The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Lwaldron on 2021/06/30

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks

Subjects

Location of subjects
United States of America
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
SARS-CoV-2 infected patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
SARS-CoV-2 recovered individuals
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
>age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2
Group 0 sample size Number of subjects in the control (unexposed) group
50
Group 1 sample size Number of subjects in the case (exposed) group
9

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
edgeR
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2021/06/30

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 3c

Description: Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples

Abundance in Group 1: decreased abundance in SARS-CoV-2 recovered individuals

NCBI Quality ControlLinks
Campylobacter
Corynebacterium
Mobiluncus
Fenollaria
Ezakiella
Murdochiella
Fastidiosipila
Facklamia
Staphylococcus
Gallicola
Lawsonella
Finegoldia
Sutterella
Peptoniphilus
Porphyromonas
Atopobium
Pseudoclavibacter
Cloacibacillus
Sellimonas
Turicibacter
Helcococcus
Anaerococcus
Dermabacter
Desulfovibrio

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2021/06/30

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 3c

Description: Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples

Abundance in Group 1: increased abundance in SARS-CoV-2 recovered individuals

NCBI Quality ControlLinks
Lactococcus
Anaerostipes
Merdimmobilis
Faecalibacterium
Escherichia
Intestinibacter
Catenibacterium
Klebsiella
Subdoligranulum
Granulicatella
Blautia
Agathobacter

Revision editor(s): Claregrieve1