ArticleNature communications2021
Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Impact of Invasive Mechanical Ventilation on the Lung Microbiome.Advances in respiratory medicine · 2025Pooled it
- Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.Nature metabolism · 2025Trial
- The Role of the Respiratory Microbiome in Pneumonia.Clinics in chest medicine · 2026Review
- Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.Cell host & microbe · 2025Article
- Lower airway microbiota compositions and diversity among ventilator-associated pneumonia patients across COVID-19 epidemic phases: a retrospective study.Microbiology spectrum · 2025Article
- Nasopharyngeal microbiome composition by SARS-CoV-2 presence and severity.Scientific reports · 2025Article
- Article
- The respiratory microbiome in patients with post-COVID-19 residual lung abnormalities resembles that of healthy individuals and is distinct from idiopathic pulmonary fibrosis.ERJ open research · 2025Article
- Mycobiome analyses of critically ill COVID-19 patients.Microbiology spectrum · 2025Article
- Assessment of upper respiratory and gut bacterial microbiomes during COVID-19 infection in adults: potential aerodigestive transmission.Scientific reports · 2025Article
- Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.Frontiers in cellular and infection microbiology · 2025Article
- Sialylation-related gene signature predict prognosis and immunotherapy efficacy in low- and high-grade glioma: a PCA-based stratification study.Frontiers in oncology · 2025Article
- Gut microbiota dysbiosis in infantile cholestatic hepatopathy.Frontiers in pediatrics · 2025Article
- Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends.Scientific reports · 2024Article
- Profiling Bacteria in the Lungs of Patients with Severe Influenza Versus COVID-19 with or without Aspergillosis.American journal of respiratory and critical care medicine · 2024Article
- Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia.Nature communications · 2024Article
- Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature.BMC infectious diseases · 2024Article
- A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models.Nature communications · 2024Article
- A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models.bioRxiv : the preprint server for biology · 2024Article
- Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.NPJ biofilms and microbiomes · 2024Article
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n = 58) and lower (n = 35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We find that time in the intensive care unit and type of oxygen support, as well as associated treatments such as antibiotic usage, explain the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load has a reduced impact. Specifically, mechanical ventilation is linked to altered community structure and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomics of the lower respiratory tract of COVID-19 patients identifies specific oral bacteria in physical association with proinflammatory immune cells, which show higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.