Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19

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Reviewed Marked as Reviewed by Fatima on 2021/09/16

Curated date: 2021/05/25

Curator: Claregrieve1

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

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 cases

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs

Group 0 sample size Number of subjects in the control (unexposed) group: 78

Group 1 sample size Number of subjects in the case (exposed) group: 87

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

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

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 Fatima on 2021/09/16

Curated date: 2021/05/28

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table 2

Description: Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples

Abundance in Group 1: increased abundance in COVID-19 cases

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Phocaeicola dorei
Phocaeicola vulgatus
Mediterraneibacter gnavus
[Ruminococcus] torques
Bacteroides ovatus
Bacteroides caccae
Akkermansia muciniphila

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2021/09/16

Curated date: 2021/05/28

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table 2

Description: Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples

Abundance in Group 1: decreased abundance in COVID-19 cases

NCBI	Quality Control	Links
Bifidobacterium adolescentis
Agathobacter rectalis CAG:36
Ruminococcus bromii
Subdoligranulum
Bifidobacterium pseudocatenulatum
Faecalibacterium prausnitzii
Collinsella aerofaciens
Blautia obeum CAG:39
Dorea longicatena
Coprococcus comes
Dorea formicigenerans

Revision editor(s): Claregrieve1

Experiment 2

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/05/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs

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): Patients whose COVID-19 treatment included antibiotics were excluded

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/05/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table 3

Description: Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery

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

NCBI	Quality Control	Links
Bifidobacterium dentium
Dorea longicatena
Enterocloster bolteae
Ligilactobacillus ruminis
Parabacteroides distasonis
Parabacteroides sp.
Segatella copri
Ruminococcus sp. 5_1_39BFAA
Streptococcus salivarius
Veillonella parvula
[Clostridium] symbiosum

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/05/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table 3

Description: Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery

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

NCBI	Quality Control	Links
Alistipes putredinis
Bifidobacterium longum subsp. longum
Bifidobacterium pseudocatenulatum
Collinsella aerofaciens
Coprococcus comes
Dorea formicigenerans
Agathobacter rectalis CAG:36
Faecalibacterium prausnitzii
Ruminococcus bromii
Blautia obeum CAG:39
Subdoligranulum

Revision editor(s): Claregrieve1

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/05/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs, treated with antibiotics during course of COVID-19

Group 1 sample size Number of subjects in the case (exposed) group: 14

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Not specified

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/05/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table 3

Description: Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery

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

NCBI	Quality Control	Links
Bifidobacterium dentium
Ligilactobacillus ruminis
Parabacteroides distasonis
Enterococcus faecalis
Parabacteroides
Enterocloster bolteae
[Clostridium] symbiosum
Veillonella parvula

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/05/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table 3

Description: Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery

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

NCBI	Quality Control	Links
Agathobacter rectalis CAG:36
Ruminococcus bromii
Faecalibacterium prausnitzii
Bifidobacterium pseudocatenulatum
Subdoligranulum
Collinsella aerofaciens
Bifidobacterium longum subsp. longum
Ruminococcus sp. 5_1_39BFAA
Blautia obeum CAG:39
Segatella copri
Coprococcus comes
Dorea formicigenerans
Dorea longicatena
Alistipes putredinis
Streptococcus salivarius
Anaerobutyricum hallii

Revision editor(s): Claregrieve1

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/10

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs, treated with antibiotics

Group 1 sample size Number of subjects in the case (exposed) group: 34

Lab analysis

Statistical Analysis

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

Statistical test: Linear Regression

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/11

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S3

Description: Differential bacterial species abundance between COVID-19 samples from patients were treated with antibiotics and non-COVID-19 samples

Abundance in Group 1: decreased abundance in COVID-19 patients treated with antibiotics

NCBI	Quality Control	Links
Bifidobacterium adolescentis
Dorea formicigenerans
Dorea longicatena
Faecalibacterium prausnitzii
Blautia obeum CAG:39
Subdoligranulum sp.
Klebsiella pneumoniae
Adlercreutzia equolifaciens
Blautia obeum
[Clostridium] leptum CAG:27
Coprococcus comes
Subdoligranulum sp. 4_3_54A2FAA
Enterococcus avium
Eubacterium ventriosum
Citrobacter sp.

Revision editor(s): Claregrieve1

Signature 2