Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/18

Curator: Victoria

Revision editor(s): Victoria

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: Surface of tongue Tongue surface,Surface of tongue,surface of tongue

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: Control group

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of 71 patients with Covid-19.

Group 0 sample size Number of subjects in the control (unexposed) group: 132

Group 1 sample size Number of subjects in the case (exposed) group: 71

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 8 weeks

Lab analysis

Sequencing type: ITS / ITS2

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

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

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/19

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 4g

Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.

Abundance in Group 1: increased abundance in Covid-19 group

NCBI	Quality Control	Links
Acrodictys
Acrodictys fluminicola
Angustimassarina
Angustimassarina camporesii
Aspergillus subflavus
Chrysosphaeria
Chrysosphaeria jannelii

Fantasmomyces hyalinus
Hydnobolites
Hydnobolites roseus
Parafuscosporella
Vanakripa mucosa
Parasympodiella
Parasympodiella longispora
Saccharomyces
Saccharomyces cerevisiae
Simplicillium
Simplicillium sympodiophorum
Tuber
Tuber alcaracense
[Cryptococcus] ater
Filobasidiaceae gen Incertae sedisFilobasidiaceae gen Incertae sedis
Candida spe Incertae sedisCandida spe Incertae sedis
Fantasmomyces

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/19

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 4g

Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.

Abundance in Group 1: decreased abundance in Covid-19 group

NCBI	Quality Control	Links
Zanclospora jonesii
Milospium graphideorum
Diversispora
Zanclospora
Diaporthe
Vanrija longa
Russula xerophila
Talaromyces
Milospium
Aspergillus amstelodami
Diversispora spurca
Cladosporium kenpeggii
Ophiostoma
Raffaelea
Arthrographis grakistii
Russula
Cryptococcus
Blumeria spe Incertae sedisBlumeria spe Incertae sedis
Blumeria
Harringtonia lauricola
Malassezia restricta
Arthrographis
Fungi gen Incertae sedisFungi gen Incertae sedis
Candida parapsilosis
Fungi spe Incertae sedisFungi spe Incertae sedis

Revision editor(s): Victoria

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/18

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Covid-19 group

Group 1 name Corresponds to the case (exposed) group for case-control studies: Post-Covid-19 group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of patients who have recovered from Covid-19.

Group 0 sample size Number of subjects in the control (unexposed) group: 71

Group 1 sample size Number of subjects in the case (exposed) group: 22

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/19

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 4g

Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.

Abundance in Group 1: increased abundance in Post-Covid-19 group

NCBI	Quality Control	Links
Actinomucor
Actinomucor elegans
Aspergillus penicillioides

Botryosphaeria
Candida
Candida albicans
Dipodascus
Galactomyces
Galactomyces pseudocandidus
Geotrichum candidum
Malassezia
Mucor
Mucor circinelloides
Mucor pseudolusitanicus
Rhodotorula
Rhodotorula mucilaginosa
Talaromyces scorteus
Udeniomyces
Udeniomyces megalosporus
Udeniomyces pyricola
Botryosphaeria spe Incertae sedisBotryosphaeria spe Incertae sedis

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/19

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 4g

Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.

Abundance in Group 1: decreased abundance in Post-Covid-19 group

NCBI	Quality Control	Links
Simplicillium sympodiophorum
Parasympodiella longispora
Chrysosphaeria
Angustimassarina camporesii
Aspergillus subflavus
Chrysosphaeria jannelii
Hydnobolites
[Cryptococcus] ater
Acrodictys
Fantasmomyces hyalinus
Saccharomyces cerevisiae
Parasympodiella
Fantasmomyces
Simplicillium
Acrodictys fluminicola
Saccharomyces
Candida spe incertae sedisCandida spe incertae sedis
Hydnobolites roseus
Filobasidiaceae gen Incertae sedisFilobasidiaceae gen Incertae sedis
Vanakripa mucosa
Tuber
Tuber alcaracense
Parafuscosporella
Entorrhiza
Angustimassarina

Revision editor(s): Victoria

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/20

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Control group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of 22 patients who have recovered from Covid-19.

Group 0 sample size Number of subjects in the control (unexposed) group: 132

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: decreased

Signature 1

Mark reviewed

Needs review

Curated date: 2024/04/24

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 4g

Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.

Abundance in Group 1: increased abundance in Post-Covid-19 group

NCBI	Quality Control	Links
Actinomucor
Actinomucor elegans
Aspergillus penicillioides

Botryosphaeria
Candida
Candida albicans
Dipodascus
Galactomyces
Galactomyces pseudocandidus
Geotrichum candidum
Malassezia
Mucor
Mucor circinelloides
Mucor pseudolusitanicus
Rhodotorula
Rhodotorula mucilaginosa
Talaromyces scorteus
Udeniomyces
Udeniomyces megalosporus
Udeniomyces pyricola
Botryosphaeria spe Incertae sedisBotryosphaeria spe Incertae sedis

Revision editor(s): Victoria

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/03

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Covid-19-N group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of 56 Covid-19 patients without comorbidities.

Group 1 sample size Number of subjects in the case (exposed) group: 56

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: increased

Signature 1

Mark reviewed

Needs review

Curated date: 2024/06/03

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: The 10 most abundant fungi among the differential fungi among the three groups at the genus and species levels.

Abundance in Group 1: increased abundance in Covid-19-N group

NCBI	Quality Control	Links
Acrodictys
Candida
Hydnobolites
Raffaelea
Harringtonia lauricola
Acrodictys fluminicola
Hydnobolites roseus
Candida albicans

Revision editor(s): Victoria

Signature 2

Mark reviewed

Needs review

Curated date: 2024/06/03

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Figure S4

Description: The 10 most abundant fungi among the differential fungi among the three groups at the genus and species levels

Abundance in Group 1: decreased abundance in Covid-19-N group

NCBI	Quality Control	Links
Zanclospora
Blumeria
Cryptococcus
Cladosporium
Malassezia
Diversispora
Zanclospora jonesii
Blumeria spe Incertae sedisBlumeria spe Incertae sedis
Vanrija longa
Malassezia restricta
Diversispora spurca
Cladosporium kenpeggii

Revision editor(s): Victoria

Experiment 5