Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome DOI Creative Commons
Tatiana Borodovich, Jason S. Wilson, Pavol Bárdy

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 16, 2024

Abstract Transducing bacteriophages and gene transfer agents (GTA) are constrained by their capsids’ structural properties in the length of host DNA they can package. Nanopore sequencing intact capsid-packaged molecules with full-sized reads be used to establish precise lengths identity individual packaged association specific bacterial hosts. This approach was validated using a few well-characterised transducing systems, then applied study encapsidation faecal microbiomes from three healthy human donors. Bacterial appears widespread microbiome up 5.4% gut virome being (non-prophage) origin. Generalised transduction GTA activity especially prevalent families Oscillospiraceae Ruminococcaceae, whereas an example lateral observed genus Bacteroides. In addition that, induction prophages variety highly bacteria observed.

Language: Английский

GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome DOI Creative Commons
Yiqi Jiang, Yanfei Wang,

Lijia Che

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D772 - D782

Published: Nov. 11, 2024

Abstract Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping gut microbiome’s capacity resilience. However, lack comprehensive data integration systematic analysis approaches has limited in-depth exploration HGT FR dynamics across large-scale microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human with analyses. contains 21 567 metagenome samples whole-genome shotgun sequencing related to various health conditions. Through analysis, characterized taxonomic profiles profiles, identified 14 636 events using shared reference genome collected samples. These been curated into 8049 clusters, which are annotated categorized mobile genetic elements, transposons, prophages, integrative mobilizable genomic islands, conjugative elements group II introns. Additionally, incorporates automated analyses visualizations for FR, serving as an efficient platform interactions among taxa their implications health.

Language: Английский

Citations

2
Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome DOI Creative Commons
Tatiana Borodovich, Jason S. Wilson, Pavol Bárdy

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 16, 2024

Abstract Transducing bacteriophages and gene transfer agents (GTA) are constrained by their capsids’ structural properties in the length of host DNA they can package. Nanopore sequencing intact capsid-packaged molecules with full-sized reads be used to establish precise lengths identity individual packaged association specific bacterial hosts. This approach was validated using a few well-characterised transducing systems, then applied study encapsidation faecal microbiomes from three healthy human donors. Bacterial appears widespread microbiome up 5.4% gut virome being (non-prophage) origin. Generalised transduction GTA activity especially prevalent families Oscillospiraceae Ruminococcaceae, whereas an example lateral observed genus Bacteroides. In addition that, induction prophages variety highly bacteria observed.

Language: Английский

Citations

1