Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients/Experiment 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Rimsha, Claregrieve1, ChiomaBlessing, Victoria

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: Mucosa of oropharynx Mucosa of oral part of pharynx,Mucosa of organ of oral part of pharynx,Mucosa of organ of oropharynx,Mucous membrane of oral part of pharynx,Mucous membrane of oropharynx,Oral part of pharynx mucosa,Oral part of pharynx mucosa of organ,Oral part of pharynx mucous membrane,Oral part of pharynx organ mucosa,Organ mucosa of oral part of pharynx,Organ mucosa of oropharynx,Oropharynx mucosa,Oropharynx mucosa of organ,Oropharynx mucous membrane,Oropharynx organ mucosa,Mucosa of oropharynx,mucosa of oropharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Pneumonia acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: elderly pneumonia patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients >= 60 years of age with pneumonia

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V5-V7

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

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, smoking behavior, comorbidity