Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma
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Clinical and Translational Allergy Open Access
RESEARCH
Fungal and bacterial microbiome dysbiosis and imbalance of trans‑kingdom network in asthma Chunrong Huang1,2†, Youchao Yu1,2†, Wei Du1,2, Yahui Liu1,2, Ranran Dai1,2, Wei Tang1,2, Ping Wang1,2, Chenhong Zhang3* and Guochao Shi1,2*
Abstract Background: Fungal and bacterial microbiota play an important role in development of asthma. We aim to characterize airway microbiome (mycobiome, bacteriome) and functional genes in asthmatics and controls. Methods: Sputum microbiome of controls, untreated asthma patients and inhaled corticosteroid (ICS) receiving patients was detected using high throughput sequencing. Metagenomic sequencing was used to examine the functional genes of microbiome. Results: 1. Mycobiome: α diversity was lower in untreated asthma group than that in controls. Mycobiome compositions differed among the three groups. Compared with controls, untreated asthma group has higher abundance of Wallemia, Mortierella and Fusarium. Compared with untreated asthma patients, ICS receiving patients has higher abundance of Fusarium and Mortierella, lower frequency of Wallemia, Alternaria and Aspergillus. 2. Bacteriome: α diversity was lower in untreated asthma group than that in controls. There are some overlaps of bacteriome compositions between controls and untreated asthma patients which were distinct from ICS receiving patients. Untreated asthma group has higher Streptococcus than controls. 3. Potential fungal and bacterial biomarkers of asthma: Trametes, Aspergillus, Streptococcus, Gemella, Neisseria, etc. 4. Correlation network: There are dense and homogenous correlations in controls but a dramatically unbalanced network in untreated asthma and ICS receiving patients, which suggested the existence of disease-specific inter-kingdom and intra-kingdom alterations. 5. Metagenomic analysis: functional pathways were associated with the status of asthma, microbiome and functional genes showed different correlations in different environment. Conclusion: We showed mycobiome and bacteriome dysbiosis in asthma featured by alterations in biodiversity, community composition, inter-kingdom and intra-kingdom network. We also observed several functional genes associated with asthma. Keywords: Mycobiome, Bacteriome, Asthma, Correlations, Metagenomics
*Correspondence: [email protected]; [email protected] † Chunrong Huang and Youchao Yu contributed equally 1 Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai 200025, People’s Republic of China 3 State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800, Dongchuan Road, Shanghai 200240, People’s Republic of China Full list of author information is available at the end of the article
Introduction Asthma is a heterogeneous disease as a result of complex interactions between genetic a
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