First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

ABSTRACT Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human...

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Autores principales:	Kaisa Koskinen, Manuela R. Pausan, Alexandra K. Perras, Michael Beck, Corinna Bang, Maximilian Mora, Anke Schilhabel, Ruth Schmitz, Christine Moissl-Eichinger
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	archaeome methanogens microbiome Archaea Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/9f98d3829af34626976f3e80cbed74c9
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spelling	oai:doaj.org-article:9f98d3829af34626976f3e80cbed74c92021-11-15T15:51:56ZFirst Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin10.1128/mBio.00824-172150-7511https://doaj.org/article/9f98d3829af34626976f3e80cbed74c92017-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00824-17https://doaj.org/toc/2150-7511ABSTRACT Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts. IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.Kaisa KoskinenManuela R. PausanAlexandra K. PerrasMichael BeckCorinna BangMaximilian MoraAnke SchilhabelRuth SchmitzChristine Moissl-EichingerAmerican Society for MicrobiologyarticlearchaeomemethanogensmicrobiomeArchaeaMicrobiologyQR1-502ENmBio, Vol 8, Iss 6 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	archaeome methanogens microbiome Archaea Microbiology QR1-502
spellingShingle	archaeome methanogens microbiome Archaea Microbiology QR1-502 Kaisa Koskinen Manuela R. Pausan Alexandra K. Perras Michael Beck Corinna Bang Maximilian Mora Anke Schilhabel Ruth Schmitz Christine Moissl-Eichinger First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
description	ABSTRACT Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts. IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.
format	article
author	Kaisa Koskinen Manuela R. Pausan Alexandra K. Perras Michael Beck Corinna Bang Maximilian Mora Anke Schilhabel Ruth Schmitz Christine Moissl-Eichinger
author_facet	Kaisa Koskinen Manuela R. Pausan Alexandra K. Perras Michael Beck Corinna Bang Maximilian Mora Anke Schilhabel Ruth Schmitz Christine Moissl-Eichinger
author_sort	Kaisa Koskinen
title	First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
title_short	First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
title_full	First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
title_fullStr	First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
title_full_unstemmed	First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
title_sort	first insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/9f98d3829af34626976f3e80cbed74c9
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First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

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