The biogeography of the mucosa-associated microbiome in health and disease/Experiment 12

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Reviewed Marked as Reviewed by KateRasheed on 2025-6-5

Curated date: 2025/05/03

Curator: Tosin

Revision editor(s): Tosin

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
Ileum , Right colon , Rectum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum,Proximal colon,Right colon,right colon,Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Response to proton-pump inhibitor Response to proton-pump inhibitor,response to proton-pump inhibitor
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low proton pump inhibitor (PPI) (lower gastrointestinal tract)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High proton pump inhibitor (PPI) (lower gastrointestinal tract)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Increased proton pump inhibitor in the lower gastrointestinal tract (GI)
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
V6-V8
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).
arcsine square-root
Statistical test
MaAsLin2
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

Reviewed Marked as Reviewed by KateRasheed on 2025-6-5

Curated date: 2025/05/03

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 4, supplementary Table 4

Description: Differentially abundant bacterial taxa associated with proton pump inhibitor (PPI) usage measured by relative abundance (lower gastrointestinal tract).

Abundance in Group 1: increased abundance in High proton pump inhibitor (PPI) (lower gastrointestinal tract)

NCBI Quality ControlLinks
Faecalibacterium
Collinsella
Negativibacillus
Coprobacter
Monoglobus
Eubacterium coprostanoligenes
Lachnospiraceae bacterium NK4A136
Odoribacter

Revision editor(s): Tosin

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-5

Curated date: 2025/05/03

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 4B, Supplementary Table 4

Description: Differentially abundant bacterial taxa associated with proton pump inhibitor (PPI) usage measured by relative abundance (lower gastrointestinal tract).

Abundance in Group 1: decreased abundance in High proton pump inhibitor (PPI) (lower gastrointestinal tract)

NCBI Quality ControlLinks
Bilophila
Thomasclavelia
Fusicatenibacter
Escherichia/Shigella sp.
Mediterraneibacter gnavus

Revision editor(s): Tosin