{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:30:00Z","timestamp":1760146200046,"version":"build-2065373602"},"reference-count":54,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T00:00:00Z","timestamp":1728259200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swiss National Science Foundation through the BRIDGE Discovery program","award":["194701","FreeNovation Program","GRS-064\/18"],"award-info":[{"award-number":["194701","FreeNovation Program","GRS-064\/18"]}]},{"DOI":"10.13039\/100008273","name":"Novartis Foundation, through the FreeNovation program","doi-asserted-by":"publisher","award":["194701","FreeNovation Program","GRS-064\/18"],"award-info":[{"award-number":["194701","FreeNovation Program","GRS-064\/18"]}],"id":[{"id":"10.13039\/100008273","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003357","name":"Gebert R\u00fcf Stiftung","doi-asserted-by":"publisher","award":["194701","FreeNovation Program","GRS-064\/18"],"award-info":[{"award-number":["194701","FreeNovation Program","GRS-064\/18"]}],"id":[{"id":"10.13039\/501100003357","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fondation Professeur Placide Nicod","award":["194701","FreeNovation Program","GRS-064\/18"],"award-info":[{"award-number":["194701","FreeNovation Program","GRS-064\/18"]}]},{"name":"Ligue Pulmonaire Neuch\u00e2teloise","award":["194701","FreeNovation Program","GRS-064\/18"],"award-info":[{"award-number":["194701","FreeNovation Program","GRS-064\/18"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Fungi of the genus Aspergillus are widespread in the environment, where they produce large quantities of airborne conidia. Inhalation of Aspergillus spp. conidia in immunocompromised individuals can cause a wide spectrum of diseases, ranging from hypersensitivity responses to lethal invasive infections. Upon deposition in the lung epithelial surface, conidia encounter and interact with complex microbial communities that constitute the lung microbiota. The lung microbiota has been suggested to influence the establishment and growth of Aspergillus spp. in the human airways. However, the mechanisms underlying this interaction have not yet been sufficiently investigated. In this study, we aimed to enrich and isolate bacterial strains capable of inhibiting the germination and growth of A. fumigatus conidia from bronchoalveolar lavage fluid (BALF) samples of lung transplant recipients using a novel enrichment method. This method is based on a soft agar overlay plate assay in which bacteria are directly in contact with conidia, allowing inhibition to be readily observed during enrichment. We isolated a total of five clonal bacterial strains with identical genotypic fingerprints, as shown by random amplified polymorphic DNA PCR (RAPD\u2013PCR). All strains were identified as Pseudomonas aeruginosa (strains b1\u2013b5). The strains were able to inhibit the germination and growth of Aspergillus fumigatus in a soft agar confrontation assay, as well as in a germination multiplate assay. Moreover, when compared with ten P. aeruginosa strains isolated from expectoration through standard methods, no significant differences in inhibitory potential were observed. Additionally, we showed inhibition of A. fumigatus growth on Calu-3 cell culture monolayers. However, the isolated P. aeruginosa strains were shown to cause significant damage to the cell monolayers. Overall, although P. aeruginosa is a known opportunistic lung pathogen and antagonist of A. fumigatus, we validated this novel one-step enrichment approach for the isolation of bacterial strains antagonistic to A. fumigatus from BALF samples as a proof-of-concept. This opens up a new venue for the targeted enrichment of antagonistic bacterial strains against specific fungal pathogens.<\/jats:p>","DOI":"10.3390\/microorganisms12102025","type":"journal-article","created":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T07:08:18Z","timestamp":1728284898000},"page":"2025","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus Conidia"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5241-6898","authenticated-orcid":false,"given":"Fabio","family":"Palmieri","sequence":"first","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00e9r\u00e9my","family":"Diserens","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manon","family":"Gresse","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margo","family":"Magnin","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julina","family":"Helle","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4682-2177","authenticated-orcid":false,"given":"Beno\u00eet","family":"Salamin","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorenzo","family":"Bisanti","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Bernasconi","sequence":"additional","affiliation":[{"name":"Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), 1066 Epalinges, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie","family":"Pernot","sequence":"additional","affiliation":[{"name":"Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), 1066 Epalinges, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Apiha","family":"Shanmuganathan","sequence":"additional","affiliation":[{"name":"Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), 1066 Epalinges, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5244-0823","authenticated-orcid":false,"given":"Aur\u00e9lien","family":"Trompette","sequence":"additional","affiliation":[{"name":"Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), 1066 Epalinges, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"von Garnier","sequence":"additional","affiliation":[{"name":"Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), 1066 Epalinges, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Junier","sequence":"additional","affiliation":[{"name":"Vital-IT, Swiss Institute of Bioinformatic (SIB), 1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4080-5546","authenticated-orcid":false,"given":"Samuel","family":"Neuenschwander","sequence":"additional","affiliation":[{"name":"Vital-IT, Swiss Institute of Bioinformatic (SIB), 1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saskia","family":"Bindschedler","sequence":"additional","affiliation":[{"name":"Laboratory of 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Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0177-4134","authenticated-orcid":false,"given":"Niki","family":"Ubags","sequence":"additional","affiliation":[{"name":"Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), 1066 Epalinges, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pilar","family":"Junier","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Institute of Biology, Faculty of Science, University of Neuch\u00e2tel, 2000 Neuch\u00e2tel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e428","DOI":"10.1016\/S1473-3099(23)00692-8","article-title":"Global incidence and mortality of severe fungal 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