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

From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-1-10
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR, Kaakoush NO
Journal
Microbiome
Year
2018
Keywords:
Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms
BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host. Here, the esophageal microbiomes of 106 prospectively recruited patients were assessed using 16S rRNA and 18S rRNA amplicon sequencing as well as shotgun sequencing, and associations with age, gender, proton pump inhibitor use, host genetics, and disease were tested. RESULTS: The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. While age was found to be a significant factor driving microbiome composition, bacterial signatures and functions such as enrichment with Gram-negative oral-associated bacteria and microbial lactic acid production were associated with the early stages of the esophageal adenocarcinoma cascade. Non-bacterial microbes such as archaea, Candida spp., and bacteriophages were also identified in low abundance in the esophageal microbiome. Specific host SNPs in NOTCH2, STEAP2-AS1, and NREP were associated with the composition of the esophageal microbiome in our cohort. CONCLUSIONS: This study provides the most comprehensive assessment of the esophageal microbiome to date and identifies novel signatures and host markers that can be investigated further in the context of esophageal adenocarcinoma development.

Experiment 1


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/11

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

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
Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cluster 1 and Cluster 3
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cluster 2
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).
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
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/16

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Source: Additional file 1, sheet 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 2

NCBI Quality ControlLinks
Bacilli
Lactobacillales
Porphyromonas
Streptococcaceae
Streptococcus
unclassified Bacillales
Bacillota

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/11

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cluster 1 and Cluster 2
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cluster 3
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.

Lab analysis

Statistical Analysis

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
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/05/16

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Source: Additional file 1, sheet 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 3

NCBI Quality ControlLinks
Actinomyces
Actinomycetaceae
Actinomycetales
Actinomycetota
Atopobium
Bacteroidales
Bacteroidia
Coriobacteriaceae
Coriobacteriales
Granulicatella
Kingella
Lachnoanaerobaculum
Lachnospiraceae
Megasphaera
Mogibacterium
Negativicutes
Prevotella
Prevotellaceae
Selenomonadales
Streptococcus
Veillonella
Veillonellaceae
unclassified Carnobacteriaceae
unclassified Lachnospiraceae
unclassified Veillonellaceae
Acidimicrobiia
Bacteroidota
unclassified Prevotellaceae

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Experiment 3


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/11

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cluster 2 and Cluster 3
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cluster 1
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.

Lab analysis

Statistical Analysis

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
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/05/16

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Source: Additional file 1, sheet 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.   

Abundance in Group 1: increased abundance in Cluster 1

NCBI Quality ControlLinks
Prevotella

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Experiment 4


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/25

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cluster 1 and Cluster 3
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cluster 2
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).

Lab analysis

Sequencing type
WMS

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
decreased

Signature 1

Needs review

Curated date: 2024/05/25

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Source: Additional file 1, sheet 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis. 

Abundance in Group 1: increased abundance in Cluster 2

NCBI Quality ControlLinks
Bacilli
Bacillota

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Experiment 5


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/25

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cluster 1 and Cluster 2
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cluster 3
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.

Lab analysis

Statistical Analysis

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
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/05/29

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Source: Additional file 1, sheet 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 3

NCBI Quality ControlLinks
Bacteroidales
Bacteroidia
Negativicutes
Prevotella histicola
Prevotella pallens
Prevotella veroralis
Selenomonadales
Veillonella
Veillonellaceae
unclassified Veillonella
Bacteroidota

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Experiment 6


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/25

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cluster 2 and Cluster 3
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cluster 1

Lab analysis

Statistical Analysis

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
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/05/29

Curator: Fiddyhamma

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Source: Additional file 1, sheet 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 1

NCBI Quality ControlLinks
Acidimicrobiia
Actinomycetales
Actinomycetota
Capnocytophaga
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Gammaproteobacteria
Haemophilus
Haemophilus parainfluenzae
Micrococcaceae
Pasteurellaceae
Pasteurellales
Pseudomonadota
Rothia mucilaginosa
unclassified Granulicatella
Rothia

Revision editor(s): WikiWorks, Victoria, Fiddyhamma, Ifeanyisam

Experiment 7


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/06/01

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Victoria, WikiWorks

Differences from previous experiment shown

Subjects

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 (Normal esophagus)
Group 1 name Corresponds to the case (exposed) group for case-control studies
GERD (Gastroesophageal reflux disease)
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.
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
29

Lab analysis

Sequencing type
16S

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/16

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Victoria, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

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

NCBI Quality ControlLinks
Acetoanaerobium
Campylobacter
Filifactor
unclassified Flavobacteriaceae

Revision editor(s): Fiddyhamma, Victoria, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/17

Curator: Victoria

Revision editor(s): Victoria, Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

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

NCBI Quality ControlLinks
Enterobacterales
Enterobacteriaceae
Escherichia/Shigella sp.
Lactobacillus

Revision editor(s): Victoria, Fiddyhamma, WikiWorks

Experiment 8


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/06/01

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

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
Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)
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(within subjects classified as PPI NO)
Group 1 sample size Number of subjects in the case (exposed) group
19

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)

NCBI Quality ControlLinks
Acetoanaerobium
Campylobacter
Cardiobacterium
Filifactor
Leptotrichia
Neisseriaceae
Neisseriales
Prevotella
Pseudomonadota incertae sedis
Rothia
Streptococcus
Veillonella
unclassified Eubacteriales
unclassified Flavobacteriaceae
unclassified Pasteurellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)

NCBI Quality ControlLinks
Centipeda
Enterobacterales
Enterobacteriaceae
Escherichia/Shigella sp.
Lactobacillus
Megasphaera
Oribacterium
Prevotella
Slackia
Streptococcus
Veillonella
unclassified Bacteroidales
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 9


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

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 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 1 sample size Number of subjects in the case (exposed) group
12

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

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

NCBI Quality ControlLinks
Capnocytophaga
Leptotrichia

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 10


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Gastroesophageal reflux disease (GERD)
Group 0 sample size Number of subjects in the control (unexposed) group
29

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

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

NCBI Quality ControlLinks
Burkholderiales
Capnocytophaga

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

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

NCBI Quality ControlLinks
Alloprevotella

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 11


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
Group 1 name Corresponds to the case (exposed) group for case-control studies
Glandular mucosa (GM)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group consists of patients with Glandular mucosa
Group 1 sample size Number of subjects in the case (exposed) group
14

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

NCBI Quality ControlLinks
Enterobacterales
Enterobacteriaceae
Prevotella
Saccharofermentans

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in Glandular mucosa (GM)

NCBI Quality ControlLinks
Acetoanaerobium
Prevotella
unclassified Prevotellaceae
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 12


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Normal
Group 0 sample size Number of subjects in the control (unexposed) group
59

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

NCBI Quality ControlLinks
Prevotella
unclassified Prevotellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in Glandular mucosa (GM)

NCBI Quality ControlLinks
unclassified Prevotellaceae
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 13


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

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 (Normal esophagus)
Group 1 name Corresponds to the case (exposed) group for case-control studies
GERD (Gastroesophageal reflux disease)
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.
Group 1 sample size Number of subjects in the case (exposed) group
29

Lab analysis

Sequencing type
WMS

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 5

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

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

NCBI Quality ControlLinks
Fusobacteriales
Fusobacteriia
Haemophilus parainfluenzae
Neisseria macacae
Neisseria meningitidis
Prevotella intermedia
Prevotella micans
Treponema medium
Fusobacteriota

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 14


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO
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(within subjects classified as PPI NO)
Group 1 sample size Number of subjects in the case (exposed) group
19

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 5

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

Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO

NCBI Quality ControlLinks
Neisseria meningitidis

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Needs review

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 5

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

Abundance in Group 1: decreased abundance in GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO

NCBI Quality ControlLinks
Megasphaera
Megasphaera micronuciformis
Prevotella pallens
unclassified Rothia (in: high G+C Gram-positive bacteria)

