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.

Project description:Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. In order to understand how archaeal histones affect transcriptional processes, we induced expression of the two histones from the archaeon Methanothermus fervidus in a naive bacterial system (E. coli) that has not evolved to integrate this kind of proteins. We show, using a series of MNase digestion experiments, that these histones bind the bacterial genome and wrap DNA in vivo in a pattern consistent with a previously proposed multimerisation model, in a similar pattern observed natively. We correlate genome-wide occupancy maps and gene expression profiles in different phases of growth to show that – although expression of archaeal histones triggers morphological changes in E. coli – there appears to only be an indirect effect on transcription. Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. In order to understand how archaeal histones affect transcriptional processes, we induced expression of the two histones from the archaeon Methanothermus fervidus in a naive bacterial system (E. coli) that has not evolved to integrate this kind of proteins. We show, using a series of MNase digestion experiments, that these histones bind the bacterial genome and wrap DNA in vivo in a pattern consistent with a previously proposed multimerisation model, in a similar pattern observed natively. We correlate genome-wide occupancy maps and gene expression profiles in different phases of growth to show that – although expression of archaeal histones triggers morphological changes in E. coli – there appears to only be an indirect effect on transcription.

			Action	DRS
	20250512_160238_b023.sne	Other
	2025_05_10_H_volcanii_plus_J2ZJU5_from_Warnecke.fasta	Fasta
	2025_05_10_visualising_distributions.R	Other
	2025_05_12_potein_report.tsv	Tabular
	b023_p005_e001_fr47.raw	Raw

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Archaea produce peptidoglycan hydrolases that kill bacteria

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Archaea produce peptidoglycan hydrolases that kill bacteria.

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