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Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases
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  • Published: 03 March 2026

Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases

  • Sanjana Fatema Chowdhury1,
  • Md. Murshed Hasan Sarkar1,
  • Syed Muktadir Al Sium1,
  • Showti Raheel Naser1,
  • Md. Saddam Hossain1,
  • Md. Ahashan Habib1,
  • Shahina Akter1,
  • Tanjina Akhtar Banu1,
  • Barna Goswami1,
  • Iffat Jahan1,
  • Tanay Chakrovarty1,2,
  • M. Maruf Ahmed Molla3,
  • Tasnim Nafisa3,
  • Mahmuda Yeasmin3,
  • Asish Kumar Ghosh3 &
  • …
  • Md. Salim Khan1 

Scientific Reports , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Computational biology and bioinformatics
  • Diseases
  • Genetics
  • Microbiology

Abstract

Coronavirus disease 2019 (COVID-19) remains a major global health concern, with emerging evidence highlighting the role of the human microbiome in influencing disease severity. While extensive research has been conducted on COVID-19, studies examining host-pathogen interactions at the transcriptomic level remain limited. In this study, we investigated the metatranscriptomic profiles of forty nasopharyngeal samples collected from COVID-19 patients across different Bangladeshi cohorts. Sequencing data were processed to analyze taxonomic composition, microbial diversity, and antimicrobial resistance gene (ARG) patterns using multiple bioinformatic pipelines. COVID-19 positive and asymptomatic patients exhibited a higher abundance of pathogenic and multidrug-resistant bacteria, whereas COVID-19 negative individuals showed increased fungal diversity. Differential gene expression analysis revealed significant upregulation of immune response related genes, including pro-inflammatory cytokines, in COVID-19 positive cases. Notably, asymptomatic patients demonstrated reduced TLR4 expression, suggesting a potential reducing of innate immune activation, which may contribute to asymptomatic clinical outcomes. Additionally, functional enrichment highlighted active ARG expression in positive cases, indicating potential links between the respiratory microbiome and host immune modulation. These findings provide insights into the host-microbiome interplay underlying COVID-19 severity and highlight the need for further validation in larger, ethnically diverse cohorts with comprehensive clinical metadata.

Data availability

All the data related to this manuscript is available in the supplement files and all the raw data is uploaded to NCBI under the accession number of PRJNA1298058. Formal permission was taken from Kanehisa laboratories to publish the result of using KEGG software, both in print and digital, under the CC BY 4.0 open access license.

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Acknowledgements

The authors would like to acknowledge National Institute of Laboratory Medicine & Referral Center (NILMRC), Dhaka, Bangladesh for the support during sample collection. The authors also acknowledge Bangladesh Council of Scientific and Industrial Research (BCSIR), Bangladesh and Ministry of Science and Technology, Bangladesh for the funding and infrastructure support.

Funding

This work has been funded by the Ministry of Science and Technology, Bangladesh.

Author information

Authors and Affiliations

  1. Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh

    Sanjana Fatema Chowdhury, Md. Murshed Hasan Sarkar, Syed Muktadir Al Sium, Showti Raheel Naser, Md. Saddam Hossain, Md. Ahashan Habib, Shahina Akter, Tanjina Akhtar Banu, Barna Goswami, Iffat Jahan, Tanay Chakrovarty & Md. Salim Khan

  2. Jashore University of Science and Technology (JUST), Jashore, Bangladesh

    Tanay Chakrovarty

  3. National Institute of Laboratory Medicine & Referral Center (NILMRC), Dhaka, Bangladesh

    M. Maruf Ahmed Molla, Tasnim Nafisa, Mahmuda Yeasmin & Asish Kumar Ghosh

Authors
  1. Sanjana Fatema Chowdhury
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Contributions

Experimental Design: Murshed Hasan Sarkar, Sanjana Fatema Chowdhury, Salim Khan Sample Collection: Md. Maruf Ahmed Molla, Tasnim Nafisa, Mahmuda Yeasmin, Asish Kumar Ghosh Library Preparation and Sequencing: Murshed Hasan Sarkar, Md. Saddam Hossain, Iffat Jahan Data Analysis and Primary Analysis: Sanjana Fatema Chowdhury, Murshed Hasan Sarkar, Syed Muktadir Al Sium, Tanay Chakrovarty Manuscript Preparation: Sanjana Fatema Chowdhury, Murshed Hasan Sarkar, Syed Muktadir Al Sium, Showti Raheel Naser Logistic Support: Md. Ahashan Habib, Shahina Akter, Tanjina Akhtar Banu, Barna Goswami.

Corresponding authors

Correspondence to Md. Murshed Hasan Sarkar or Md. Salim Khan.

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The ethical permission of the protocol for sample collection from patients, sample processing, and other consecutive laboratory work was taken from the National Institute of Laboratory Medicine and Referral Center (NILMRC) of Bangladesh.

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Chowdhury, S.F., Sarkar, M.H., Al Sium, S.M. et al. Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases. Sci Rep (2026). https://doi.org/10.1038/s41598-026-40563-x

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  • Received: 25 August 2025

  • Accepted: 13 February 2026

  • Published: 03 March 2026

  • DOI: https://doi.org/10.1038/s41598-026-40563-x

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Keywords

  • COVID-19
  • Metatranscriptomics
  • Immunological signaling
  • Differential gene expression
  • Transcriptome
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