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

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2021/07/16

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: Non-infected patients with unrelated respiratory medical conditions

Group 1 name Corresponds to the case (exposed) group for case-control studies: SARS-CoV-2 infected patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: >age 18, positive nasopharyngeal swab for SARS-CoV-2 by PCR, COVID-19 related symptoms present, weight > 110 pounds

Group 0 sample size Number of subjects in the control (unexposed) group: 34

Group 1 sample size Number of subjects in the case (exposed) group: 50

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 2c

Description: Differential abundance of microbial genera in COVID-19 infected cases and controls

Abundance in Group 1: increased abundance in SARS-CoV-2 infected patients

NCBI	Quality Control	Links
Corynebacterium
Campylobacter
Finegoldia
Mobiluncus
Anaerococcus
Ezakiella
Porphyromonas
Prevotella
Murdochiella
Fastidiosipila
Facklamia
Gallicola
Staphylococcus
Atopobium
Christensenella
Dialister
Parasutterella
Hungatella
Intestinimonas

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 2c

Description: Differential abundance of microbial genera in COVID-19 infected cases and controls

Abundance in Group 1: decreased abundance in SARS-CoV-2 infected patients

NCBI	Quality Control	Links
Lactobacillus
Intestinibacter
Dorea
Blautia
Rothia
Faecalibacterium
Lachnospiraceae
Escherichia
Monoglobus
Subdoligranulum
Streptococcus
Veillonella
Roseburia
Fusicatenibacter
Agathobacter
Klebsiella

Revision editor(s): Claregrieve1

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

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

Statistical Analysis

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 Control	Links
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 Control	Links
Lactococcus
Anaerostipes
Merdimmobilis
Faecalibacterium
Escherichia
Intestinibacter
Catenibacterium
Klebsiella
Subdoligranulum
Granulicatella
Blautia
Agathobacter

Revision editor(s): Claregrieve1

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-infected patients with unrelated respiratory medical conditions

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

Group 0 sample size Number of subjects in the control (unexposed) group: 38

Lab analysis

Statistical Analysis

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 4c

Description: Differential abundance in microbial taxa between recovered COVID-19 patients and non-infected controls

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

NCBI	Quality Control	Links
Anaerostipes
Merdimmobilis
rumen bacterium NK4A214

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 4c

Description: Differential abundance in microbial genera between recovered COVID-19 patients and non-infected controls

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

NCBI	Quality Control	Links
Marvinbryantia
Lachnospiraceae
Candidatus Stoquefichus
Bilophila
Paraprevotella
Dialister
Sutterella
Ruminococcus

Revision editor(s): Claregrieve1

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

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

Statistical Analysis

Statistical test: PERMANOVA

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 Control	Links
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