ArticleGene reports2021
Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases.
Article in Gene reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- A retrospective clinical risk prediction model for co‑infection with Mycoplasma pneumoniae in patients with COVID‑19 based on restricted cubic splines.Scientific reports · 2026Article
- Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases.Scientific reports · 2026Article
- Machine learning-based classification of COVID-19 severity using respiratory microbiome profiles from shotgun metagenomic sequencing.Frontiers in bioinformatics · 2026Article
- Co-infection models ofFrontiers in cellular and infection microbiology · 2026Article
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.Scientific reports · 2025Article
- The Discovery of Phages in the Substantia Nigra and Its Implication for Parkinson's Disease.Research (Washington, D.C.) · 2025Article
- Article
- SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia.Journal of Taibah University Medical Sciences · 2024Article
- Review
- Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater.BMC microbiology · 2023Article
- Temporal dynamics and fatality of SARS-CoV-2 variants in Bangladesh.Health science reports · 2023Article
- Artificial Intelligence: A Next-Level Approach in Confronting the COVID-19 Pandemic.Healthcare (Basel, Switzerland) · 2023Review
- Explainable artificial intelligence model for identifying COVID-19 gene biomarkers.Computers in biology and medicine · 2023Article
- GCRV NS38 counteracts SVCV proliferation by intracellular antagonization during co-infection.Virologica Sinica · 2023Article
- Article
- The impact of infection with COVID-19 on the respiratory microbiome: A narrative review.Virulence · 2022Review
- Bacterial Co-Infection in Patients with COVID-19 Hospitalized (ICU and Not ICU): Review and Meta-Analysis.Antibiotics (Basel, Switzerland) · 2022Review
- HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach.Viruses · 2022Article
- Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: Insights from machine learning and bioinformatics approaches.Frontiers in immunology · 2022Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesize that microbiome diversity and composition, and their genomic features are associated with different pathological conditions of these human respiratory tract diseases. To test this hypothesis, we analyzed 21 RNASeq metagenomic data including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the microbiome diversity and related genomic metabolic functions. The metagenomic data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19 > COPD > URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively. However, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID samples, respectively, and of them 34.50% strains shared between the conditions. Functional annotation of the metagenomic data identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, virulence, disease and defense, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, we detected comparatively higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful in developing microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.
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