bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria

Nature Communications, vol. 15, pp. 2072

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.

Authors 12

1. Guillermo Guerrero-Egido Aachen Institute of Biology, Leiden University

   Leiden University · Consejo Superior de Investigaciones Científicas · Netherlands Institute of Ecology · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Universidad de Málaga

   Affiliation as printed

   Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain

   Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands

   Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

2. Adrián Pintado Aachen Institute of Biology, Leiden University

   Leiden University · Consejo Superior de Investigaciones Científicas · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Universidad de Málaga

   Affiliation as printed

   Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain

   Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain

   Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

3. Kevin M. Bretscher Aachen Institute of Biology, Leiden University

   Leiden University · Consejo Superior de Investigaciones Científicas · Netherlands Institute of Ecology · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Universidad de Málaga

   Affiliation as printed

   Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain

   Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands

   Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

4. Luisa M. Arias-Giraldo

   Netherlands Institute of Ecology

   Affiliation as printed

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands

5. Joseph Nathaniel Paulson
   Affiliation as printed

   Department of Data Sciences, N-Power Medicine, Redwood City, CA, 94063, USA

6. Herman P. Spaink Aachen Institute of Biology, Leiden University

   Leiden University

   Affiliation as printed

   Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

7. Dennis Claessen Aachen Institute of Biology, Leiden University

   Leiden University

   Affiliation as printed

   Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

8. Cayo Ramos

   Consejo Superior de Investigaciones Científicas · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Universidad de Málaga

   Affiliation as printed

   Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain

   Área de Genética, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain

9. Francisco Manuel Cazorla

   Consejo Superior de Investigaciones Científicas · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Universidad de Málaga

   Affiliation as printed

   Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain

   Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain

10. Marnix H. Medema Aachen Institute of Biology, Leiden University

    Leiden University · Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

    Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

11. Jos M. Raaijmakers Aachen Institute of Biology, Leiden University

    Leiden University · Netherlands Institute of Ecology

    Affiliation as printed

    Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands

    Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

12. Víctor J. Carrión corresponding Aachen Institute of Biology, Leiden University

    Leiden University · Consejo Superior de Investigaciones Científicas · Netherlands Institute of Ecology · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Universidad de Málaga

    Affiliation as printed

    Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain. vcarrion@uma.es

    Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain. vcarrion@uma.es

    Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands. vcarrion@uma.es

    Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. vcarrion@uma.es

    Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands