Signatures within the esophageal microbiome are associated with host genetics, age, and disease/Experiment 22

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Curated date: 2024/09/24

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

Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease

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

Normal (Cluster 2)

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

GERD(Gastroesophageal reflux disease) (Cluster 2)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Gastroesophageal reflux disease.

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Signature 1

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Curated date: 2024/09/24

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Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)

NCBI	Quality Control	Links
Actinomycetales
Actinomycetota
Bacteria
Eubacteriales Family XIII. Incertae Sedis
Leptotrichia
Leptotrichia wadei
Leptotrichiaceae
Micrococcaceae
Prevotella denticola
Prevotella nigrescens
Rothia mucilaginosa
Segatella oris
Streptococcus salivarius
Streptococcus vestibularis
[Eubacterium] infirmum
unclassified Leptotrichia
Clostridiales Family XIII incertae sedis nonameClostridiales Family XIII incertae sedis noname
Rothia

Revision editor(s): Fiddyhamma

Signature 2

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Mark reviewed

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Needs review

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)

NCBI	Quality Control	Links
Haemophilus parahaemolyticus

Revision editor(s): Fiddyhamma