ArticleMicrobiome2019
MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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78 citing papers in PubMed, 159 citations in OpenAlex.
- DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.Briefings in bioinformatics · 2026Article
- Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.Nature communications · 2026Article
- Systematic citywide analysis reveals ecological connectivity of antimicrobial resistance genes across urban water systems.Nature communications · 2026Article
- Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Alternating High-Fat and Polysaccharide Diets Modulates Gut Phage-Bacterial Interplay.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.mSystems · 2026Article
- Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.NPJ biofilms and microbiomes · 2026Article
- TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.bioRxiv : the preprint server for biology · 2026Article
- Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.Communications biology · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.The ISME journal · 2026Article
- Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.The ISME journal · 2026Article
- Genomic adaptation strategies to habitat switching in Korarchaeota.Science advances · 2026Article
- A metagenomic snapshot of metabolic potentials in wintertime eutrophic sediments of Lake Taihu inferred from metagenome-assembled genomes.Frontiers in microbiology · 2026Article
- Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.BMC microbiology · 2025Article
- Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau.Science China. Life sciences · 2025Article
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- Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.Nature communications · 2025Article
- Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.Nature communications · 2025Article
- DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils.Nature communications · 2025Article
- Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.Microbiome · 2025Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.
resultsAssessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms.
conclusionMetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .
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