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

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks, 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 Control	Links
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
Candidatus 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 Control	Links
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
Faecalicatena
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

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: COVID-positive patients admitted to infectious disease ward (w-COVID-19)

Group 0 sample size Number of subjects in the control (unexposed) group: 9

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 Fatima on 2022/06/1

Curated date: 2021/07/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S6, S9, S12

Description: Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19)

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

NCBI	Quality Control	Links
unclassified Burkholderiales
Nocardiaceae
unclassified Alphaproteobacteria
Pseudonocardiaceae
unclassified Erysipelotrichales
Mycobacteriaceae
unclassified Hyphomicrobiales
unclassified Erysipelotrichia
Aeromonadaceae
Rhodospirillaceae
Micrococcaceae
Brevibacteriaceae
Corynebacteriaceae
Staphylococcaceae
Microbacteriaceae
Paenibacillaceae
Arthrobacter
unclassified Micrococcaceae
Slackia
unclassified Erysipelotrichaceae
Vagococcus
Microbacterium
Paenibacillus
Micrococcus
Rhodococcus
unclassified Corynebacteriaceae
Kocuria
Streptomyces
Candidatus Phytoplasma
unclassified Flavobacteriaceae
Mycobacterium
Aeromonas
Mogibacterium
Howardella
Fonticella
Haemophilus
Ihubacter
Staphylococcus
Corynebacterium
Brevibacterium
Corynebacterium imitans
Enterococcus sp. DJF_SLA47
Slackia sp.
Fusobacterium sp.
Lactobacillus gasseri
Clostridium fusiformis
Peptoniphilus sp. S362
Corynebacterium aurimucosum
Anaerococcus provencensis
Staphylococcus aureus
Corynebacterium afermentans
Enterococcus durans
Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Corynebacterium tuscaniense
[Ruminococcus] lactaris
Prevotella sp. S4-8
Bacteroides sp. MANG
unclassified Bifidobacteriaceae (miscellaneous)
Butyrivibrio crossotus
Senegalimassilia anaerobia
unclassified Vagococcus
Gorbachella
Howardella ureilytica
Enterococcus casseliflavus
unclassified Mogibacterium
unclassified Fonticella
Clostridium sp. TM-40
unclassified Parasutterella
Staphylococcus sp.
Staphylococcus epidermidis

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/06/1

Curated date: 2021/07/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S6, S9, S12

Description: Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19)

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

NCBI	Quality Control	Links
Aerococcus
Alcanivoracaceae
Alcanivorax
Alterileibacterium massiliense
Anaerococcus degeneri
Anaerostipes hadrus
Campylobacter hominis
Carnobacteriaceae
Citrobacter
Eubacteriales Family XIII. Incertae Sedis
Collinsella
Collinsella aerofaciens
Coprobacillus
Coprobacillus cateniformis
Coprobacter
Coprobacter fastidiosus
Coriobacteriaceae
Coriobacteriia
Cronobacter
Desulfovibrio
Dialister micraerophilus
Enterocloster clostridioformis
Eubacterium ramulus
Faecalibacterium
Faecalibacterium sp.
Fenollaria
Fenollaria massiliensis
Flavonifractor
Granulicatella
Ileibacterium
Kallipyga massiliensis
Lachnospira
Lachnospira pectinoschiza
Lactococcus
Lagierella massiliensis
Metaprevotella
Metaprevotella massiliensis
Micromonosporaceae
Moritellaceae
Murdochiella
Olsenella
Parabacteroides johnsonii
Pectobacteriaceae
Phocaeicola massiliensis
Hallella colorans
Prevotella disiens
Prevotella sp. DJF_RP53
Roseburia faecis
Salmonella
Selenomonadaceae
Selenomonas
Subdoligranulum
Sutterella
Varibaculum anthropi
Vibrio
[Eubacterium] siraeum
unclassified Acidaminococcaceae
unclassified Coriobacteriaceae
unclassified Coriobacteriia
unclassified Deltaproteobacteria
unclassified Fenollaria
unclassified Peptostreptococcaceae
unclassified Phascolarctobacterium
Bacteroides sp. DJF_B097
[Lactobacillus] rogosae
Faecalibacterium prausnitzii
Prevotella bivia
Roseburia sp.
Klebsiella aerogenes
Salmonella enterica
Dorea longicatena
Anaerobutyricum hallii
Roseburia sp. 1120
Hallella bergensis
Streptococcus thermophilus
unclassified Butyricimonas
unclassified Enterobacter
unclassified Collinsella
unclassified Escherichia
Prevotella sp. S8 F8
Escherichia sp. C71
Anaerostipes sp. 992a
unclassified Hungatella
Ruminococcus sp. Marseille-P328
unclassified Ruminiclostridium
Clostridium sp. BPY5
Alistipes sp. enrichment culture clone
Pantoea agglomerans
Shigella sonnei
Marseillibacter massiliensis
Coprococcus sp.
unclassified Desulfovibrio
Moritella abyssi
Clostridium sp. enrichment culture clone 7-14
Granulicatella sp.
Blautia sp. Marseille-P2398
unclassified Anaerostipes
Oscillibacter sp. Marseille-P3260
Enterobacter cloacae

