16S rRNA gene sequencing of rectal swab in patients affected by COVID-19/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Fatima on 2022/05/4

Curated date: 2021/07/04

Curator: Claregrieve1

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

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
Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
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
Pneumonia control patients (COVID-negative)
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-positive patients admitted to ICU (i-COVID-19)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
6

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).
raw counts
Statistical test
DESeq2
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
Chao1 Abundance-based estimator of species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/05/25

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S5, Table S8, Table S11

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

Abundance in Group 1: increased abundance in COVID-positive patients admitted to ICU (i-COVID-19)

NCBI Quality ControlLinks
Dermabacteraceae
unclassified Micrococcales
Nocardiaceae
unclassified Alphaproteobacteria
unclassified Actinomycetota
Pseudonocardiaceae
Streptomycetaceae
unclassified Erysipelotrichales
Mycobacteriaceae
unclassified Hyphomicrobiales
Veillonellales
unclassified Erysipelotrichia
Rhodospirillaceae
Brevibacteriaceae
Staphylococcaceae
Micrococcaceae
Erysipelotrichaceae
unclassified Burkholderiales
Microbacteriaceae
Corynebacteriaceae
Aerococcaceae
unclassified Negativicutes
Paenibacillaceae
unclassified Bacilli
Bacillaceae
unclassified Enterococcaceae
Arthrobacter
Negativicoccus
unclassified Dermabacteraceae
Vagococcus
Slackia
Micrococcales
Micrococcus
Rhodococcus
Kocuria
unclassified Flavobacteriaceae
Streptomyces
unclassified Erysipelotrichaceae
Phytoplasma
Mycobacterium
unclassified Sutterellaceae
Mogibacterium
Erysipelotrichia
Angelakisella
Howardella
Fonticella
Haemophilus
Ihubacter
Brevibacterium
Enterococcus
Corynebacterium
Facklamia
Burkholderiales
unclassified Mycobacteriales
Paenibacillus
Bacillus
Enterococcus faecium
Corynebacterium amycolatum
Anaerococcus octavius
Corynebacterium imitans
Facklamia hominis
Fusobacterium nucleatum
Enterococcus hirae
Enterococcus rivorum
Hoylesella buccalis
Candidatus Anaerococcus phoceensis
unclassified Vagococcus
Corynebacterium tuscaniense
Lactobacillus helveticus
Corynebacterium sp. IrT-R5M2-141
Peptoniphilus sp. S362
Slackia sp.
Micrococcus luteus
Anaerococcus provencensis
Corynebacterium sundsvallense
Corynebacterium afermentans
Prevotella sp. S4-8
Butyrivibrio crossotus
unclassified Angelakisella
unclassified Bifidobacteriaceae (miscellaneous)
Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Gorbachella
Hyphomicrobiales
Senegalimassilia anaerobia
Veillonella parvula
Howardella ureilytica
Enterococcus casseliflavus
Klebsiella oxytoca
unclassified Fonticella
unclassified Mogibacterium
Clostridium sp. TM-40
unclassified Parasutterella
Clostridium fusiformis
Enterococcus sp.
Corynebacterium sp.

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/05/25

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S5, S8, S11

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

Abundance in Group 1: decreased abundance in COVID-positive patients admitted to ICU (i-COVID-19)

NCBI Quality ControlLinks
Acetivibrio
Alistipes putredinis
Anaerobutyricum hallii
Anaerostipes hadrus
Anaerotruncus
Anaerotruncus colihominis
Atopobium deltae
Bacteroides clarus
Bacteroides eggerthii
Bacteroides fragilis
Bacteroides nordii
Bacteroides salyersiae
Bacteroides sp.
Bacteroides stercoris
Butyricicoccus sp.
Carnobacteriaceae
Christensenellaceae
Citrobacter
Eubacteriales Family XIII. Incertae Sedis
Clostridium sp.
Collinsella
Coprobacter
Coprobacter fastidiosus
Coriobacteriaceae
Desulfovibrio
Dorea longicatena
Eisenbergiella
Enterocloster bolteae
Enterocloster clostridioformis
Enterocloster lavalensis
Faecalibacterium
Faecalibacterium prausnitzii
Faecalibacterium sp.
Fenollaria
Fenollaria massiliensis
Flavonifractor
Flavonifractor plautii
Fusicatenibacter
Granulicatella
Halanaerobium
Leuconostoc
Mycoplasma
Mycoplasmataceae
Oribacterium
Oribacterium sp.
Oscillospira guilliermondii
Peptococcus
Phocaeicola massiliensis
Prevotella bivia
Pseudoflavonifractor
Pyramidobacter
Pyramidobacter piscolens
Robinsoniella
Salmonella
Subdoligranulum
Vibrio
Thomasclavelia spiroformis
unclassified Coriobacteriaceae
unclassified Oscillospiraceae
unclassified Coriobacteriia
Actinotignum
Metaprevotella
unclassified Rikenellaceae
Caproiciproducens
Peptoniphilus gorbachii
Prevotella sp. MC_18
Prevotella sp. DJF_RP53
Corynebacterium pyruviciproducens
Corynebacterium sp. NML96-0085
Metaprevotella massiliensis
Peptoniphilus sp. S470
Peptoniphilus sp. gpac007
Prevotella sp. BI-42
Anaerobium acetethylicum
Actinotignum schaalii
Saccharofermentans acetigenes
unclassified Hungatella
unclassified Collinsella
unclassified Butyricimonas
Clostridium sp. A9
Anaerostipes sp. 992a
Clostridium sp. enrichment culture clone 7-14
unclassified Desulfovibrio
Varibaculum cambriense
Fusicatenibacter saccharivorans
unclassified Ruminiclostridium
Clostridium sp. 14505
Intestinimonas sp. FSAA-17
unclassified Tyzzerella
Bacteroides finegoldii
unclassified Anaerostipes
Clostridium sp. BPY5
Prevotella sp. oral taxon G70
unclassified Caproiciproducens
unclassified Klebsiella

Revision editor(s): Claregrieve1