ArticlemBio2021
Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome.
Erratum issuedOpen access · goldAbstract read
In one paragraph
Article in mBio, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 90 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
90citing papers in PubMed, 2 pooled it
14.6field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
90 citing papers in PubMed, 2 syntheses or guidelines pooled it, 122 citations in OpenAlex.
- Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis.BMC infectious diseases · 2023Pooled it
- COVID-19 alters human microbiomes: a meta-analysis.Frontiers in cellular and infection microbiology · 2023Pooled it
- Effects of Mask Reuse on the Oropharyngeal, Skin, and Mask Microbiome.The Journal of infectious diseases · 2023Trial
- Dynamic balance of the lung microbiome in health and respiratory diseases.Chinese medical journal · 2026Review
- Lower Respiratory Microbiome Dysbiosis Is Associated With Poor Prognosis in Acute Severe Lower Respiratory Tract Infection.MedComm · 2026Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- Lung Microbiome Diversity, Infection Dynamics, and Microbe-Mediated Cross-Protection.MicrobiologyOpen · 2026Review
- The Role of the Respiratory Microbiome in Pneumonia.Clinics in chest medicine · 2026Review
- Pathogen-specific immune responses might underlie divergent outcomes of coronavirus and influenza infection in the natural porcine host.Communications biology · 2026Article
- The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.Microorganisms · 2026Review
- Oropharyngeal Microbiota Associated with Sore Throat in Acute Upper Respiratory Tract Infections.Current microbiology · 2026Article
- Structures of nucleotide-bound Redondovirus Rep protein link conformation and function.PLoS pathogens · 2026Article
- The impact of COVID-19 on the incidence of allergic diseases in the pediatric population: A retrospective cohort study from TriNetX United States collaborative network.Asia Pacific allergy · 2025Article
- The Human Respiratory Virome in Health and Disease: Interactions, Dysbiosis, and Methodological Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren's disease.Nature microbiology · 2025Article
- Lung microbiota of patients with ARDS due to coronavirus disease 2019 receiving ECMO.Scientific reports · 2025Article
- 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
- Oral microbiota and respiratory diseases: advances and perspectives.Clinical microbiology reviews · 2025Review
- Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.Microbiome · 2025Article
- Pathogenic profiles and lower respiratory tract microbiota in severe pneumonia patients using metagenomic next-generation sequencing.Advanced biotechnology · 2025Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Update of
Authors and funding
21 authors at 3 institutions in 1 country.
Carter Merenstein *Department of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Guanxiang Liang *Department of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Samantha A Whiteside *Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Ana G Cobián-GüemesDepartment of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Madeline S MerlinoDepartment of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Louis J TaylorDepartment of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Abigail GlascockDepartment of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Kyle BittingerDivision of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Ceylan TanesDivision of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Jevon Graham-WootenPulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Layla A KhatibPulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Ayannah S FitzgeraldPulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Shantan ReddyDepartment of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Amy E BaxterDepartment of Systems Pharmacology and Translational Therapeutics, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Josephine R GilesDepartment of Systems Pharmacology and Translational Therapeutics, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Derek A OldridgeInstitute for Immunology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Nuala J MeyerPulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
E John WherryDepartment of Systems Pharmacology and Translational Therapeutics, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
John E McGinnissPulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Frederic D BushmanDepartment of Microbiology, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
Ronald G CollmanPulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvaniagrid.25879.31 Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
University of Pennsylvania · USTranslational Therapeutics (United States) · USChildren's Hospital of Philadelphia · US
Funding
Virology CoreU19AI082630 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI RAYMOND T CHUNG, GEORG Michael LAUER · 2009 to 2026
$48.1MIMMUNOBIOLOGY OF NORMAL AND NEOPLASTIC LYMPHOCYTEST32CA009140 · NCI · UNIVERSITY OF PENNSYLVANIA · PI Malay Haldar, WARREN S PEAR · 1985 to 2026
$16.1MTRAINING PROGRAM IN CELL AND MOLECULAR BIOLOGYT32GM007229 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI BARTOLOMEI, MARISA S. · 1985 to 2023
$14.0MInstitutional Clinical and Translational Science AwardKL2TR001879 · NCATS · UNIVERSITY OF PENNSYLVANIA · PI MEAGHER, EMMA ANNE · 2016 to 2025
$13.7MTargeting Angiopoietin-2 in ARDSR01HL137006 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI MEYER, NUALA JENNINGS · 2017 to 2021
$2.5MThe Lung DNA Virome in Health and DiseaseR33HL137063 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI BUSHMAN, FREDERIC D, COLLMAN, RONALD G · 2019 to 2021
$2.3MReconsidering the IL-1 axis in sepsis-associated ARDSR01HL137915 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI MEYER, NUALA JENNINGS · 2017 to 2020
$2.1MCellular and transcriptional control of exhausted CD8 T cells lineage dynamicsR01AI105343 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI WHERRY, E. JOHN · 2014 to 2017
$1.6MThe Lung DNA Virome in Health and DiseaseR61HL137063 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI BUSHMAN, FREDERIC D, COLLMAN, RONALD G · 2017 to 2018
$605kMOLECULAR MECHANISMS OF FC (GAMMA) RECEPTOR COOPORATIONF32AI010534 · NIAID · UNIVERSITY OF CALIFORNIA SAN FRANCISCO · PI GREEN, JENNIFER M · 1999 to 1999
–Allen Institute for ImmunologyHHS | National Institutes of Health (NIH) AI10534HHS | National Institutes of Health (NIH) HL137063HHS | National Institutes of Health (NIH) KL2-TR001879HHS | National Institutes of Health (NIH) T32-CA009140Mark Foundation for Cancer Research InstituteNCATS NIH HHS KL2 TR001879NCI NIH HHS T32 CA009140NHLBI NIH HHS R01 HL137006NHLBI NIH HHS R01 HL137915NHLBI NIH HHS R33 HL137063NHLBI NIH HHS R61 HL137063NIAID NIH HHS F32 AI010534NIAID NIH HHS R01 AI105343NIAID NIH HHS U19 AI082630NIGMS NIH HHS T32 GM007229Parker Institute for Cancer Immunotherapy (Parker Institute)
Abstract
Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated the respiratory tract microbiome in coronavirus disease 2019 (COVID-19) and its relationship to disease severity, systemic immunologic features, and outcomes. We examined 507 oropharyngeal, nasopharyngeal, and endotracheal samples from 83 hospitalized COVID-19 patients as well as non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, and the commensal DNA viruses
Indexed as
AdultAgedAged, 80 and overAnelloviridaeBacteriaCOVID-19DysbiosisFemaleHumansLungLymphocyte CountMaleMicrobiotaMiddle AgedNasopharynxOropharynxRNA, Ribosomal, 16S16S rRNA gene sequencinganelloviruscoronavirusredondovirusrespiratory microbiomeSARS-CoV-2
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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.