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

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
Neisseria
Corynebacterium
Actinobacillus
Moryella
Aggregatibacter
Prevotella intermedia
Treponema
Pseudomonas
Treponema amylovorum

Revision editor(s): Claregrieve1

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
Treponema
Aggregatibacter
Aggregatibacter segnis
Prevotella intermedia
Streptococcus anginosus
Selenomonas
Filifactor
Treponema amylovorum
Peptococcus

Revision editor(s): Claregrieve1

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
Moryella
Treponema
Prevotella intermedia

Revision editor(s): Claregrieve1

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
Blautia
Coprococcus
Bacteroides caccae
Blautia obeum
[Clostridium] colinum
Collinsella
Phocaeicola coprophilus

Revision editor(s): Claregrieve1

Experiment 5