{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T15:07:12Z","timestamp":1787065632880,"version":"build-2736575974"},"reference-count":60,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T00:00:00Z","timestamp":1769040000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>The nasopharyngeal microbiome presents an important environmental human interface and a window in the fight against chronic diseases like asthma, respiratory infections, and antimicrobial resistance. To identify the microbial structure and function, we designed a pilot study with individuals with asthma, COVID-19 infection, and healthy controls.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We compare the microbial and resistome profiles of healthy individuals, patients with asthma, and patients with PCR-confirmed COVID-19 using shotgun metagenome sequencing. Additionally, metagenome-assembled genomes were generated to assess the virulence potential of the bacteria identified in the nasopharynx.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We found different patterns in microbial diversity, richness, and structure between individuals with asthma and those who are healthy, but not for those with COVID-19. Our results revealed unexpected insights into the quite diverse nasopharynx resistome encompassing 23 distinct drug classes, mainly based on antibiotic efflux (63.9%) and antibiotic inactivation (24.6%), regardless of the disease state. The majority of the antimicrobial resistance genes (ARGs) confer resistance to multidrug (45%), followed by those genes that confer resistance to aminoglycosides, tetracyclines, polymyxin, beta-lactam, and macrolide-lincosamide-streptogramin. A high proportion of ARGs was associated with various\n                      <jats:italic>Pseudomonas<\/jats:italic>\n                      species, which was confirmed by analysing metagenome-assembled genomes.\n                      <jats:italic>Pseudomonas brenneri<\/jats:italic>\n                      exhibited the highest number of ARGs and virulence factors, indicating notable pathogenic potential.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      The study reveals distinct bacterial community compositions in healthy individuals and individuals with asthma.\n                      <jats:italic>Pseudomonadales<\/jats:italic>\n                      , particularly\n                      <jats:italic>Pseudomonas<\/jats:italic>\n                      species, contribute to the nasopharyngeal resistome. No association was found between nasopharyngeal resistome profiles and asthma development. Future research may explore airway microbial functions\u2019 influence on asthma development.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1729707","type":"journal-article","created":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T06:51:59Z","timestamp":1769064719000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Metagenomic analysis of the nasopharyngeal microbiomes and resistomes in asthma, COVID-19 infected, and healthy individuals"],"prefix":"10.3389","volume":"17","author":[{"given":"Wisnu Adi","family":"Wicaksono","sequence":"first","affiliation":[{"name":"Institute of Environmental Biotechnology, Graz University of Technology","place":["Graz, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Thorsen","sequence":"additional","affiliation":[{"name":"COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital - Herlev and Gentofte","place":["Copenhagen, Denmark"]},{"name":"Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen","place":["Copenhagen, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakob","family":"Stokholm","sequence":"additional","affiliation":[{"name":"COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital - Herlev and Gentofte","place":["Copenhagen, Denmark"]},{"name":"Department of Food Science, University of Copenhagen","place":["Copenhagen, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriele","family":"Berg","sequence":"additional","affiliation":[{"name":"Institute of Environmental Biotechnology, Graz University of Technology","place":["Graz, Austria"]},{"name":"Leibniz-Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB)","place":["Potsdam, Germany"]},{"name":"Institute for Biochemistry and Biology, University of Potsdam","place":["Potsdam, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,22]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s40413-015-0074-z","article-title":"The microbiome of the human lower airways: a next generation sequencing perspective","volume":"8","author":"Aho","year":"2015","journal-title":"World Allergy Organ. 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