Proteomic and Metabolomic Profiling of Archaeal Extracellular Vesicles from the Human Gut

Weinberger V, Darnhofer B, Thapa HB, Mertelj P, Stentz R, Jones E, Grabmann G, Mohammadzadeh R, Shinde T, Karner C, Ober J, Juodeikis R, Pernitsch D, Hingerl K, Zurabishvili T, Kumpitsch C, Kuehnast T, Rinner B, Strohmaier H, Kolb D, Gotts K, Weichhart T, Köcher T, Köfeler H, Carding S, Schild S, Moissl-Eichinger C. (2025)

Nature Communications, Article number: 5094 (2025)

Gastrointestinal bacteria interact with the host and each other through various mechanisms, 33 including bacterial extracellular vesicles (BEVs). Archaea remain poorly studied in host 34 microbiomes, therefore their interactive potential is largely unknown. 35 Here we report the capability of several archaea, M. smithii ALI, M. smithii GRAZ-2, 36 Candidatus M. intestini, and Methanosphaera stadtmanae, to produce archaeal extracellular 37 vesicles (AEVs). 38 While the size (~130 nm) and morphology of these AEVs were comparable to BEVs, proteomic 39 and metabolomic analyses revealed unique traits. AEV proteins (n=229) of both M. smithii and 40 Cand. M. intestini revealed a massive accumulation of adhesins/adhesin-like proteins, which 41 may mediate AEV-bacteria and AEV-host interactions. Additionally, the AEVs contained free 42 glutamic and aspartic acid and choline glycerophosphate, compounds which may be involved 43 in gut-brain signaling. 44 AEVs were efficiently taken up by macrophages and elicited species-specific responses in 45 both immune and epithelial cells. They triggered chemokines, including CXCL9, CXCL11, and 46 CX3CL1, implicating a role in immune cell recruitment. While AEVs of Cand. M. intestini 47 strongly induced pro-inflammatory cytokine IL-8 in epithelial cells, others exhibited lower 48 inflammatory potential, demonstrating distinct immunostimulatory properties among species. 49 The characterization of AEVs may offer novel paths to modulate vesicle-mediated impacts on 50 host health through an archaeal lens.

Nature Communications, Article number: 5094 (2025)

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