Fig. 2: Main archaeal lineages in the gut and proposed independent events of adaptation to the gut in the domain Archaea.

a Distribution of archaeal 16S rRNA gene sequences in the gut and other environments based on sequences obtained from the Silva database and this study. The archaeal tree is based on Borrel et al.¹¹² enriched with DPANN lineages. Large arrows on the tree indicate five main events of adaptation to the gut environment, small arrows indicate four other possible events of adaptation to the gut. Fully orange triangles indicate that gut adaptation likely occurred at the base of the lineage while blue triangles with an orange spot indicate that gut adaptation occurred within the lineage. The histogram shows the proportion of sequences (from the Silva database) of a given lineage present in either animal digestive tract (“Gut”, orange), open natural environment (“Environment”, blue) or built environment (“Engineered”, grey). Orange circle surface area represents the percentage of reads attributed to each taxon in our study (gut-related samples only). b Proportion of archaea corresponding to the dominant methanogen lineages (green), Nitrososphaeraceae (purple) and rarest taxa (light blue) in samples, based on amplicon sequencing (Miseq) with archaea-specific primers, according to absolute abundance of archaea in the sample (qPCR). Dots indicate the relative abundance of these three groups of archaea in each sample. Coloured lines indicate the moving averages of the relative abundance of these three groups on a subset size of 25 samples. The dominant methanogen lineages category contains Methanobrevibacter, Methanosphaera, “Ca. Methanomethylophilaceae”, Methanocorpusculum, Methanimicrococcus. The rarest taxa category contains Methanobacterium, Methanothermobacter, Methanomassiliicoccaceae, Methanosarcina, Methanoregulaceae, Methanospirillaceae, Methanosaeta, Methanocellales, Nitrosopumilaceae, Nitrosotaleaceae, Bathyarchaeota, Halobacteriales. c Correlation between the absolute abundance (16S rRNA copies/gram of faeces) of archaea and bacteria (black), summed methanogen lineages (Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, Methanimicrococcus; green) and Thaumarchaeota (purple), all determined by qPCR using lineage-specific primers. Same samples (n = 176) are plotted in panels b) and c) and correspond to those with amplified archaea in deep sequencing (Miseq). The scale of the absolute abundance of archaea is the same than in b, c. d Phylogenetic position of dominant gut Thaumarchaeota (this study, ASV4, ASV20 and ASV21, purple, bold) and dominant soil archaea⁴⁴ (DSC1 and DSC2, brown, bold). ASV4/ASV20 are practically identical to DSC2 representative sequence (only 1 indel in a 4/5Gs homopolymer region, which may be due to a 454-sequencing error in DSC2¹²⁹). ASV21 shares 99.2% identity with the DSC1 representative sequence.