Evidence map›Paper›PMID 37294090›Full record

ArticlemBio2023

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

Vaibhav Upadhyay, Rahul K Suryawanshi, Preston Tasoff, Maria McCavitt-Malvido, Renuka G Kumar, Victoria Wong Murray, Cecilia Noecker, Jordan E Bisanz, Yulin Hswen, Connie W Y Ha and 6 more

Open access · goldAbstract read
In one paragraph

Article in mBio, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
26citing papers in PubMed, 1 pooled it
5.4field-weighted citation impact, top 4% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

26 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.

  1. Gut distress and interventionFrontiers in public health · 2023
    Pooled it
  2. Article
  3. Oral and plasma microbiome in the context of acute febrile illness.medRxiv : the preprint server for health sciences · 2026
    Article
  4. Review
  5. Frontiers in microbiology · 2026
    Article
  6. Review
  7. Article
  8. Microbiome and Long COVID-19: Current Evidence and Insights.International journal of molecular sciences · 2025
    Review
  9. Article
  10. Article
  11. Quantifying compositional variability in microbial communities with FAVA.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  12. Observational
  13. Review
  14. Article
  15. Article
  16. Human microbiome in post-acute COVID-19 syndrome (PACS).Current research in microbial sciences · 2025
    Article
  17. Virulence · 2024
    Review
  18. Article
  19. Quantifying compositional variability in microbial communities with FAVA.bioRxiv : the preprint server for biology · 2024
    Article
  20. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors at 2 institutions in 1 country.

Vaibhav Upadhyay *Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California , San Francisco, California, USA.ORCID 0000-0002-7652-1043
Rahul K Suryawanshi *Gladstone Institutes , San Francisco, California, USA.
Preston TasoffDepartment of Medicine, Benioff Center for Microbiome Medicine, University of California , San Francisco, California, USA.
Maria McCavitt-MalvidoGladstone Institutes , San Francisco, California, USA.
Renuka G KumarGladstone Institutes , San Francisco, California, USA.
Victoria Wong MurrayDepartment of Medicine, University of California San Francisco, University of California , San Francisco, California, USA.
Cecilia NoeckerDepartment of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California , San Francisco, California, USA.
Jordan E BisanzDepartment of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California , San Francisco, California, USA.ORCID 0000-0002-8649-1706
Yulin HswenDepartment of Epidemiology and Biostatistics and the Bakar Computational Health Institute, University of California San Francisco , San Francisco, California, USA.
Connie W Y HaDepartment of Medicine, Benioff Center for Microbiome Medicine, University of California , San Francisco, California, USA.
Bharath SreekumarGladstone Institutes , San Francisco, California, USA.
Irene P ChenGladstone Institutes , San Francisco, California, USA.
Susan V LynchDepartment of Medicine, University of California San Francisco, University of California , San Francisco, California, USA.
Melanie OttDepartment of Medicine, University of California San Francisco, University of California , San Francisco, California, USA.
Sulggi LeeDepartment of Medicine, University of California San Francisco, University of California , San Francisco, California, USA.
Peter J TurnbaughDepartment of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California , San Francisco, California, USA.ORCID 0000-0002-0888-2875
University of California, San Francisco · USGladstone Institutes · US

Funding

Predicting and preventing drug metabolism by the human gut microbiomeR01HL122593 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Peter James Turnbaugh · 2016 to 2026
$5.7M
Employing the gut microbiome to accelerate effective initiation of rheumatoid arthritis therapyR01AR074500 · NIAMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Renuka Rajendra Nayak, Jose U. Scher · 2019 to 2026
$4.1M
Host-microbiome interactions shape the metabolic effects of ketogenic dietsR01DK114034 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TURNBAUGH, PETER JAMES · 2020 to 2024
$2.5M
Establishing the feasibility of editing the human gut microbiomeR01AT011117 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TURNBAUGH, PETER JAMES · 2020 to 2023
$1.6M
Impact of gut bacterial metabolites on lung function and diseaseK08HL165106 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Vaibhav Upadhyay · 2023 to 2026
$676k
Suppression of Host Antiviral Responses by a SARS-CoV-2 Histone MimeticF31AI164671 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHEN, IRENE PO-RU · 2021 to 2022
$82k
NCCIH NIH HHS R01 AT011117NHLBI NIH HHS K08 HL165106NHLBI NIH HHS R01 HL122593NIAID NIH HHS F31 AI164671NIAMS NIH HHS R01 AR074500NIDDK NIH HHS R01 DK114034
6 · The paper itself

Abstract

Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in

Indexed as

COVID-19MicrobiotaAnimalsMammalsMiceMice, Inbred C57BLSARS-CoV-2COVID-19gastrointestinal symptomshuman gut microbiomemicrobial ecologynon-hospitalized patientsSARS-CoV-2

Identifiers

PMID37294090
PMCPMC10470529
OpenAlexW4379966260

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.