Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity
Objective The study objective was to compare gut microbiome diversity and composition in SARS-CoV-2 PCR-positive patients whose symptoms ranged from asymptomatic to severe versus PCR-negative exposed controls.Design Using a cross-sectional design, we performed shotgun next-generation sequencing on s...
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BMJ Publishing Group
2022-04-01
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| Series: | BMJ Open Gastroenterology |
| Online Access: | https://bmjopengastro.bmj.com/content/9/1/e000871.full |
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| author | Eamonn MM Quigley Thomas J Borody Sabine Hazan Neil Stollman Huseyin S Bozkurt Sonya Dave Andreas J Papoutsis Jordan Daniels Brad D Barrows |
| author_facet | Eamonn MM Quigley Thomas J Borody Sabine Hazan Neil Stollman Huseyin S Bozkurt Sonya Dave Andreas J Papoutsis Jordan Daniels Brad D Barrows |
| author_sort | Eamonn MM Quigley |
| collection | DOAJ |
| description | Objective The study objective was to compare gut microbiome diversity and composition in SARS-CoV-2 PCR-positive patients whose symptoms ranged from asymptomatic to severe versus PCR-negative exposed controls.Design Using a cross-sectional design, we performed shotgun next-generation sequencing on stool samples to evaluate gut microbiome composition and diversity in both patients with SARS-CoV-2 PCR-confirmed infections, which had presented to Ventura Clinical Trials for care from March 2020 through October 2021 and SARS-CoV-2 PCR-negative exposed controls. Patients were classified as being asymptomatic or having mild, moderate or severe symptoms based on National Institute of Health criteria. Exposed controls were individuals with prolonged or repeated close contact with patients with SARS-CoV-2 infection or their samples, for example, household members of patients or frontline healthcare workers. Microbiome diversity and composition were compared between patients and exposed controls at all taxonomic levels.Results Compared with controls (n=20), severely symptomatic SARS-CoV-2-infected patients (n=28) had significantly less bacterial diversity (Shannon Index, p=0.0499; Simpson Index, p=0.0581), and positive patients overall had lower relative abundances of Bifidobacterium (p<0.0001), Faecalibacterium (p=0.0077) and Roseburium (p=0.0327), while having increased Bacteroides (p=0.0075). Interestingly, there was an inverse association between disease severity and abundance of the same bacteria.Conclusion We hypothesise that low bacterial diversity and depletion of Bifidobacterium genera either before or after infection led to reduced proimmune function, thereby allowing SARS-CoV-2 infection to become symptomatic. This particular dysbiosis pattern may be a susceptibility marker for symptomatic severity from SARS-CoV-2 infection and may be amenable to preinfection, intrainfection or postinfection intervention.Trial registration number NCT04031469 (PCR−) and 04359836 (PCR+). |
| format | Article |
| id | doaj-art-4f2ed47536cd4ecdb984fbb4acdd41b6 |
| institution | Kabale University |
| issn | 2054-4774 |
| language | English |
| publishDate | 2022-04-01 |
| publisher | BMJ Publishing Group |
| record_format | Article |
| series | BMJ Open Gastroenterology |
| spelling | doaj-art-4f2ed47536cd4ecdb984fbb4acdd41b62025-02-07T16:55:09ZengBMJ Publishing GroupBMJ Open Gastroenterology2054-47742022-04-019110.1136/bmjgast-2022-000871Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severityEamonn MM Quigley0Thomas J Borody1Sabine Hazan2Neil Stollman3Huseyin S Bozkurt4Sonya Dave5Andreas J Papoutsis6Jordan Daniels7Brad D Barrows8Division of Gastroenterology and Hepatology, The Methodist Hospital, Weill Cornell Medical College, Houston, Texas, USACentre for Digestive Diseases, Sydney, New South Wales, AustraliaN/A, ProgenaBiome LLC, Ventura, California, USADivision of Gastroenterology, Alta Bates Summit Medical Center, Berkeley, California, USAClinic of Gastroenterology, Istanbul Maltepe University, Istanbul, TurkeyN/A, Microbiome Research, Inc, Ventura, California, USAN/A, ProgenaBiome LLC, Ventura, California, USAN/A, ProgenaBiome LLC, Ventura, California, USAN/A, ProgenaBiome LLC, Ventura, California, USAObjective The study objective was to compare gut microbiome diversity and composition in SARS-CoV-2 PCR-positive patients whose symptoms ranged from asymptomatic to severe versus PCR-negative exposed controls.Design Using a cross-sectional design, we performed shotgun next-generation sequencing on stool samples to evaluate gut microbiome composition and diversity in both patients with SARS-CoV-2 PCR-confirmed infections, which had presented to Ventura Clinical Trials for care from March 2020 through October 2021 and SARS-CoV-2 PCR-negative exposed controls. Patients were classified as being asymptomatic or having mild, moderate or severe symptoms based on National Institute of Health criteria. Exposed controls were individuals with prolonged or repeated close contact with patients with SARS-CoV-2 infection or their samples, for example, household members of patients or frontline healthcare workers. Microbiome diversity and composition were compared between patients and exposed controls at all taxonomic levels.Results Compared with controls (n=20), severely symptomatic SARS-CoV-2-infected patients (n=28) had significantly less bacterial diversity (Shannon Index, p=0.0499; Simpson Index, p=0.0581), and positive patients overall had lower relative abundances of Bifidobacterium (p<0.0001), Faecalibacterium (p=0.0077) and Roseburium (p=0.0327), while having increased Bacteroides (p=0.0075). Interestingly, there was an inverse association between disease severity and abundance of the same bacteria.Conclusion We hypothesise that low bacterial diversity and depletion of Bifidobacterium genera either before or after infection led to reduced proimmune function, thereby allowing SARS-CoV-2 infection to become symptomatic. This particular dysbiosis pattern may be a susceptibility marker for symptomatic severity from SARS-CoV-2 infection and may be amenable to preinfection, intrainfection or postinfection intervention.Trial registration number NCT04031469 (PCR−) and 04359836 (PCR+).https://bmjopengastro.bmj.com/content/9/1/e000871.full |
| spellingShingle | Eamonn MM Quigley Thomas J Borody Sabine Hazan Neil Stollman Huseyin S Bozkurt Sonya Dave Andreas J Papoutsis Jordan Daniels Brad D Barrows Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity BMJ Open Gastroenterology |
| title | Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity |
| title_full | Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity |
| title_fullStr | Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity |
| title_full_unstemmed | Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity |
| title_short | Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity |
| title_sort | lost microbes of covid 19 bifidobacterium faecalibacterium depletion and decreased microbiome diversity associated with sars cov 2 infection severity |
| url | https://bmjopengastro.bmj.com/content/9/1/e000871.full |
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