Oral lesion and microbiome diversity in COVID-19 hospitalized patients/Experiment 6

From BugSigDB


Needs review

Curated date: 2024/03/29

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Subjects

Location of subjects
Brazil
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
Diet Dietary,Diets,Diet,diet
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non enteral diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Covid-19 patients on enteral diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
COVID-19 patients who were on the enteral diet.

Lab analysis

Sequencing type
16S
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

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
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)


Signature 1

Needs review

Curated date: 2024/03/29

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section

Description: Significant differences found in Covid-10 patients who were on enteral diet.

Abundance in Group 1: increased abundance in Covid-19 patients on enteral diet

NCBI Quality ControlLinks
Cardiobacterium
Granulicatella
Haemophilus
Lactobacillus
Leptotrichia
Porphyromonas
Rothia
Streptococcus
Veillonella

Revision editor(s): Aleru Divine