PXD053245-1

PXD053245 is an original dataset announced via ProteomeXchange.

Title	Interacting archaea: Extracellular Vesicle formation in two major human gut Methanobrevibacter species
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.
HostingRepository	PRIDE
AnnounceDate	2025-06-10
AnnouncementXML	Submission_2025-06-10_02:21:06.343.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbara Darnhofer
SpeciesList	scientific name: Methanobrevibacter smithii; NCBI TaxID: 2173; scientific name: Archaea; NCBI TaxID: NCBITaxon:2157;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	maXis

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-19 22:26:49	ID requested
⏵ 1	2025-06-10 02:21:06	announced

10.1038/S41467-025-60271-W;

submitter keyword: extracellular vesicle, proteomics,archaea

Harald Koefeler
contact affiliation	Priv. Doz. Dr. Harald C. Köfeler Director Core Facility Mass Spectrometry Medical University Graz Center for Medical Research (ZMF) Neue Stiftingtalstrasse 6 8010 Graz AUSTRIA
contact email	harald.koefeler@medunigraz.at
lab head
Barbara Darnhofer
contact affiliation	Omics Center Graz
contact email	barbara.darnhofer@klinikum-graz.at
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/06/PXD053245

PRIDE project URI

• PRIDE
  1. PXD053245
     1. Label: PRIDE project
     2. Name: Interacting archaea: Extracellular Vesicle formation in two major human gut Methanobrevibacter species