Joon Yong Kim1,†, Tae Woong Whon1,†, Mi Young Lim2, Yeon Bee Kim1, Namhee Kim1, Min-Sung Kwon1, Juseok Kim1, Se Hee Lee1, Hak-Jong Choi1, In-Hyun Nam3, Won-Hyong Chung2, Jung-Ha Kim4, Jin-Woo Bae5, Seong Woon Roh1,* and Young-Do Nam2,*
1Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea. 2Research Group of Healthcare, Research Division of Food Functionality, Korea Food Research Institute, Jeollabuk-do 55365, Republic of Korea. 3Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea. 4Department of Family Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea. 5Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea.
*Correspondence : Seong Woon Roh, Young-Do Nam
†Joon Yong Kim and Tae Woong Whon contributed equally to this work.
Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is available.
We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living in South Korea. In total, 42.47% faecal samples were positive for archaeal colonisation; these were subsequently subjected to archaeal 16S rRNA gene deep sequencing and real-time quantitative polymerase chain reaction-based abundance estimation. The mean archaeal relative abundance was 10.24 ± 4.58% of the total bacterial and archaeal abundance. We observed extensive colonisation of haloarchaea (95.54%) in the archaea-positive faecal samples, with 9.63% mean relative abundance in archaeal communities. Haloarchaea were relatively more abundant than methanogens in some samples. The presence of haloarchaea was also verified by fluorescence in situ hybridisation analysis. Owing to large inter-individual variations, we categorised the human gut archaeome into four archaeal enterotypes.
The study demonstrated that the human gut archaeome is indigenous, responsive, and functional, expanding our understanding of the archaeal signature in the gut of human individuals.