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 15


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

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 1 sample size Number of subjects in the case (exposed) group
12

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/08/18

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 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
Streptococcus sanguinis
Veillonella sp. oral taxon 780
unclassified Gemella

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 16


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
Group 1 name Corresponds to the case (exposed) group for case-control studies
Glandular mucosa (GM)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group consists of patients with Glandular mucosa
Group 1 sample size Number of subjects in the case (exposed) group
14

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Ifeanyisam, WikiWorks

Source: Additional file 3, sheet 5

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

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

NCBI Quality ControlLinks
Abiotrophia
Abiotrophia defectiva
Aerococcaceae
Anaeroglobus
Anaeroglobus geminatus
Betapapillomavirus
Betapapillomavirus 3
Burkholderia
Deltaproteobacteria
Desulfobacterales
Desulfobulbaceae
Desulfobulbus
Desulfobulbus sp. oral taxon 041
Eggerthia
Eggerthia catenaformis
Fusobacterium necrophorum
Gammapapillomavirus
Helicobacter
Helicobacter pylori
Helicobacteraceae
Hoylesella oralis
Neisseria cinerea
Neisseria flavescens
Papillomaviridae
Prevotella multiformis
Streptococcus australis
Streptococcus gordonii
Treponema socranskii
human papillomavirus 128
unclassified Burkholderia
virus nonamevirus noname
Bacteroidetes bacterium oral taxon 272

Revision editor(s): Fiddyhamma, Ifeanyisam, WikiWorks

Experiment 17


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
GERD(Gastroesophageal reflux disease)
Group 0 sample size Number of subjects in the control (unexposed) group
29

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Ifeanyisam, WikiWorks

Source: Additional file 3, sheet 5

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

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

NCBI Quality ControlLinks
Abiotrophia
Abiotrophia defectiva
Aerococcaceae
Aggregatibacter aphrophilus
Betapapillomavirus
Betapapillomavirus 3
Eggerthia
Eggerthia catenaformis
Fusobacterium necrophorum
Gammapapillomavirus
Helicobacter
Helicobacter pylori
Helicobacteraceae
Hoylesella oralis
Kingella
Neisseria cinerea
Papillomaviridae
Selenomonas noxia
Streptococcus gordonii
human papillomavirus 128
unclassified Kingella (in: b-proteobacteria)
virus nonamevirus noname
Bacteroidetes bacterium oral taxon 272

Revision editor(s): Fiddyhamma, Ifeanyisam, WikiWorks

Signature 2

Needs review

Curated date: 2025/01/03

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 5

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

Abundance in Group 1: decreased abundance in Glandular mucosa (GM)

NCBI Quality ControlLinks
Porphyromonas gingivalis

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 18


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

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 1)
Group 1 name Corresponds to the case (exposed) group for case-control studies
GERD(Gastroesophageal reflux disease) (Cluster 1)
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.
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified
Group 1 sample size Number of subjects in the case (exposed) group
Not specified

Lab analysis

Sequencing type
16S

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 6

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 1)

NCBI Quality ControlLinks
Streptococcus
Veillonella
unclassified Flavobacteriaceae

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Needs review

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 6

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 1)

NCBI Quality ControlLinks
Enterobacterales
Enterobacteriaceae
Lactobacillus

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 19


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

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)

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 6

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 ControlLinks
Brachymonas
Corynebacterium
Erysipelotrichaceae
Erysipelotrichales
Erysipelotrichia
Filifactor
Leptotrichiaceae
Neisseria
Oribacterium
Prevotella
Selenomonas
Solobacterium
Veillonella
unclassified Actinomycetales
unclassified Bacillota
unclassified Pasteurellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 6

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 ControlLinks
Gammaproteobacteria
Pasteurellaceae
Pasteurellales
Prevotella
unclassified Pasteurellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 20


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Normal (Cluster 3)
Group 1 name Corresponds to the case (exposed) group for case-control studies
GERD(Gastroesophageal reflux disease) (Cluster 3)

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 6

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 3)

