The biogeography of the mucosa-associated microbiome in health and disease/Experiment 15
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
- Duodenum , Esophagus , Mucosa of pyloric antrum Proximal intestine,Upper intestine,Duodenum,duodenum,Gullet,Oesophagus,Esophagus,esophagus,Antral mucosa,Antrum of stomach mucosa,Antrum of stomach mucosa of organ,Antrum of stomach mucous membrane,Antrum of stomach organ mucosa,Gastric antrum mucosa,Mucosa of antrum of stomach,Mucosa of organ of antrum of stomach,Mucosa of organ of pyloric antrum,Mucosa of organ of stomach pyloric antrum,Mucosa of stomach pyloric antrum,Mucous membrane of antrum of stomach,Mucous membrane of pyloric antrum,Mucous membrane of stomach pyloric antrum,Organ mucosa of antrum of stomach,Organ mucosa of pyloric antrum,Organ mucosa of stomach pyloric antrum,Pyloric antrum mucosa,Pyloric antrum mucosa of organ,Pyloric antrum mucous membrane,Pyloric antrum organ mucosa,Stomach pyloric antrum mucosa,Stomach pyloric antrum mucosa of organ,Stomach pyloric antrum mucous membrane,Stomach pyloric antrum organ mucosa,Mucosa of pyloric antrum,mucosa of pyloric antrum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Abnormality of the gastrointestinal tract Abnormality of the gastrointestinal tract,Abnormality of the GI tract,Digestive system disease,Gastrointestinal disease,abnormality of the gastrointestinal tract
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Increased structural assessment of gastrointestinal symptom (SAGIS) scores ≥12 in the upper 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
Source: Figure 5B, Supplementary Table 5
Description: Differentially abundant bacterial taxa associated with higher structured assessment of gastrointestinal symptom (SAGIS) scores measured by relative abundance (upper gastrointestinal tract).
Abundance in Group 1: increased abundance in High structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Roseateles | ||
| Dechloromonas |
Revision editor(s): Tosin
Signature 2
Source: Figure 5B, Supplementary Table 5
Description: Differentially abundant bacterial taxa associated with higher structured assessment of gastrointestinal symptom (SAGIS) scores measured by relative abundance (upper gastrointestinal tract).
Abundance in Group 1: decreased abundance in High structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract)
| NCBI | Quality Control | Links |
|---|---|---|
| [Eubacterium] brachy | ||
| Lentimicrobium | ||
| Prevotella | ||
| Filifactor | ||
| Megasphaera | ||
| Atopobium | ||
| Alloprevotella |
Revision editor(s): Tosin
