Evidence map›Paper›PMID 37438797›Full record

ArticleGenome medicine2023

Metagenomic assessment of gut microbial communities and risk of severe COVID-19.

Long H Nguyen, Daniel Okin, David A Drew, Vincent M Battista, Sirus J Jesudasen, Thomas M Kuntz, Amrisha Bhosle, Kelsey N Thompson, Trenton Reinicke, Chun-Han Lo and 15 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
5.5field-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

16 citing papers in PubMed, 32 citations in OpenAlex.

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  4. Microbiome-Metabolome Crosstalk as a Driver of COVID-19 Severity.Medical sciences (Basel, Switzerland) · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors at 3 institutions in 1 country.

Long H Nguyen *Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-5436-4219
Daniel Okin *Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
David A Drew *Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Vincent M BattistaDivision of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Sirus J JesudasenDepartment of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Thomas M KuntzHarvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Amrisha BhosleHarvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Kelsey N ThompsonHarvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Trenton ReinickeDivision of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Chun-Han LoDivision of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Jacqueline E WooDivision of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Alexander CaraballoDivision of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Lorenzo BerraDepartment of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Jacob VieiraDivision of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Ching-Ying HuangDivision of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Upasana Das AdhikariRagon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA.
Minsik KimDivision of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Hui-Yu SuiDivision of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Marina Magicheva-GuptaDivision of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Lauren McIverDepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Marcia B GoldbergDivision of Infectious Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Douglas S KwonRagon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA.
Curtis HuttenhowerHarvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Andrew T Chan *Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. achan@mgh.harvard.edu.
Peggy S Lai *Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. plai@mgh.harvard.edu.
Harvard University · USBroad Institute · USRagon Institute of MGH, MIT and Harvard · US

Funding

The Harvard Clinical and Translational Science CenterUL1TR002541 · NCATS · HARVARD MEDICAL SCHOOL · PI NADLER, LEE MARSHALL · 2018 to 2022
$93.0M
Research Training in Pulmonary Immunology and Allergy at MGHT32HL116275 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI David C Christiani, ANDREW D LUSTER · 2013 to 2026
$8.6M
Dietary strategies for rational manipulation of the gut microbiome in inflammatory bowel diseaseK23DK125838 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI NGUYEN, LONG H · 2020 to 2024
$1.0M
Impact of Aspirin on the Gut Microbiome and Mucosal MicroenvironmentK01DK120742 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI DREW, DAVID A · 2020 to 2024
$793k
NCATS NIH HHS UL1 TR002541NHLBI NIH HHS T32 HL116275NIDDK NIH HHS K01 DK120742NIDDK NIH HHS K23 DK125838
6 · The paper itself

Abstract

backgroundThe gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.

methodsWe profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.

resultsForty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.

conclusionsHere, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.

Indexed as

COVID-19Gastrointestinal MicrobiomeMicrobiotaHumansMetagenomePost-Acute COVID-19 SyndromeMachine learningMicrobiomeSARS-CoV-2

Identifiers

PMID37438797
PMCPMC10337137
OpenAlexW4384030780

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.