NCBI Quality ControlLinks
Capnocytophaga
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Prevotella
unclassified Flavobacteriaceae
unclassified Pseudomonadaceae
unclassified Bacilli

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 6

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 3)

NCBI Quality ControlLinks
Peptostreptococcaceae
unclassified sequences

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 21


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Normal (Cluster 1)
Group 1 name Corresponds to the case (exposed) group for case-control studies
GERD(Gastroesophageal reflux disease) (Cluster 1)

Lab analysis

Sequencing type
WMS

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 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 1)

NCBI Quality ControlLinks
Alloprevotella tannerae
Eubacteriaceae
Eubacterium
unclassified Alloprevotella

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 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 1)

NCBI Quality ControlLinks
Alloprevotella

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 22


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

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)

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Ifeanyisam, WikiWorks

Source: Additional file 3, sheet 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 ControlLinks
Actinomycetales
Actinomycetota
Bacteria
Eubacteriales Family XIII. Incertae Sedis
Leptotrichia
Leptotrichia wadei
Leptotrichiaceae
Micrococcaceae
Prevotella denticola
Prevotella nigrescens
Rothia
Rothia mucilaginosa
Segatella oris
Streptococcus salivarius
Streptococcus vestibularis
[Eubacterium] infirmum
unclassified Leptotrichia
Clostridiales Family XIII bacterium

Revision editor(s): Fiddyhamma, Ifeanyisam, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 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 ControlLinks
Haemophilus parahaemolyticus

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 23


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Normal (Cluster 3)
Group 1 name Corresponds to the case (exposed) group for case-control studies
GERD(Gastroesophageal reflux disease) (Cluster 3)

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 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 3)

NCBI Quality ControlLinks
Bacillales
Gammaproteobacteria
Gemella
Haemophilus
Haemophilus parainfluenzae
Neisseria
Neisseria macacae
Neisseria meningitidis
Neisseriaceae
Neisseriales
Pasteurellales
Pasteuriaceae
Pseudomonadota
Treponema medium
unclassified Bacillales

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional file 3, sheet 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 3)

NCBI Quality ControlLinks
Atopobium
Bacteroidales
Bacteroidia
Coriobacteriaceae
Coriobacteriales
Lancefieldella parvula
Prevotella
Prevotellaceae

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 24


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Subjects with normal esophagus on PPI-No
Group 1 name Corresponds to the case (exposed) group for case-control studies
Subjects with normal esophagus on PPI-Yes
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group consists of patients with normal esophagus

Lab analysis

Sequencing type
16S

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional figure 3 A

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: increased abundance in Subjects with normal esophagus on PPI-Yes

NCBI Quality ControlLinks
Prevotella dentalis
Streptococcus vestibularis

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional figure 3A

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: decreased abundance in Subjects with normal esophagus on PPI-Yes

NCBI Quality ControlLinks
Peptostreptococcus
Haemophilus influenzae
Segatella salivae

Revision editor(s): Fiddyhamma, WikiWorks

Experiment 25


Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Subjects with GERD on PPI-No
Group 1 name Corresponds to the case (exposed) group for case-control studies
Subjects with GERD on PPI-Yes
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

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional figure 3B

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: increased abundance in Subjects with GERD on PPI-Yes

NCBI Quality ControlLinks
Actinomyces graevenitzii
Alloprevotella
Gemella morbillorum
Lachnospiraceae
Megasphaera
Megasphaera micronuciformis
Negativicutes
Prevotella histicola
Prevotella pallens
Segatella salivae
Selenomonadales
Stomatobaculum
Stomatobaculum longum
Streptococcus constellatus
Veillonella
Veillonellaceae
unclassified Rothia (in: high G+C Gram-positive bacteria)

Revision editor(s): Fiddyhamma, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/09/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, WikiWorks

Source: Additional figure 3B

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: decreased abundance in Subjects with GERD on PPI-Yes

NCBI Quality ControlLinks
Neisseria meningitidis

Revision editor(s): Fiddyhamma, WikiWorks