Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples

Summary: Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sarah Ahannach, Lize Delanghe, Irina Spacova, Stijn Wittouck, Wannes Van Beeck, Ilke De Boeck, Sarah Lebeer
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Body substance sample Microbiology Omics Science Q
Acceso en línea:	https://doaj.org/article/bd85c065daa540a6ae41b90970f2cc00
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:bd85c065daa540a6ae41b90970f2cc00
record_format	dspace
spelling	oai:doaj.org-article:bd85c065daa540a6ae41b90970f2cc002021-11-20T05:09:43ZMicrobial enrichment and storage for metagenomics of vaginal, skin, and saliva samples2589-004210.1016/j.isci.2021.103306https://doaj.org/article/bd85c065daa540a6ae41b90970f2cc002021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S258900422101275Xhttps://doaj.org/toc/2589-0042Summary: Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and host DNA depletion on microbiome profiling. Vaginal, skin, and saliva samples were analyzed using 16S rRNA gene amplicon and metagenomic shotgun sequencing, and qPCR. Of the two tested storage buffers, the eNAT buffer could keep the microbial composition stable during various conditions. All three tested host DNA-depletion approaches showed a bias against Gram-negative taxa. However, using the HostZERO Microbial DNA and QIAamp DNA Microbiome kits, samples still clustered according to body site and not by depletion approach. Therefore, our study showed the effectiveness of these methods in depleting host DNA. Yet, a suitable approach is recommended for each habitat studied based on microbial composition.Sarah AhannachLize DelangheIrina SpacovaStijn WittouckWannes Van BeeckIlke De BoeckSarah LebeerElsevierarticleBody substance sampleMicrobiologyOmicsScienceQENiScience, Vol 24, Iss 11, Pp 103306- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Body substance sample Microbiology Omics Science Q
spellingShingle	Body substance sample Microbiology Omics Science Q Sarah Ahannach Lize Delanghe Irina Spacova Stijn Wittouck Wannes Van Beeck Ilke De Boeck Sarah Lebeer Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
description	Summary: Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and host DNA depletion on microbiome profiling. Vaginal, skin, and saliva samples were analyzed using 16S rRNA gene amplicon and metagenomic shotgun sequencing, and qPCR. Of the two tested storage buffers, the eNAT buffer could keep the microbial composition stable during various conditions. All three tested host DNA-depletion approaches showed a bias against Gram-negative taxa. However, using the HostZERO Microbial DNA and QIAamp DNA Microbiome kits, samples still clustered according to body site and not by depletion approach. Therefore, our study showed the effectiveness of these methods in depleting host DNA. Yet, a suitable approach is recommended for each habitat studied based on microbial composition.
format	article
author	Sarah Ahannach Lize Delanghe Irina Spacova Stijn Wittouck Wannes Van Beeck Ilke De Boeck Sarah Lebeer
author_facet	Sarah Ahannach Lize Delanghe Irina Spacova Stijn Wittouck Wannes Van Beeck Ilke De Boeck Sarah Lebeer
author_sort	Sarah Ahannach
title	Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
title_short	Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
title_full	Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
title_fullStr	Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
title_full_unstemmed	Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
title_sort	microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/bd85c065daa540a6ae41b90970f2cc00
work_keys_str_mv	AT sarahahannach microbialenrichmentandstorageformetagenomicsofvaginalskinandsalivasamples AT lizedelanghe microbialenrichmentandstorageformetagenomicsofvaginalskinandsalivasamples AT irinaspacova microbialenrichmentandstorageformetagenomicsofvaginalskinandsalivasamples AT stijnwittouck microbialenrichmentandstorageformetagenomicsofvaginalskinandsalivasamples AT wannesvanbeeck microbialenrichmentandstorageformetagenomicsofvaginalskinandsalivasamples AT ilkedeboeck microbialenrichmentandstorageformetagenomicsofvaginalskinandsalivasamples AT sarahlebeer microbialenrichmentandstorageformetagenomicsofvaginalskinandsalivasamples
_version_	1718419563553488896

Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples

Ejemplares similares