Archaea in mammalian gut microbiomes

Abstract

Archaea are the most enigmatic of the three domains of life. Most archaea are extremophiles found in highly acidic, high-salt, or high-temperature environments. However, members of the archaea also have been discovered in animal and human intestines, albeit their functional roles in host health or disease are poorly understood. Interestingly, archaea are now considered as indigenous microorganisms of the human gut microbiota and their biological importance has recently been reevaluated. Targeted sequencing of the 16S rRNA gene, metagenomic shotgun sequencing, or other metaomic approaches are used to define the composition, activity, and dynamics of the microbial communities. Archaea themselves are not known to be pathogenic; however. the presence of methanogens, a group of archaea in the human gut, has been linked to several digestive disorders such as IBD and IBS and metabolic diseases such as obesity and diabetes. Our study aimed to mine rat 16S rRNA gene amplicon and shotgun metagenomic sequencing datasets in our laboratory for the presence of archaeal sequence reads. Additionally, we investigated whether these sequences are present in 16S sequencing data from pig fecal DNA samples. Taxonomic profiling workflows in the Qiagen CLC Genomics Workbench were used to elucidate the relative abundances of archaeal and bacterial reads in the sequence datasets. Our results showed that archaeal sequences were either absent or present in extremely low abundance in the investigated rat metagenomes. In contrast, we found evidence that methanogens were abundant in sow and piglet fecal microbiotas. The correlation of sow and offspring archaea profiles was evaluated using longitudinal sequence data and quantitative PCR with group-specific primers. The genus Methanobrevibacter was dominant in sows and piglets, while Methanosphaera and Methanomethylophilaceae showed disparate abundances. Future studies will include investigation of archaeome inheritance and development as well as study of archaea-bacteria co-occurrence networks and correlations with host health status.