Differential methanogenic archaea-induced TLR8-dependent signaling is governed by NF-κB p65- and STAT1/2-controlled gene classes

Abstract

Prevalent in the human gut yet lacking canonical cell wall-derived host-recognition motifs found in bacteria, human-associated archaea Methanosphaera stadtmanae and Methanobrevibacter smithii show immune activity and disease links but remain largely underexplored. Time-resolved RNA-seq in human PBMCs identified an immune program shared with bacterial or viral stimuli across both archaeal species, yet their kinetics diverged, with M. stadtmanae inducing earlier and stronger activation and M. smithii eliciting more gradual responses. Among conserved early-upregulated genes, two classes emerged: Class I was preferentially induced by M. stadtmanae, whereas Class II was similarly induced by both species. To investigate the origin of the Class I/II phenotype, we measured uptake and applied TLR8 inhibition, finding greater early uptake with M. stadtmanae and broad TLR8 dependence across readouts. Consistent with this gene-class separation, ChIP-qPCR showed that M. stadtmanae, but not M. smithii, strongly induced NF-{kappa}B p65 binding at representative Class I promoters, while STAT1/2 binding at representative Class II promoters occurred with both stimuli. Dose-response analyses with RNA inputs established distinct activation thresholds, with Class II at low dose (via STAT1/2) and Class I only at higher dose (via p65). Together, these findings support an input-tuned logic in which archaeal inputs and RNA sensing gate TLR8-dependent immune programs.