The biogeography of the mucosa-associated microbiome in health and disease/Experiment 12
From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-6-5
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
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 Control | Links |
---|---|---|
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
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 Control | Links |
---|---|---|
Bilophila | ||
Thomasclavelia | ||
Fusicatenibacter | ||
Escherichia/Shigella sp. | ||
Mediterraneibacter gnavus |
Revision editor(s): Tosin