ena-STUDY-Medical University of Graz-21-02-2017-13:34:08:018-815
Tackling the human archaeome: specific archaea detection in the gastrointestinal tract, lung, nose and on skin
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea have been found to be regular commensals of the human gut, and 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 other parts of the human body, besides the gastro-intestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable to characterize the full spectrum of Archaea.The goal of this study was to critically assess PCR-based methods for specific Archaea detection in human tissue samples. We tested approaches to specifically detect M. smithii, M. stadtmanae and M. luminyensis, and to assess the overall archaeal abundance and diversity using next generation sequencing based technology. To test our established protocols, we determined the archaeal diversity associated with human skin, lung (bronchoalveolar lavage), gastrointestinal tract, stool and nose.Detection of Archaea was highly dependent on primer selection and sequence processing pipeline. Our proposed protocol enabled us to retrieve a novel picture of the human archaeome, as we identified 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 GIT, (iii) a mixed skin/GIT landscape for the nose, and (iv) a woesearchaeal lung landscape.Our study highlights the importance of primer and bioinformatics pipeline choice for studying the human archaeome. We were able to establish protocols that enlightened the presence of yet undetected Archaea in all investigated tissue samples and to detect biogeographic patterns of the human archaeome in respiratory tract, the gastrointestinal tract and on skin. Our results are a solid basis for further investigation of the human archaeome, and in the long term to uncover the potential  archaeal role in human health and disease.
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea have been found to be regular commensals of the human gut, and 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 other parts of the human body, besides the gastro-intestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable to characterize the full spectrum of Archaea.The goal of this study was to critically assess PCR-based methods for specific Archaea detection in human tissue samples. We tested approaches to specifically detect M. smithii, M. stadtmanae and M. luminyensis, and to assess the overall archaeal abundance and diversity using next generation sequencing based technology. To test our established protocols, we determined the archaeal diversity associated with human skin, lung (bronchoalveolar lavage), gastrointestinal tract, stool and nose.Detection of Archaea was highly dependent on primer selection and sequence processing pipeline. Our proposed protocol enabled us to retrieve a novel picture of the human archaeome, as we identified 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 GIT, (iii) a mixed skin/GIT landscape for the nose, and (iv) a woesearchaeal lung landscape.Our study highlights the importance of primer and bioinformatics pipeline choice for studying the human archaeome. We were able to establish protocols that enlightened the presence of yet undetected Archaea in all investigated tissue samples and to detect biogeographic patterns of the human archaeome in respiratory tract, the gastrointestinal tract and on skin. Our results are a solid basis for further investigation of the human archaeome, and in the long term to uncover the potential  archaeal role in human health and disease.