ArticleScientific reports2021
SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- COVID-19 alters human microbiomes: a meta-analysis.Frontiers in cellular and infection microbiology · 2023Pooled it
- Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases.Scientific reports · 2026Article
- Fecal Microbiome in Women With Fibromyalgia: Functional Composition and Symptom Correlations.ACR open rheumatology · 2025Article
- Is meningococcal B vaccination needed in the post-COVID-19 world?Biomedica : revista del Instituto Nacional de Salud · 2025Review
- Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon.Microorganisms · 2025Article
- Age- and disease severity-associated changes in the nasopharyngeal microbiota of COVID-19 patients.iScience · 2025Article
- Article
- Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies.Current microbiology · 2024Review
- The Human Nasal Microbiome: A Perspective Study During the SARS-CoV-2 Pandemic in Malta.Microorganisms · 2024Article
- The Link between Inflammation, Lipid Derivatives, and Microbiota Metabolites in COVID-19 Patients: Implications on Eating Behaviors and Nutritional Status.International journal of molecular sciences · 2024Review
- 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
- The nasopharyngeal microbiome in COVID-19.Emerging microbes & infections · 2023Article
- Proteome based analysis of circulating SARS-CoV-2 variants: approach to a universal vaccine candidate.Genes & genomics · 2023Article
- Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults.EBioMedicine · 2023Article
- Gut microbiota in colorectal cancer development and therapy.Nature reviews. Clinical oncology · 2023Review
- A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness.Cell reports methods · 2023Article
- A multicentre study reveals dysbiosis in the microbial co-infection and antimicrobial resistance gene profile in the nasopharynx of COVID-19 patients.Scientific reports · 2023Article
- Gut microbiota and COVID-19: A systematic review.Health science reports · 2023Article
- Review
- A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
21 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.
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Registered trials
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