Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing/Experiment 1

From BugSigDB


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 ControlLinks
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 ControlLinks
Dermabacteraceae
Erwiniaceae
Nocardiaceae
Pectobacteriaceae
Campylobacterales
Xanthomonadaceae
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