Dataset Information

Proteomic and metabolomic profiling of extracellular vesicles produced by human gut archaea

ABSTRACT:

Gastrointestinal bacteria interact with the host and each other through various mechanisms, including the production of extracellular vesicles (EVs). However, the composition and potential roles of EVs released by gut archaea are poorly understood. Here, we study EVs produced by four strains of human gut-derived methanogenic archaea: Methanobrevibacter smithii ALI, M. smithii GRAZ-2, Candidatus Methanobrevibacter intestini and Methanosphaera stadtmanae. The size (~130 nm) and morphology of these EVs are comparable to those of bacterial EVs. Proteomic and metabolomic analyses reveal that the archaeal EVs are enriched in putative adhesins or adhesin-like proteins, free glutamic and aspartic acid, and choline glycerophosphate. The archaeal EVs are taken up by macrophages in vitro and elicit species-specific responses in immune and epithelial cell lines, including production of chemokines such as CXCL9, CXCL11 and CX3CL1. The EVs produced by Ca. M. intestini strongly induce pro-inflammatory cytokine IL-8 in epithelial cells. Future work should examine whether archaeal EVs play roles in the interactions of archaea with other gut microbes and with the host.

INSTRUMENT(S): Liquid Chromatography MS - alternating - hilic

PROVIDER: MTBLS12422 | MetaboLights | 2025-07-01

REPOSITORIES: MetaboLights

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			Action	DRS
	20240416_Ext_blank_HILIC_D_sw_R01_11.raw	Raw
	20240416_Ext_blank_HILIC_D_sw_R02_20.raw	Raw
	20240416_MSMedia_HILIC_D_S007_Media_R01_10.raw	Raw
	20240416_MSMedia_HILIC_D_sw_S007_Media_R01_19.raw	Raw
	20240416_QCVWeinberger_HILIC_D_sw_R01_12.raw	Raw

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Publications

Proteomic and metabolomic profiling of extracellular vesicles produced by human gut archaea.

Weinberger Viktoria V Darnhofer Barbara B Thapa Himadri B HB Mertelj Polona P Stentz Régis R Jones Emily E Grabmann Gerlinde G Mohammadzadeh Rokhsareh R Shinde Tejus T Karner Christina C Ober Jennifer J Juodeikis Rokas R Pernitsch Dominique D Hingerl Kerstin K Zurabishvili Tamara T Kumpitsch Christina C Kuehnast Torben T Rinner Beate B Strohmaier Heimo H Kolb Dagmar D Gotts Kathryn K Weichhart Thomas T Köcher Thomas T Köfeler Harald H Carding Simon R SR Schild Stefan S Moissl-Eichinger Christine C

Nature communications 20250603 1

PMID: 40461460

Similar Datasets

Project description:Within the gut microbiome, Methanobrevibacter and Methanosphaera species are the prevailing methanogenic archaea. In general, these archaeal species interact widely with other members of the gut microbiome, subsequently facilitating the processes of digestion and fermentation within humans, thereby playing a significant role in the gut. Despite their significance, detailed characteristics and microbiome-host interactions remain largely unexplored. One potential mechanism for microbiome-host interaction and communication involves extracellular vesicles, which play a crucial role in both inter- and intra-kingdom interactions as well as intercellular communication. The production of extracellular vesicles has been confirmed for representatives of all three domains of life, eukaryotes, bacteria, and archaea. In this study, we report for the first time that human gut-derived archaea are capable of producing extracellular vesicles. Here, we present the ultrastructure, composition, proteome, and metabolome of these newly discovered archaeal extracellular vesicles (AEV) of M. smithii (strains ALI and GRAZ-2), Candidatus M. intestini, and Methanosphaera stadtmanae. Here, we describe their morphology, contents of archaeal extracellular vesicles (AEV) produced by the major methanogenic archaea of the human gut, namely Methanobrevibacter smithii (strains ALI and GRAZ-2), Candidatus M. intestini, and Methanosphaera stadtmanae. We also describe their interaction with human cell lines and ability to trigger immune responses. The findings show a high similarity of AEVs to their bacterial counterparts in size, morphology, and composition. Proteome and metabolome analysis demonstrate high similarities between vesicles derived from Methanobrevibacter species and are highly enriched in adhesin or adhesin-like proteins, suggesting an important role for archaeal-bacterial and archaeal-host interactions. Unless the specific role of AEVs could not be identified, their production itself suggests an intricate network of interdomain interactions shaping the dynamics of the human microbiome.