Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing

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Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/06/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Atrayees

Subjects

Location of subjects: Italy

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: Nasopharynx , Oropharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx,Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx

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: ICU COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 patients admitted to intensive care unit

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V2-V9

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Ion Torrent

Statistical Analysis

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

Statistical test: Kruskall-Wallis

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: decreased

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/06/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S1

Description: Differential microbial abundance between healthy controls and ICU COVID-19 patients

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

NCBI	Quality Control	Links
Candidatus Saccharibacteria
Deinococcota
Aeromonadaceae
Alicyclobacillaceae
Caulobacteraceae
Chromobacteriaceae
Deinococcaceae
Helicobacteraceae
Hydrogenophilaceae
Intrasporangiaceae
Oxalobacteraceae
Rubrobacteraceae
Sporomusaceae
Thermoanaerobacteraceae
Thermoanaerobacterales Family III. Incertae Sedis
Acinetobacter
Aeromonas
Arthrobacter
Bergeyella
Bifidobacterium
Burkholderia
Butyrivibrio
Clostridium
Deinococcus
Filifactor
Gulbenkiania
Johnsonella
Microbacterium
Pasteurella
Roseateles
Ralstonia
Rubrobacter
Snodgrassella
Tepidiphilus
Thermoanaerobacter
Thermoanaerobacterium
Thermosinus
Flavobacteriaceae
Mollicutes
Neisseriales
Porphyromonadaceae
Selenomonadaceae
Tissierellia
Variovorax

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/06/30

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S1

Description: Differential microbial abundance between healthy controls and ICU COVID-19 patients

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

NCBI	Quality Control	Links
Dermabacteraceae
Erwiniaceae
Nocardiaceae
Pectobacteriaceae
Campylobacterales
Lysobacteraceae
Yersiniaceae
Enterobacter
Escherichia
Klebsiella
Lachnoclostridium
Lawsonella
Micrococcus
Olsenella
Paenibacillus
Pantoea
Rhodococcus
Salmonella
Scardovia
Serratia
Stenotrophomonas
Eubacteriales Family XIII. Incertae Sedis
Mycobacteriales
Enterococcaceae
Pseudomonadaceae
Staphylococcaceae

Revision editor(s): Claregrieve1

Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 patients with mild to moderate symptoms that were not admitted to an intensive care unit

Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S1

Description: Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases

Abundance in Group 1: decreased abundance in Mild-moderate COVID-19 patients

NCBI	Quality Control	Links
Deinococcota
Alicyclobacillaceae
Caulobacteraceae
Chromobacteriaceae
Hydrogenophilaceae
Intrasporangiaceae
Microbacteriaceae
Oxalobacteraceae
Rubrobacteraceae
Sporomusaceae
Thermoanaerobacteraceae
Thermoanaerobacterales Family III. Incertae Sedis
Burkholderiales
Arthrobacter
Bulleidia
Burkholderia
Deinococcus
Gulbenkiania
Johnsonella
Kocuria
Lactococcus
Okadaella
Roseateles
Ralstonia
Rubrobacter
Snodgrassella
Tepidiphilus
Thermoanaerobacter
Thermoanaerobacterium
Thermosinus
Burkholderiaceae
Clostridiaceae
Mycobacteriales
Enterobacteriaceae
Campylobacterota
Propionibacteriaceae
Selenomonadaceae
Variovorax

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S1

Description: Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases

Abundance in Group 1: increased abundance in Mild-moderate COVID-19 patients

NCBI	Quality Control	Links
Deinococcaceae
Methylobacteriaceae
Alphaproteobacteria
Campylobacterales
Campylobacterota
Flavobacteriales
Mycoplasmatota
Halanaerobium
Methylobacterium
Streptobacillus
Eubacteriales Family XIII. Incertae Sedis
Enterococcaceae
Eubacteriaceae
Moraxellaceae
Mycoplasmataceae
Staphylococcaceae

Revision editor(s): Claregrieve1

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Mild-Moderate COVID-19 patients

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 patients admitted to intensive care unit

