{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T19:06:54Z","timestamp":1788376014445,"version":"build-2803163510"},"posted":{"date-parts":[[2025,6,2]]},"group-title":"Microbiology","reference-count":53,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,6,2]],"date-time":"2025-06-02T00:00:00Z","timestamp":1748822400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  <jats:italic>Aspergillus fumigatus<\/jats:italic>\n                  is a filamentous fungus found in compost and soil that can cause invasive and\/or chronic disease in a broad spectrum of individuals. Diagnosis and treatment of aspergillosis often occur during stages of infection when\n                  <jats:italic>A. fumigatus<\/jats:italic>\n                  has formed dense networks of hyphae within the lung. These dense hyphal networks are multicellular, encased in a layer of extracellular matrix, and have reduced susceptibility to contemporary antifungal drugs, characteristics which are defining features of a microbial biofilm. A mode of growth similar to these dense hyphal networks observed\n                  <jats:italic>in vivo<\/jats:italic>\n                  can be recapitulated\n                  <jats:italic>in vitro<\/jats:italic>\n                  using a static, submerged biofilm culture model. The mechanisms underlying filamentous fungal cell physiology at different stages of biofilm development remain to be defined. Here, we utilized an RNA sequencing approach to evaluate changes in transcript levels during\n                  <jats:italic>A. fumigatus<\/jats:italic>\n                  biofilm development. These analyses revealed an increase in transcripts associated with fermentation and a concomitant decrease in oxidative phosphorylation related transcripts. Further investigation revealed that ethanol and butanediol fermentation is important for mature biofilm biomass maintenance. Correspondingly, a gene (silG), a predicted transcription factor, was observed to also be required for mature biofilm biomass maintenance. Taken together, these data suggest temporal changes in\n                  <jats:italic>A. fumigatus<\/jats:italic>\n                  metabolism during biofilm development are required to maintain a fully mature biofilm.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>IMPORTANCE<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Aspergillus fumigatus<\/jats:italic>\n                    is the most common etiological agent of a collection of diseases termed aspergillosis. Invasive\n                    <jats:underline>P<\/jats:underline>\n                    ulmonary\n                    <jats:underline>A<\/jats:underline>\n                    spergillosis (IPA), a severe form of aspergillosis, is highlighted by invasive growth of fungal hyphae into host lung tissue. Strains that are susceptible to antifungal therapies\n                    <jats:italic>in vitro<\/jats:italic>\n                    frequently fail to respond to treatment\n                    <jats:italic>in<\/jats:italic>\n                    vivo, resulting in high mortality rates even with treatment. It is now appreciated that this decreased antifungal efficacy\n                    <jats:italic>in vivo<\/jats:italic>\n                    is, in part, likely due to biofilm-like growth of the fungus.\n                    <jats:italic>A. fumigatus<\/jats:italic>\n                    biofilms have been shown to develop regions of limited oxygen availability that are hypothesized to induce cell quiescence and drug resistance. Understanding the mechanisms by which\n                    <jats:italic>A. fumigatus<\/jats:italic>\n                    induces, develops, and maintains biofilms to evade antifungal therapies is expected to illuminate biofilm-specific therapeutic targets. Here we present transcriptomics data of developing\n                    <jats:italic>A. fumigatus<\/jats:italic>\n                    biofilms and from these data define genes related to fungal fermentation and regulation of transcription important for maintenance of mature\n                    <jats:italic>A. fumigatus<\/jats:italic>\n                    biofilms.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.06.02.657448","type":"posted-content","created":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T00:10:21Z","timestamp":1748909421000},"source":"Crossref","is-referenced-by-count":2,"title":["Transcriptional analysis of developing\n                  <i>Aspergillus fumigatus<\/i>\n                  biofilms reveals metabolic shifts required for biofilm maintenance"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4402-0295","authenticated-orcid":false,"given":"Charles","family":"Puerner","sequence":"first","affiliation":[{"name":"Geisel School of Medicine, and Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaesi A.","family":"Morelli","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine, and Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755 USA"},{"name":"Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, VT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua D.","family":"Kerkaert","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine, and Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755 USA"},{"name":"School of Integrative Plant Sciences Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane T.","family":"Jones","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine, and Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine G.","family":"Quinn","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine, and Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandeep","family":"Vellanki","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine, and Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5503-5006","authenticated-orcid":false,"given":"Robert A.","family":"Cramer","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine, and Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755 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