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The lung microbiome framework offers a unifying model: altered microbial immigration, elimination, and growth can produce dysbiosis with pathobiont expansion and antimicrobial resistance (AMR). We propose that pediatric NMD may follow a distinct developmental trajectory in which early-life secretion stasis, viral insults, and frequent antibiotics perturb immune\u2013microbiome crosstalk during lung growth, potentially \u201cimprinting\u201d long-term community structure. However, NMD-specific airway microbiome data remain sparse because most studies rely on culture or upper-airway sampling. Oxford Nanopore Technologies (ONT) long-read sequencing enables real-time metagenomics with AMR gene detection and can deliver same-day profiles (as short as\u2009~\u20096 h from sample to result in optimized workflows), but requires robust low-biomass controls and, in some settings, polishing or hybrid strategies to mitigate higher per-read error. A major limitation of metagenomic sequencing of respiratory samples is the high proportion of host DNA, bacterial reads may account for only about 1\u20135% of the total sequencing reads. We review microbiome principles relevant to pediatric NMD, summarize current evidence, and outline ONT-enabled study designs and translational priorities.<\/jats:p>","DOI":"10.1186\/s40348-026-00261-0","type":"journal-article","created":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T03:15:41Z","timestamp":1789787741000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing"],"prefix":"10.1186","volume":"13","author":[{"given":"Sebahattin","family":"Cirak","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vivien","family":"Grieshaber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"M\u00fcller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cho-Ming","family":"Chao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,19]]},"reference":[{"issue":"4","key":"261_CR1","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1164\/rccm.200307-885ST","volume":"170","author":"JD Finder","year":"2004","unstructured":"Finder JD, Birnkrant D, Carl J, Farber HJ, Gozal D, Iannaccone ST et al (2004) Respiratory care of the patient with Duchenne muscular dystrophy: ATS consensus statement. 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