Group 0 sample size Number of subjects in the control (unexposed) group: 11

Group 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S1

Description: Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients

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

NCBI	Quality Control	Links
Acinetobacter
Aeromonadaceae
Aeromonas
Bergeyella
Bifidobacterium
Bulleidia
Butyrivibrio
Candidatus Saccharibacteria
Clostridium
Filifactor
Flavobacteriales
Halanaerobiaceae
Halanaerobium
Helicobacteraceae
Methylobacterium
Mycoplasmataceae
Pasteurella
unclassified Mycoplasmataceae
unclassified Mollicutes
unclassified Moraxellaceae
unclassified Micrococcaceae
unclassified Fusobacteriales
unclassified Fusobacteriaceae
unclassified Flavobacteriaceae
unclassified Eubacteriaceae
unclassified Campylobacterota
unclassified Alphaproteobacteria
unclassified Bifidobacteriaceae (miscellaneous)
unclassified Neisseriales
unclassified Porphyromonadaceae
unclassified Mycoplasmatota
unclassified Tissierellia

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S1

Description: Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients

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

NCBI	Quality Control	Links
Enterobacter
Erwiniaceae
Escherichia
Klebsiella
Kocuria
Lachnoclostridium
Lactococcus
Lawsonella
Microbacteriaceae
Micrococcus
Nocardiaceae
Okadaella
Olsenella
Paenibacillus
Pantoea
Pectobacteriaceae
Rhodococcus
Salmonella
Scardovia
Serratia
Stenotrophomonas
Lysobacteraceae
Yersiniaceae
unclassified Corynebacteriaceae
unclassified Mycobacteriales
unclassified Enterobacteriaceae
unclassified Propionibacteriaceae
unclassified Pseudomonas
unclassified Lysobacteraceae

Revision editor(s): Claregrieve1

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Patients infected with other human coronaviruses

Group 0 sample size Number of subjects in the control (unexposed) group: 8

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/07/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Atrayees

Source: Table S1

Description: Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients

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

NCBI	Quality Control	Links
Acetobacteraceae
Acinetobacter
Actinomyces sp.
Aeromonadaceae
Aeromonas
Alcaligenaceae
Alistipes
Anaerostipes
Arsenophonus
Arthrobacter
Bergeyella
Bifidobacterium
Blastococcus
Blautia
Brevibacteriaceae
Brevibacterium
Brevundimonas
Burkholderia
Casaltella
Caulobacter
Caulobacteraceae
Cellvibrionaceae
Chitinophagaceae
Christensenellaceae
Chryseobacterium
Clostridium
Coriobacteriaceae
Cupriavidus
Demequinaceae
Desulfovibrionaceae
Dorea
Facklamia
Filifactor
Geodermatophilaceae
Holdemanella
Intrasporangiaceae
Janibacter
Massilia
Methylobacteriaceae
Methylobacterium
Microbacterium
Morganellaceae
Mycobacteriaceae
Mycobacterium
Negativicoccus
Nocardioidaceae
Nocardioides
Odoribacter
Odoribacteraceae
Oxalobacteraceae
Parabacteroides
Paracoccus
Pedobacter
Roseateles
Planococcaceae
Pseudonocardiaceae
Ralstonia
Rhizobiaceae
Rikenellaceae
Roseburia
Rubrobacter
Rubrobacteraceae
Ruminiclostridium
Ruminococcus
Saccharopolyspora
Snodgrassella
Sphingobacteriaceae
Sphingomonadaceae
Sphingomonas
Tyzzerella
Xanthomonas
unclassified Actinomycetales
unclassified Alphaproteobacteria
unclassified Bacillaceae
unclassified Burkholderiaceae
unclassified Burkholderiales
unclassified Clostridiaceae
unclassified Dermabacteraceae
unclassified Erysipelotrichaceae
unclassified Erysipelotrichales
unclassified Erysipelotrichia
unclassified Eubacteriaceae
unclassified Flavobacteriaceae
unclassified Intrasporangiaceae
unclassified Microbacteriaceae
unclassified Micrococcaceae
unclassified Neisseriales
unclassified Nocardiaceae
unclassified Paracoccaceae
unclassified Peptoniphilaceae
unclassified Ruminococcus
unclassified Sphingomonadaceae
unclassified Tissierellia
Oscillospiraceae

Revision editor(s): Claregrieve1, Atrayees

Signature 2