Revision editor(s): Claregrieve1

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Fatima on 2022/06/1

Curated date: 2021/07/04

Curator: Claregrieve1

Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Pneumonia controls (COVID-negative)

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-positive patients admitted to infectious disease ward (w-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 infectious disease ward

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: 9

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: unchanged

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 S1, S4, S7, S10

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

Abundance in Group 1: increased abundance in COVID-positive patients admitted to infectious disease ward (w-COVID-19)

NCBI	Quality Control	Links
Pseudomonadota
Alcanivoracaceae
unclassified Actinomycetota
unclassified Micrococcales
unclassified Deltaproteobacteria
unclassified Acidaminococcaceae
unclassified Veillonellaceae
Pectobacteriaceae
Syntrophomonadaceae
Streptomycetaceae
Selenomonadaceae
Dermabacteraceae
unclassified Sphingobacteriia
Acidithiobacillaceae
Peptostreptococcaceae
Enterobacteriaceae
unclassified Negativicutes
Aerococcaceae
Staphylococcaceae
Atopobiaceae
Vibrionaceae
Alcanivorax
Aerococcus
Sutterella
Syntrophobotulus
Coprobacillus
unclassified Peptostreptococcaceae
Olsenella
Actinomycetota
unclassified Sutterellaceae
Negativicoccus
Lactococcus
Candidatus Syntrophonatronum
Angelakisella
Acidaminococcus
Pacaella
Selenomonas
unclassified Enterococcaceae
Holdemanella
Hespellia
Acidithiobacillus
Megasphaera
Bilophila
Escherichia
unclassified Enterobacteriaceae
unclassified Streptococcaceae
Vibrio
Prevotella disiens
Hallella colorans
Dialister micraerophilus
Peptostreptococcus anaerobius
Anaerococcus octavius
Parabacteroides johnsonii
Murdochiella asaccharolytica
Alterileibacterium massiliense
Alistipes senegalensis
Peptoniphilus sp. oral taxon 375
Peptoniphilus sp. S276
Megasphaera sp. DNF00912
Bacteroides sp. DJF_B097
Coprobacillus cateniformis
Holdemanella biformis
Anaerococcus obesiensis
Kallipyga massiliensis
Megasphaera sp.
Enterococcus faecium
Atopobium sp.
Hoylesella buccalis
Streptococcus thermophilus
Facklamia hominis
Enterococcus hirae
Prevotella sp. S8 F8
Porphyromonas asaccharolytica
Escherichia sp. C71
Ruminococcus sp. Marseille-P328
Corynebacterium amycolatum
Shigella sonnei
Pantoea agglomerans
unclassified Facklamia
Syntrophobotulus glycolicus
Blautia sp. Marseille-P2398
Staphylococcus hominis
Candidatus Syntrophonatronum acetioxidans
unclassified Angelakisella
Megasphaera massiliensis
Dialister succinatiphilus
Serratia marcescens
Acidaminococcus intestini
Dialister sp. S7D
Pacaella massiliensis
Candidatus Peptoniphilus massiliensis
unclassified Sutterella
Oscillibacter sp. Marseille-P3260
Klebsiella oxytoca
Butyricimonas phoceensis
Alistipes sp. enrichment culture clone
Paraprevotella clara
Selenomonas ruminantium
Corynebacterium sp. IrT-R5M2-141
Streptococcus anginosus
unclassified Escherichia
unclassified Enterobacter
Cronobacter sakazakii
Roseburia sp.
Eubacterium coprostanoligenes
Staphylococcus sp.

Revision editor(s): Claregrieve1

Signature 2