Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/03

Curator: Claregrieve1

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

Subjects

Location of subjects: India

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: 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

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: Asymptomatic COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Asymptomatic COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with no symptoms

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

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)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Merit

Source: Figure 3a

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

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

NCBI	Quality Control	Links
Clostridiaceae
Collinsella aerofaciens
Compsobata cibaria
Eggerthella
Enterobacter
Enterocloster citroniae
Enterococcaceae
Enterococcus
Lactobacillaceae
Lactobacillus helveticus
Ovatus
Parabacteroides distasonis
Porphyromonadaceae
Ruminococcus
Shigella
Shigella dysenteriae
Weissella
Mediterraneibacter gnavus
unclassified Enterobacteriaceae
Clostridia
Clostridiales bacterium
Clostridium
Clostridium sp.
Ruminococcus sp.
unclassified Ruminococcus
Enterococcus sp.

Revision editor(s): Claregrieve1, Merit

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Fatima, Claregrieve1

Source: Figure 3a

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

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

NCBI	Quality Control	Links
Acidaminococcus
Aeromonadales
Anaerostipes
Bifidobacterium adolescentis
Campylobacter
Campylobacteraceae
Campylobacterales
Enterocloster clostridioformis
Campylobacterota
Haemophilus parainfluenzae
Lachnospira
Lactobacillaceae
Megasphaera
Mitsuokella
Mitsuokella multacida
Olsenella
Pasteurellaceae
Pasteurellales
Segatella copri
Roseburia
Roseburia faecis
Roseburia inulinivorans
Ruminococcus callidus
Succinivibrio
Succinivibrionaceae
Veillonellaceae
unclassified Lactobacillaceae
unclassified Pasteurellaceae
unclassified Veillonellaceae

Revision editor(s): Fatima, Claregrieve1

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with mild symptoms and no requirement of oxygen support/ventilator

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Merit

Source: Figure 3b

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

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

NCBI	Quality Control	Links
Acinetobacter
Acinetobacter guillouiae
Enterocloster citroniae
Enterococcaceae
Enterococcus
Lactobacillaceae
Lactobacillus helveticus
Melissococcus
Melissococcus plutonius
Micrococcaceae
Moraxellaceae
Pseudomonadales
Shigella
Shigella sonnei
Streptophyta
Weissella
unclassified Enterobacteriaceae
unclassified Streptophyta
Enterococcus sp.
Lactobacillus
Lactobacillales
Lactobacillus sp.

Revision editor(s): Claregrieve1, Merit

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): Fatima, Claregrieve1

Source: Figure 3b

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

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

NCBI	Quality Control	Links
Acidaminococcus
Aeromonadales
Anaerostipes
Campylobacterales
Clostridia
Clostridiaceae
Clostridium
Coprococcus
Coriobacteriaceae
Coriobacteriales
Dialister
Dorea
Enterobacter
Enterocloster clostridioformis
Campylobacterota
Eubacteriales
Faecalibacterium
Helicobacteraceae
Lachnospira
Lachnospira pectinoschiza
Lachnospiraceae
Megasphaera
Mitsuokella
Olsenella
Pasteurellaceae
Pasteurellales
Rikenellaceae
Roseburia
Ruminococcus
Selenomonas
Subdoligranulum
Succinivibrio
Succinivibrionaceae
Veillonellaceae
Verrucomicrobiota
unclassified Clostridia
unclassified Lactobacillaceae
unclassified Pasteurellaceae
unclassified Veillonellaceae

Revision editor(s): Fatima, Claregrieve1

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Severe COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with severe disease and requiring oxygen support/ventilator

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/11

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 3c

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

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

NCBI	Quality Control	Links
Bacteroides
Bacteroidia
Bacteroidales
Bacteroidota
Enterobacteriaceae
Enterobacterales
unclassified Enterobacteriaceae
Actinomycetota
Bifidobacteriales
Bifidobacteriaceae
Enterococcaceae
Enterococcus
Lactobacillaceae
Bacteria
Shigella
Shigella sonnei
unclassified Lactobacillales
Lactobacillus helveticus
Atopobium
Melissococcus
Enterocloster citroniae
unclassified Enterococcaceae
Shigella dysenteriae

Revision editor(s): Claregrieve1

Signature 2