The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort/Experiment 4

From BugSigDB


Reviewed Marked as Reviewed by Fatima on 2021/10/20

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): 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
Negative for COVID-19 viral RNA in feces
Group 1 name Corresponds to the case (exposed) group for case-control studies
Positive for COVID-19 viral RNA in feces
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
COVID-19 viral RNA present in feces sample
Group 0 sample size Number of subjects in the control (unexposed) group
26
Group 1 sample size Number of subjects in the case (exposed) group
24

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
PERMANOVA
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 5c

Description: Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples

Abundance in Group 1: increased abundance in Positive for COVID-19 viral RNA in feces

NCBI Quality ControlLinks
Comamonas
Sphaerochaeta
Synergistes
Megamonas
Robinsoniella
Defluviitaleaceae
Intestinibacter
Klebsiella
Clostridium sp.
Paraprevotella
Dolosicoccus
Clostridioides
Proteus
Fusobacterium
Thomasclavelia
Holdemanella
Sellimonas
Ureaplasma
Agathobacter

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 5c

Description: Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples

Abundance in Group 1: decreased abundance in Positive for COVID-19 viral RNA in feces

NCBI Quality ControlLinks
Eremococcus
Propioniferax
Adlercreutzia
Tessaracoccus
Micrococcus
Lactococcus
Soonwooa
Merdimmobilis
Dysgonomonas
Sneathia
Dermabacter
Romboutsia
Enterobacter
Terrisporobacter
Stomatobaculum
Anaerosphaera
Brevibacterium
Cutibacterium
Pseudoclavibacter

Revision editor(s): Claregrieve1