Background: Archaea are the most enigmatic domain of the three domains of life. Archaea are unique in that they share some characteristics with bacteria and others with eukaryotes while they are also distinct from these two domains. Mostarchaea are extremophiles that are found in highly acidic, high-salt, or high-temperature environments. However, recent microbiome research has revealed that these prokaryotes are also a part of the gut microbiota, albeit their functional roles in gut health or disease are unclear. Archaea could be keystone species in the gut that engage in important syntrophic relationships with other gut microbes. The recent proposal of archaeal strains as a new class of probiotics (archaebiotics) could be of interest for improving gut pathophysiology and overall human health. The main aim of this study is to mine extant microbiome data sets in our laboratory for the presence of archaeal sequences.

Method: Metagenomic data sets from mammalian microbiome studies (e.g., mouse, rat, prairie voles) based on 16S rRNA amplicon or whole-genome shotgun sequencing approaches are screened for archaeal sequences. Taxonomic profiling workflows in the Qiagen CLC Genomics Workbench and other bioinformatics software such as MetaPhlan are used to elucidate the relative abundances of these enigmatic microorganisms.

Results: Archaeal sequences have been found in DNA isolated from digesta and feces at relatively low abundances. Most sequence variants are derived from methanogens, a subgroup of archaea, while we also found indications for the presence of halophilic archaea.

Conclusion: Our experiments demonstrate that archaeal sequences, specifically from methanogens and halophiles, are found in our mammalian gut microbiome data sets. Future studies will include confirmation of archaeal presence using quantitative PCR (qPCR) and, if possible, in vitro culture. Predictions on the functional roles of archaea in the gut will also be conducted to help characterize the impact of these microorganisms on gut health.
Original languageAmerican English
StatePublished - 18 Feb 2022
EventOklahoma State University Center for Health Sciences Research Week 2022 : Poster Presentation - Oklahoma State University Center for Health Sciences, Tulsa, United States
Duration: 14 Feb 202218 Feb 2022


ConferenceOklahoma State University Center for Health Sciences Research Week 2022
Country/TerritoryUnited States


  • Archaea
  • Microbiota
  • Microbiome
  • Metagenome
  • Intestine


Dive into the research topics of 'Archaea in Mammalian Gut Microbiomes'. Together they form a unique fingerprint.

Cite this