dc.contributor.author	Huseyin, Chloe E.
dc.contributor.author	Rubio, Raul Cabrera
dc.contributor.author	O'Sullivan, Orla
dc.contributor.author	Cotter, Paul D.
dc.contributor.author	Scanlan, Pauline D.
dc.contributor.funder	Science Foundation Ireland
dc.contributor.funder	Royal Society
dc.date.accessioned	2017-09-26T11:39:21Z
dc.date.available	2017-09-26T11:39:21Z
dc.date.issued	2017
dc.description.abstract	The human gut is host to a diverse range of fungal species, collectively referred to as the gut "mycobiome". The gut mycobiome is emerging as an area of considerable research interest due to the potential roles of these fungi in human health and disease. However, there is no consensus as to what the best or most suitable methodologies available are with respect to characterizing the human gut mycobiome. The aim of this study is to provide a comparative analysis of several previously published mycobiome-specific culture-dependent and -independent methodologies, including choice of culture media, incubation conditions (aerobic versus anaerobic), DNA extraction method, primer set and freezing of fecal samples to assess their relative merits and suitability for gut mycobiome analysis. There was no significant effect of media type or aeration on culture-dependent results. However, freezing was found to have a significant effect on fungal viability, with significantly lower fungal numbers recovered from frozen samples. DNA extraction method had a significant effect on DNA yield and quality. However, freezing and extraction method did not have any impact on either alpha or beta diversity. There was also considerable variation in the ability of different fungal-specific primer sets to generate PCR products for subsequent sequence analysis. Through this investigation two DNA extraction methods and one primer set was identified which facilitated the analysis of the mycobiome for all samples in this study. Ultimately, a diverse range of fungal species were recovered using both approaches, with Candida and Saccharomyces identified as the most common fungal species recovered using culture-dependent and culture-independent methods, respectively. As has been apparent from ecological surveys of the bacterial fraction of the gut microbiota, the use of different methodologies can also impact on our understanding of gut mycobiome composition and therefore requires careful consideration. Future research into the gut mycobiome needs to adopt a common strategy to minimize potentially confounding effects of methodological choice and to facilitate comparative analysis of datasets.	en
dc.description.sponsorship	Royal Society/Science Foundation Ireland (University Research Fellowship)	en
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	1432
dc.identifier.citation	Huseyin, C. E., Rubio, R. C., O’Sullivan, O., Cotter, P. D. and Scanlan, P. D. (2017) 'The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome', Frontiers in Microbiology, 8, 1432. (15pp). doi: 10.3389/fmicb.2017.01432	en
dc.identifier.doi	10.3389/fmicb.2017.01432
dc.identifier.issn	1664-302X
dc.identifier.journaltitle	Frontiers in Microbiology	en
dc.identifier.uri	https://hdl.handle.net/10468/4798
dc.identifier.volume	8
dc.language.iso	en	en
dc.publisher	Frontiers Media S.A.	en
dc.relation.project	info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.uri	http://journal.frontiersin.org/article/10.3389/fmicb.2017.01432/full
dc.rights	© 2017, Huseyin, Rubio, O’Sullivan, Cotter and Scanlan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.	en
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/
dc.subject	Mycobiome	en
dc.subject	Gut microbiota	en
dc.subject	Mycobiota	en
dc.subject	Fungi	en
dc.subject	Human	en
dc.subject	Healthy	en
dc.subject	Methodology	en
dc.subject	Commensal fungi	en
dc.subject	Fecal samples	en
dc.subject	Identification	en
dc.subject	Metagenomics	en
dc.subject	Extraction	en
dc.subject	Microbiota	en
dc.subject	Diversity	en
dc.subject	Infection	en
dc.subject	Community	en
dc.subject	Primers	en
dc.title	The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome	en
dc.type	Article (peer-reviewed)	en

The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome

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