Extended human gut microbiome resource associated with bacterial CRISPR-Cas immune repertoires targeting viral and plasmid MGEs

This repository contains sequence data and metadata for microbial and mobile genetic element (MGE) populations reconstructed from human gut metagenomes and used in the study:“CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.” by Avershina et al., 2026The resource provides an extended catalogue of bacterial genomes, viruses, plasmids, and CRISPR-Cas immune elements identified from fecal shotgun metagenomes of Norwegian individuals. In addition to FASTA sequence files, the repository includes detailed metadata and derived interaction tables linking bacterial hosts to mobile genetic elements through CRISPR-Cas spacer targeting.ContentsThe dataset includes the following components:1. Prokaryotic species-level units (mOTUs)mOTUs_seqs_lim5.fasta: FASTA files of representative genomes used to define mOTUs; only mOTUs detected in >=5 individuals are includedmOTUs_meta.csv: Metadata table containing identifiers, taxonomic annotations, and additional characteristics of each mOTU (number of genomes; CRISPR-Cas detection, and number of spacers detected)2. Viral operational taxonomic units (vOTUs)vOTUs_seqs_lim5.fasta: FASTA sequences of viral populations detected in the dataset; only vOTUs detected in >=5 individuals are includedvOTUs_meta.csv: Metadata including identifiers, viral taxonomy, bacterial genome integration status, and CRISPR-Cas targeting (whether vOTU contained CRISPR, whether it was targeted by CRISPR, and by which bacterial species)3. Plasmid taxonomic units (PTUs)PTUs_seqs_lim5.fasta: FASTA sequences of plasmid populations; only PTUs detected in >=5 individuals are includedPTUs_meta.csv: Metadata with plasmid classification, host prediction, mobility prediction and CRISPR-Cas targeting (whether PTU contained CRISPR, whether it was targeted by CRISPR, and by which bacterial species)4. CRISPR-Cas elementsSpacers_seqs_lim5.fasta: FASTA sequences of CRISPR spacers recovered from metagenomes; only spacers detected in >=5 individuals are includedCassettes_meta.csv: Cassettes metadata describing cassette structure, associated host mOTUs, and CRISPR-Cas spacersSpacers_meta.csv: Spacers metadata describing spacers length and dereplicated cluster size, and associated host mOTUs, and targeted vOTUs and PTUs5. Bacteria-MGE interaction tablemOTU_MGE_interactions.csv: Aggregated interaction files describing relationships between:mOTUs and vOTU targetsmOTUs and PTU targetsDNA sequencing data generated in this study are deposited in Federated EGA under accession code EGAS50000000170. Processing of data from this study must comply with the General Data Protection Regulation (GDPR). Access to DNA sequencing data can be obtained by following the procedure described here: https://www.mn.uio.no/bils/english/groups/rounge-group/crcbiome/.Data generationSequences were reconstructed from fecal shotgun metagenomic data and clustered into operational taxonomic units representing bacterial species (mOTUs), viral populations (vOTUs), and plasmid taxonomic units (PTUs). CRISPR-Cas cassettes and spacers were identified from assembled microbial genomes, and spacer sequences were matched to viral and plasmid sequences to infer historical host-MGE interactions.Together, these resources enable investigation of microbial community composition, mobile genetic element diversity, and CRISPR-based interaction networks in the human gut microbiome.ReuseThis dataset provides a resource for studies of:human gut microbial ecologybacteria-phage and bacteria-plasmid interactionsCRISPR-Cas immune repertoiresmobile genetic element dynamics in microbial communities