{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T22:19:46Z","timestamp":1792189186145,"version":"4.4.0"},"reference-count":44,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:00:00Z","timestamp":1736985600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Ministry of Health"},{"name":"RSA 2021"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Pneumonia caused by Pneumocystis jirovecii infection (PCP) is a potentially life-threatening illness, particularly affecting the immunocompromised. The past two decades have shown an increase in PCP incidence; however, the underlying factors that promote disease severity and fatality have yet to be fully elucidated. Recent evidence suggests that the microbiota of the respiratory tract may play a role in stimulating or repressing pulmonary inflammation, as well as the progression of both bacterial and viral pneumonia. Here, we employed 16S rRNA metataxonomic sequencing to profile the respiratory microbiota of patients with mild-moderate and severe PCP. Our results show that the upper and lower airways of PCP patients have bacterial profiles which have been associated with a pro-inflammatory response. Furthermore, we find that severe PCP is associated with lower bacterial diversity and an increase in Prevotella and a decrease in Neisseria. Functionally, severe PCP was associated with a decrease in metabolic pathways of molecules with anti-inflammatory and antimicrobial properties. To our knowledge, this is the first study showing an association of PCP severity with shifts in the respiratory microbiome and may provide some insight into which patients are more susceptible to the more severe manifestations of the disease.<\/jats:p>","DOI":"10.3390\/pathogens14010082","type":"journal-article","created":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T10:44:23Z","timestamp":1737024263000},"page":"82","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pneumocystis Pneumonia Severity Is Associated with Taxonomic Shifts in the Respiratory Microbiota"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-1667-8338","authenticated-orcid":false,"given":"Valentina","family":"Del Prete","sequence":"first","affiliation":[{"name":"Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7591-6473","authenticated-orcid":false,"given":"Antonia","family":"Piazzesi","sequence":"additional","affiliation":[{"name":"Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00144 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6266-2884","authenticated-orcid":false,"given":"Matteo","family":"Scanu","sequence":"additional","affiliation":[{"name":"Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00144 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8976-9013","authenticated-orcid":false,"given":"Francesca","family":"Toto","sequence":"additional","affiliation":[{"name":"Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00144 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8936-895X","authenticated-orcid":false,"given":"Stefania","family":"Pane","sequence":"additional","affiliation":[{"name":"Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00144 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Berrilli","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovangiacinto","family":"Paterno","sequence":"additional","affiliation":[{"name":"Hematology, Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0134-2830","authenticated-orcid":false,"given":"Lorenza","family":"Putignani","sequence":"additional","affiliation":[{"name":"Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00144 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"di Cave","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.idc.2009.10.010","article-title":"Pneumocystis jirovecii Pneumonia","volume":"24","author":"Catherinot","year":"2010","journal-title":"Infect. 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