Oral lesion and microbiome diversity in COVID-19 hospitalized patients/Experiment 3

Needs review

Curated date: 2024/03/07

Curator: Nekembe

Revision editor(s): Nekembe, Aleru Divine

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: Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent

Group 0 name Corresponds to the control (unexposed) group for case-control studies: No antibiotics use

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 patients who had antibiotic therapy in the previous 3 months.

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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

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

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex, Confounders controlled for: "immunosuppression" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.immunosuppression, Confounders controlled for: "virus detection in saliva (Oral RT-PCR)" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.virus detection in saliva (Oral RT-PCR)