ArticleBMC bioinformatics2019
LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Comparative metagenomics using pan-metagenomic graphs.bioRxiv : the preprint server for biology · 2025Article
- Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.Nature communications · 2025Article
- A survey of computational approaches for characterizing microbial interactions in microbial mats.Genome biology · 2025Review
- Profiling lateral gene transfer events in the human microbiome using WAAFLE.Nature microbiology · 2025Article
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.Nucleic acids research · 2024Article
- Article
- Deep learning for HGT insertion sites recognition.BMC genomics · 2020Article
- Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism.FEMS microbiology ecology · 2020Review
- Understanding Horizontal Gene Transfer network in human gut microbiota.Gut pathogens · 2020Article
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3 authors.
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Abstract
backgroundHorizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of microorganisms, especially the gut microbiomes which the human body harbors. The transferred segments may lead to complicated local genome structural variations. Details of the local genome structure can elucidate the effects of the HGTs.
resultsIn this work, we propose a graph-based method to reconstruct the local strains from the gut metagenomics data at the HGT sites. The method is implemented in a package named LEMON. The simulated results indicate that the method can identify transferred segments accurately on reference sequences of the microbiome. Simulation results illustrate that LEMON could recover local strains with complicated structure variation. Furthermore, the gene fusion points detected in real data near HGT breakpoints validate the accuracy of LEMON. Some strains reconstructed by LEMON have a replication time profile with lower standard error, which demonstrates HGT events recovered by LEMON is reliable.
conclusionsThrough LEMON we could reconstruct the sequence structure of bacteria, which harbors HGT events. This helps us to study gene flow among different microbial species.
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