Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization/Experiment 5

From BugSigDB


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

Curated date: 2021/08/02

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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
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
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
32
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

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

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


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