ArticleNature communications2024
bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Integrated genomic and experimental assessment of the biosafety of Paraburkholderia sacchari as a promising microbial chassis.World journal of microbiology & biotechnology · 2026Article
- Biosynthetic diversity and antifungal potential of soil-derivedApplied and environmental microbiology · 2026Article
- Functional diversity and ecological consequences of endophytic Bacillus-plant interactions.Folia microbiologica · 2026Review
- Horizontal acquisition of nicotine catabolism gene cluster enhances Arthrobacter fitness within tobacco root microbiota.Microbiome · 2026Article
- Genome-based insights into metal co-resistance in Amazonian mercury-resistant bacteria: ecological lifestyle and biosafety implications for bioremediation.Microbiology spectrum · 2026Article
- A 'Genome-First' Framework for Next-Generation Bioinputs: From Functional Mining to Rational Synthetic Microbial Communities.Environmental microbiology · 2026Review
- PaVarDB: a database and web platform for missense variant analysis in Pseudomonas aeruginosa using an end-to-end BVbase pipeline.Database : the journal of biological databases and curation · 2026Article
- Identifying phenotypic and genetic traits for assessing pathogenic potential and biocontrol capacity in Burkholderia sensu lato strains.The ISME journal · 2026Article
- Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas.Microbiome · 2025Article
- Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH.Nature communications · 2025Article
- microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.Genome biology · 2025Article
- The soil-plant-human gut microbiome axis into perspective.Nature communications · 2025Review
- Rapid identification platform of spores based on Raman spectroscopy.Food chemistry: X · 2025Article
- Uncovering encrypted antimicrobial peptides in health-associated Lactobacillaceae by large-scale genomics and machine learning.Microbiome · 2025Article
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12 authors.
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Abstract
Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.com/Carrion-lab/bacLIFE ) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.
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