{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T17:13:03Z","timestamp":1788455583279,"version":"build-2803163510"},"reference-count":50,"publisher":"Microbiology Society","issue":"9","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science Foundation","award":["2334721"],"award-info":[{"award-number":["2334721"]}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"crossref","award":["2024-67013-43202"],"award-info":[{"award-number":["2024-67013-43202"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,3]]},"abstract":"<jats:p>\n                    The environmental bacterium\n                    <jats:italic>Pseudomonas protegens<\/jats:italic>\n                    PBL3 has antagonistic activity against the plant pathogenic bacterium\n                    <jats:italic>Burkholderia glumae<\/jats:italic>\n                    , an important pathogen in rice. The antimicrobial activity of\n                    <jats:italic>P. protegens<\/jats:italic>\n                    PBL3 was found in the bacteria-free secreted fraction (secretome), but the specific molecules, as well as the genetic basis of that activity, have not been identified. In this study, we integrated genomic information with antimicrobial assays on\n                    <jats:italic>P. protegens<\/jats:italic>\n                    PBL3 and additional six\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    spp. strains, to identify putative genomic regions in\n                    <jats:italic>P. protegens<\/jats:italic>\n                    PBL3 associated with antimicrobial activity. We hypothesized that\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    spp. strains with antimicrobial activity against\n                    <jats:italic>B. glumae<\/jats:italic>\n                    have conserved genes with\n                    <jats:italic>P. protegens<\/jats:italic>\n                    PBL3 that are absent in strains lacking activity. Comparative genomics analyses with anvi\u2019o and progressiveMauve, and using\n                    <jats:italic>P. protegens<\/jats:italic>\n                    PBL3 as the reference genome, revealed 188 genes uniquely present in antimicrobial-producing strains. Seven of those genes were annotated as biosynthetic gene clusters predicted to encode secondary metabolites; additional genes were grouped into 25 contiguous clusters with functions annotated as secretion, signal transduction, regulation, transport\/efflux, carbohydrate metabolism and one with an additional uncharacterized function. Altogether, this study uncovered a complex and multi-functional network of candidate genes, suggesting that the antimicrobial activity in\n                    <jats:italic>P. protegens<\/jats:italic>\n                    PBL3 is not limited to biosynthetic pathways but also involves additional regulatory, metabolic and export modules to synthesize and deploy antimicrobials.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001827","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T16:15:31Z","timestamp":1788452131000},"source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomics approaches to identify genomic regions associated with the antimicrobial activity of Pseudomonas protegens PBL3"],"prefix":"10.1099","volume":"12","author":[{"given":"Shilu","family":"Dahal","sequence":"first","affiliation":[{"name":"Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA"},{"name":"Department of Plant 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