The lung microbiome in moderate and severe chronic obstructive pulmonary disease/Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Subjects

Location of subjects
United States of America
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
Lung Pulmo,Lung,lung
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Chronic obstructive pulmonary disease Airflow Obstruction, Chronic,Airflow Obstructions, Chronic,CAFL - Chronic airflow limitation,CAL - Chronic airflow limitation,CAO - Chronic airflow obstruction,Chronic airflow limitation,Chronic Airflow Obstruction,Chronic Airflow Obstructions,Chronic airway disease,Chronic airway obstruction,chronic airway obstruction, NEC in ICD9CM_2006,chronic airway obstruction, not elsewhere classified,Chronic irreversible airway obstruction,CHRONIC OBSTRUCTIVE AIRWAY DIS,chronic obstructive airway disease,Chronic Obstructive Airways Disease,chronic obstructive airways disease,chronic obstructive airways disease NOS,chronic obstructive airways disease NOS (disorder),CHRONIC OBSTRUCTIVE LUNG DIS,Chronic Obstructive Lung Disease,chronic obstructive lung disease,chronic obstructive lung disease (disorder),chronic obstructive lung disease [Ambiguous],Chronic obstructive lung disease, NEC,Chronic obstructive lung disease, NOS,CHRONIC OBSTRUCTIVE PULM DIS,chronic obstructive pulmonary disease,Chronic Obstructive Pulmonary Disease (COPD),chronic obstructive pulmonary disease (COPD),chronic obstructive pulmonary disease and allied conditions,Chronic obstructive pulmonary disease finding,Chronic obstructive pulmonary disease finding (finding),Chronic obstructive pulmonary disease NOS,CHRONIC OBSTRUCTIVE PULMONARY DISEASE, (COPD),chronic obstructive pulmonary disease, (COPD),COAD,COAD - Chronic obstructive airways disease,COLD,cold,COLD (chronic obstructive lung disease),cold (chronic obstructive lung disease),COLD - Chronic obstructive lung disease,COPD,COPD - Chronic obstructive pulmonary disease,COPD NOS,COPD, CHRONIC OBSTRUCTIVE PULMONARY DISEASE,COPD, chronic obstructive pulmonary disease,DISEASE (COPD), CHRONIC OBSTRUCTIVE,disease (COPD), chronic obstructive,Dops,obstructive lung disease, chronic,OBSTRUCTIVE PULMONARY DISEASE (COPD), CHRONIC,obstructive pulmonary disease (COPD), chronic,PULM DIS CHRONIC OBSTRUCTIVE,PULMONARY DISEASE (COPD), CHRONIC OBSTRUCTIVE,pulmonary disease (COPD), chronic obstructive,Pulmonary Disease, Chronic Obstructive,Chronic obstructive pulmonary disease
Group 0 name Corresponds to the control (unexposed) group for case-control studies
controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Chronic obstructive pulmonary disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients who have Chronic obstructive pulmonary disease
Group 0 sample size Number of subjects in the control (unexposed) group
10
Group 1 sample size Number of subjects in the case (exposed) group
22
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.1
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Lwaldron, Fatima, WikiWorks

Source: Table 2

Description: Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls

Abundance in Group 1: increased abundance in Chronic obstructive pulmonary disease

NCBI Quality ControlLinks
Abiotrophia
Actinomyces
Actinomycetaceae
Aerococcaceae
Aeromonadaceae
Aeromonadales
Aeromonas
Anaerosporobacter
Atopobium
Bifidobacterium
Bulleidia
Butyrivibrio
Campylobacter
Campylobacteraceae
Campylobacterales
Capnocytophaga
Catonella
Centipeda
Coriobacteriaceae
Cryptobacterium
Desulfobacteraceae
Desulfobacterales
Desulfobulbus
Dialister
Dysgonomonas
Campylobacterota
Erysipelotrichaceae
Erysipelotrichales
Eubacteriaceae
Eubacterium
Fusobacteriota
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacterium
Hallella
Lachnospiraceae
Lactobacillales
Leptotrichia
Leptotrichiaceae
Micrococcaceae
Microvirga
Neisseriaceae
Neisseriales
Nocardioides
Olsenella
Oribacterium
Parvimonas
Peptostreptococcus
Prevotella
Rhodospirillales
Rothia
Selenomonas
Serratia
Solobacterium
Streptococcaceae
Streptococcus
Tannerella
Veillonella
Veillonellaceae
Coriobacteriales

Revision editor(s): Lwaldron, Fatima, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Table 2

Description: Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls

Abundance in Group 1: decreased abundance in Chronic obstructive pulmonary disease

NCBI Quality ControlLinks
Clostridium
Candidatus Blastococcus massiliensis
Modestobacter
Nakamurellaceae
Thermoactinomyces
Thermoactinomycetaceae
Citrobacter
Arthrobacter

Revision editor(s): WikiWorks