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The human respiratory tract, comprising the upper and lower segments, serves as a critical interface with the external environment. The upper respiratory tract (URT)—including the nostrils, sinuses, pharynx, and oropharynx—is heavily colonized by microbes, while the lower respiratory tract (LRT), composed of the larynx, trachea, bronchi, and lungs, was long thought to be sterile. However, recent molecular studies have revealed that the lungs are not devoid of microbes but act more...
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Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity,...
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Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.

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This study reveals that Moraxella catarrhalis bacteria are more abundant in children with asthma. Their presence is linked to a distinct host gene expression signature, offering new insights into asthma development.

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Area of Science:

  • Microbiology
  • Immunology
  • Genomics

Background:

  • The link between early-life infections and asthma remains unclear.
  • The role of respiratory tract microbial communities in asthma is not fully understood.
  • Previous studies noted increased gamma-Proteobacteria and Firmicutes in respiratory samples.

Purpose of the Study:

  • To introduce a novel approach combining RNA microbial identification and host gene expression.
  • To characterize and validate metagenomic taxonomic profiling in asthma patients.
  • To explore differences in microbial communities and host immune responses between asthmatic and healthy individuals.

Main Methods:

  • Whole metagenomic shotgun RNA sequencing was used to analyze microbial communities in children with asthma and controls.
  • Human and microbial reads were separated to assess microbial diversity and host gene expression.
  • Differential gene expression analysis identified host immune responses to specific pathogens.

Main Results:

  • Significant differences in nasal microbial communities were observed between asthmatic children and controls.
  • Bacterial species like Escherichia coli and Psychrobacter were overrepresented in asthma patients.
  • Moraxella catarrhalis showed a 14-fold higher abundance in asthmatics and was associated with a specific host gene expression signature.

Conclusions:

  • This study demonstrates the efficacy of combining RNA taxonomic profiling with host gene expression for microbial identification.
  • The approach validates microbial findings by correlating them with host immune responses.
  • Moraxella catarrhalis is significantly abundant in asthma patients and elicits a specific host gene expression signature.