{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T18:28:13Z","timestamp":1773685693436,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,5,29]],"date-time":"2025-05-29T00:00:00Z","timestamp":1748476800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Neonatal pneumonia is a leading cause of infant mortality worldwide; however, a lack of microbial profiling, especially of low-abundance species, makes accurate diagnosis challenging. Traditional methods can fail to capture the complexity of the neonatal respiratory microbiota, thereby obscuring its role in disease progression. Here, we describe a novel approach that combines high-throughput sequencing with droplet-based microfluidic cultivation to investigate microbiome shifts in neonates with pneumonia. Using 16S ribosomal RNA (rRNA) gene sequencing of 71 pneumonia cases and 49 controls, we identified 1009 genera, including 930 low-abundance taxa, which showed significant compositional differences between groups. Linear discriminant analysis effect size identified key pneumonia-associated genera, such as Streptococcus, Rothia, and Corynebacterium. Droplet-based cultivation recovered 299 strains from 94 taxa, including rare species and ESKAPE pathogens, thereby supporting targeted antimicrobial management. Host\u2013pathogen interaction assays showed that Rothia and Corynebacterium induced inflammation in lung epithelial cells, likely via dysregulation of the PI3K-Akt pathway. Integrating these marker taxa with clinical factors, such as gestational age and delivery type, offers the potential for precise diagnosis and treatment. The recovery of diverse species can support the construction of a biobank of neonatal respiratory microbiota to advance mechanistic studies and therapeutic strategies.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf047","type":"journal-article","created":{"date-parts":[[2025,5,29]],"date-time":"2025-05-29T07:04:37Z","timestamp":1748502277000},"source":"Crossref","is-referenced-by-count":2,"title":["Unveiling Neonatal Pneumonia Microbiome by High-throughput Sequencing and Droplet Culturomics"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1535-8772","authenticated-orcid":false,"given":"Zerui","family":"Wang (\u738b\u5219\u9510)","sequence":"first","affiliation":[{"name":"Biomedical Sciences College & Shandong Medical Biotechnology Center, Shandong First Medical University & Shandong Academy of Medical Sciences , Jinan 250117,","place":["China"]},{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9325-3351","authenticated-orcid":false,"given":"Xin","family":"Cheng (\u7a0b\u6b23)","sequence":"additional","affiliation":[{"name":"Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University , Beijing 100050,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7591-2421","authenticated-orcid":false,"given":"Yibin","family":"Xu (\u5f90\u4e49\u658c)","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1302-8215","authenticated-orcid":false,"given":"Zhiyi","family":"Wang (\u6c6a\u4e4b\u4e00)","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-9816-0134","authenticated-orcid":false,"given":"Liyan","family":"Ma (\u9a6c\u7acb\u8273)","sequence":"additional","affiliation":[{"name":"Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University , Beijing 100050,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8355-0109","authenticated-orcid":false,"given":"Caiming","family":"Li (\u674e\u57f0\u660e)","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-7288-9549","authenticated-orcid":false,"given":"Shize","family":"Jiang (\u59dc\u4e16\u6cfd)","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-1049-9861","authenticated-orcid":false,"given":"Yuchen","family":"Li (\u9ece\u96e8\u5c18)","sequence":"additional","affiliation":[{"name":"Biomedical Sciences College & Shandong Medical Biotechnology Center, Shandong First Medical University & Shandong Academy of Medical Sciences , Jinan 250117,","place":["China"]},{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6705-9339","authenticated-orcid":false,"given":"Shuilong","family":"Guo (\u90ed\u6c34\u9f99)","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University , Beijing 100050,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7401-1410","authenticated-orcid":false,"given":"Wenbin","family":"Du (\u675c\u6587\u658c)","sequence":"additional","affiliation":[{"name":"Biomedical Sciences College & Shandong Medical Biotechnology Center, Shandong First Medical University & Shandong Academy of Medical Sciences , Jinan 250117,","place":["China"]},{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]},{"name":"Medical School and College of Life Sciences, University of the Chinese Academy of Sciences , Beijing 100049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,5,29]]},"reference":[{"key":"2025122219015644300_qzaf047-B1","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.prrv.2007.07.001","article-title":"Congenital and neonatal pneumonia","volume":"8","author":"Nissen","year":"2007","journal-title":"Paediatr Respir Rev"},{"key":"2025122219015644300_qzaf047-B2","doi-asserted-by":"crossref","first-page":"e01318-17","DOI":"10.1128\/JCM.01318-17","article-title":"Community-acquired pneumonia in children: the challenges of microbiological diagnosis","volume":"56","author":"Rodrigues","year":"2018","journal-title":"J Clin Microbiol"},{"key":"2025122219015644300_qzaf047-B3","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.gpb.2014.06.001","article-title":"Human pharyngeal microbiome may play a 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