Signatures within the esophageal microbiome are associated with host genetics, age, and disease/Experiment 15

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Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Subjects

Location of subjects
Australia
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
Esophagus Gullet,Oesophagus,Esophagus,esophagus
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Barrett's esophagus (ulcerative esophagitis) or (Barrett's esophagus),adenocarcinoma of esophagus,Barrett Epithelium,Barrett Esophagus,Barrett esophagus,Barrett metaplasia,Barrett Syndrome,Barrett's esophagus,Barrett's esophagus (disorder),Barrett's esophagus (disorder) [Ambiguous],Barrett's esophagus with esophagitis,Barrett's esophagus with esophagitis (disorder),Barrett's oesophagus,Barrett's Syndrome,Barrett's ulcer of esophagus,Barrett's ulcer of esophagus (disorder),Barretts Esophagus,Barretts syndrome,BE,cello,CLE,columnar epithelial-lined Lower esophagus,columnar-lined esophagus,Epithelium, Barrett,Esophagus, Barrett,Esophagus, Barrett's,Syndrome, Barrett,Syndrome, Barrett's,ulcerative esophagitis,barrett's esophagus
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Normal
Group 1 name Corresponds to the case (exposed) group for case-control studies
Barrett’s Esophagus (BE)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group consists of patients with Barrett’s Esophagus
Group 0 sample size Number of subjects in the control (unexposed) group
59
Group 1 sample size Number of subjects in the case (exposed) group
12
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
WMS
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


Signature 1

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 3, page 5

Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).

Abundance in Group 1: increased abundance in Barrett’s Esophagus (BE)

NCBI Quality ControlLinks
unclassified Gemella
Streptococcus sanguinis
Veillonella sp. oral taxon 780

Revision editor(s): Fiddyhamma