoharaCheolwoon WooNaomichi YamamotoKazuhiro HashimotoHiroko Yoshida-OhuchiYuji KawakamiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Naohide Shinohara Cheolwoon Woo Naomichi Yamamoto Kazuhiro Hashimoto Hiroko Yoshida-Ohuchi Yuji Kawakami Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities
description	Abstract Culture-independent DNA sequencing of fungal internal transcribed spacer 2 (ITS2) region was compared to a culture-dependent morphological identification technique to characterize house dust-borne fungal communities. The abundant genera were Aspergillus, Wallemia, Cladosporium, and Penicillium. Statistically significant between-method correlations were observed for Wallemia and Cladosporium (Spearman’s ρ = 0.75 and 0.72, respectively; p < 0.001). Penicillium tended to be detected with much higher (averaged 26-times) relative abundances by the culture-based method than by the DNA-based method, although statistically significant inter-method correlation was observed with Spearman’s ρ = 0.61 (p = 0.002). Large DNA sequencing-based relative abundances observed for Alternaria and Aureobasidium were likely due to multicellularity of their spores with large number of per-spore ITS2 copies. The failure of the culture-based method in detectiing Toxicocladosporium, Verrucocladosporium, and Sterigmatomyces was likely due to their fastidiousness growth on our nutrient medium. Comparing between the two different techniques clarified the causes of biases in identifying environmental fungal communities, which should be amended and/or taken into consideration when the methods are used for future fungal ecological studies.
format	article
author	Naohide Shinohara Cheolwoon Woo Naomichi Yamamoto Kazuhiro Hashimoto Hiroko Yoshida-Ohuchi Yuji Kawakami
author_facet	Naohide Shinohara Cheolwoon Woo Naomichi Yamamoto Kazuhiro Hashimoto Hiroko Yoshida-Ohuchi Yuji Kawakami
author_sort	Naohide Shinohara
title	Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities
title_short	Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities
title_full	Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities
title_fullStr	Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities
title_full_unstemmed	Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities
title_sort	comparison of dna sequencing and morphological identification techniques to characterize environmental fungal communities
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d2d4024f820344429d3ecf2af9b62a40
work_keys_str_mv	AT naohideshinohara comparisonofdnasequencingandmorphologicalidentificationtechniquestocharacterizeenvironmentalfungalcommunities AT cheolwoonwoo comparisonofdnasequencingandmorphologicalidentificationtechniquestocharacterizeenvironmentalfungalcommunities AT naomichiyamamoto comparisonofdnasequencingandmorphologicalidentificationtechniquestocharacterizeenvironmentalfungalcommunities AT kazuhirohashimoto comparisonofdnasequencingandmorphologicalidentificationtechniquestocharacterizeenvironmentalfungalcommunities AT hirokoyoshidaohuchi comparisonofdnasequencingandmorphologicalidentificationtechniquestocharacterizeenvironmentalfungalcommunities AT yujikawakami comparisonofdnasequencingandmorphologicalidentificationtechniquestocharacterizeenvironmentalfungalcommunities
_version_	1718393122108473344

Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities

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