Altered Phage-Related Gene Profiles in Asthmatic Airways

Sep 29, 2026

Altered Phage-Related Gene Profiles in Asthmatic Airways investigates airway microbiome functions in asthma using gene-level metagenomic sequencing. Induced sputum from healthy controls and non-severe versus severe asthma patients shows similar overall bacterial composition but distinct phage- and anti-phage–related functional disruption patterns. Functional variability increases with disease severity, with greater beta-diversity dispersion and rising within-group dissimilarity. Phage-related genes decrease in asthma, while CRISPR-related genes increase, with prophage and CRISPR profiles differing across severity states.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages4

Reading Time10 min

AccessFree to download

Background and Study Aim

Functional gene profiling by metagenomic sequencing

Methods

Participant groups and sample analysis

Results

Bacterial composition and genera-level findings

Viral composition and combined viral presence

Functional variability across severity

Phage-related and CRISPR-associated gene changes

Data Summary

Allergy LETTER OPEN ACCESS Altered Phage-Related Gene Profiles in Asthmatic Airways Min-Gyung Baek1 | Sangcheol Park1 | Young-Chan Kim2,3 | Kyoung-Hee Sohn4 | Jung Wook Kim5 | Kwang Jun Lee5 | Sang-Heon Cho2,3 | Hye-Ryun Kang2,3 | Hana Yi1,6 1Institute for Biomaterials, Korea University, Seoul, Korea | 2Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea | 3Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea | 4Department of Internal Medicine, Kyung Hee University Hospital, Seoul, Korea | 5Division of Zoonotic and Vector Borne Diseases Research, Center for Infectious Disease Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Korea | 6School of Biosystems and Biomedical Sciences, Korea University, Seoul, Korea Correspondence: Hye-Ryun Kang ([helenmed@snu.ac.kr](helenmed@snu.ac.kr)) | Hana Yi ([hanayi@korea.ac.kr](hanayi@korea.ac.kr)) Received: 31 December 2024 | Revised: 16 July 2025 | Accepted: 31 July 2025 Funding: This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Ministry of Science and ICT of Korea (MSIT)(No. 2022R1A2C1007966 and No. RS-2023-00217157) and by the National Institute of Health (NIH) research project (No. 2024-ER2105-00) . Keywords: asthma | biomarkers | microbiome To the Editor, This study provides a functional perspective on the airway microbiome in asthma by analyzing gene-level features through metagenomic sequencing. While prior studies have largely focused on taxonomic composition, our findings reveal functionlevel disruptions—particularly in phage-related and anti-phage gene profiles—that distinguish asthmatic airways from healthy controls. Induced sputum samples from patients with non-severe and severe asthma and healthy controls (17 per group) were analyzed (Table 1) . Overall bacterial composition was similar across groups (Figure S1A) . No genera differed significantly by disease severity, though Actinomyces showed a marginal difference between control and non-severe groups (Table S1A). Actinomyces, Selenomonas [1] and GGB4533 were relatively enriched in controls (Figure 1A), but their associations with clinical parameters were not statistically significant (Figure S1B) . Viral composition analysis showed an overall abundance of bacteriophages across all groups (Figure S2A) . Notably, the combined presence of both viruses (Cytomegalovirus and Epstein–Barr virus) showed a significant difference between controls and non-severe patients (Q = 0.083) (Figure S2B; Table S1B), consistent with our prior findings [2] . To evaluate microbial functional variability across asthma severity, we analyzed beta-diversity of functional gene profiles. PCoA based on Bray-Curtis distances showed greater dispersion in asthma samples compared to controls (p = 0.049)(Figure S3A) . Linear regression analysis further demonstrated that within-group functional dissimilarity increased with severity (p = 0.001) (Figure S3B) . These findings suggest that airway microbial function becomes increasingly heterogeneous as asthma progresses. Elevated within-group variability may indicate disrupted microbial homeostasis and potentially reflect functional dysbiosis [3] associated with disease severity. Among the functional genes examined, two phage-related genes showed significant reduction in asthma, while certain CRISPRrelated genes were relatively increased (Figure 1B; Table S1C) . A broader analysis showed that prophage-related genes were more abundant in controls, whereas CRISPR-associated genes were enriched in severe asthma (Figure 1C) . Bacteria possess | Min-gyung Baek and Sangcheol Park contributed equally as first authors. | | --- | | This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits u

FAQs

What approach does the study use to analyze asthma-related airway changes?

The study uses metagenomic sequencing to analyze airway microbiome gene-level features, focusing on functional characteristics rather than only taxonomy.

How do bacterial and viral compositions differ among healthy controls and asthma severity groups?

Overall bacterial composition is similar across groups, with limited marginal differences. Viral composition shows overall bacteriophage abundance across groups, with a significant difference in combined viral presence between controls and non-severe patients.

Which functional gene patterns are associated with asthma severity?

Beta-diversity dispersion and within-group functional dissimilarity increase with severity, suggesting growing heterogeneity. Phage-related genes decrease in asthma, while CRISPR-related genes are relatively increased, and prophage versus CRISPR-associated profiles differ between controls and severe asthma.

Sep 29, 2026

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