Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H, Huang X
Journal
NPJ biofilms and microbiomes
Year
2021
The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests
Group 0 sample size Number of subjects in the control (unexposed) group
44
Group 1 sample size Number of subjects in the case (exposed) group
140
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls)

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
Linear Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 2D

Description: Differential microbial abundance between healthy controls and COVID-19 patients

Abundance in Group 1: increased abundance in COVID-19 patients

NCBI Quality ControlLinks
Haemophilus parainfluenzae
Veillonella
Campylobacter
Rothia mucilaginosa
Granulicatella
Neisseria subflava
Kingella
Filifactor

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 2D

Description: Differential microbial abundance between healthy controls and COVID-19 patients

Abundance in Group 1: decreased abundance in COVID-19 patients

NCBI Quality ControlLinks
Neisseria
Corynebacterium
Actinobacillus
Moryella
Aggregatibacter
Prevotella intermedia
Treponema
Pseudomonas
Treponema amylovorum

Revision editor(s): Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
COVID-19 patients (mild/moderate)
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients (severe/critical)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests deemed to have severe/critical disease
Group 0 sample size Number of subjects in the control (unexposed) group
30
Group 1 sample size Number of subjects in the case (exposed) group
22

Lab analysis

Statistical Analysis

Alpha Diversity

Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 3

Description: Differential microbial abundance between mild/moderate and severe/critical COVID-19 patients

Abundance in Group 1: decreased abundance in COVID-19 patients (severe/critical)

NCBI Quality ControlLinks
Treponema
Aggregatibacter
Aggregatibacter segnis
Prevotella intermedia
Streptococcus anginosus
Selenomonas
Filifactor
Treponema amylovorum
Peptococcus

Revision editor(s): Claregrieve1

Experiment 3


Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients not treated with antibiotics
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics
Group 0 sample size Number of subjects in the control (unexposed) group
44
Group 1 sample size Number of subjects in the case (exposed) group
17
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls)

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 3

Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls

Abundance in Group 1: increased abundance in COVID-19 patients not treated with antibiotics

NCBI Quality ControlLinks
Neisseria subflava
Granulicatella
Veillonella
Campylobacter
Rothia mucilaginosa
Veillonella dispar
Peptoniphilus

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 3

Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls

Abundance in Group 1: decreased abundance in COVID-19 patients not treated with antibiotics

NCBI Quality ControlLinks
Moryella
Treponema
Prevotella intermedia

Revision editor(s): Claregrieve1

Experiment 4


Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests
Group 0 sample size Number of subjects in the control (unexposed) group
32
Group 1 sample size Number of subjects in the case (exposed) group
81
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls)

Lab analysis

Statistical Analysis

Alpha Diversity

Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 4

Description: Differential microbial abundance between healthy controls and COVID-19 patients

Abundance in Group 1: increased abundance in COVID-19 patients

NCBI Quality ControlLinks
Streptococcus
Weissella
Enterococcus
Enterocloster citroniae
Bifidobacterium longum
Rothia mucilaginosa
Rothia
Lactobacillus
Actinomyces
Granulicatella

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 4

Description: Differential microbial abundance between healthy controls and COVID-19 patients

Abundance in Group 1: decreased abundance in COVID-19 patients

NCBI Quality ControlLinks
Blautia
Coprococcus
Bacteroides caccae
Blautia obeum
[Clostridium] colinum
Collinsella
Phocaeicola coprophilus

Revision editor(s): Claregrieve1

Experiment 5


Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients not treated with antibiotics
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics
Group 1 sample size Number of subjects in the case (exposed) group
13
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls)

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 5

Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls

Abundance in Group 1: increased abundance in COVID-19 patients not treated with antibiotics

NCBI Quality ControlLinks
Streptococcus
Enterocloster citroniae
Anaerococcus
Streptococcus anginosus
Peptoniphilus
Campylobacter
Atopobium

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Table 5

Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls

Abundance in Group 1: decreased abundance in COVID-19 patients not treated with antibiotics

NCBI Quality ControlLinks
Blautia
Coprococcus
Bacteroides eggerthii
Phocaeicola coprophilus
Blautia obeum
Blautia producta
Anaerostipes
[Clostridium] colinum
Neisseria

Revision editor(s): Claregrieve1