A history of repeated antibiotic usage leads to microbiota-dependent mucus defects/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-12-20
Subjects
- Location of subjects
- Estonia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT-C (control transplant mice)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT- ABX (antibiotic transplant mice)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal microbiota transplant (FMT) from the hABX (humans with a history of repeated antibiotic used) pool.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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).
- centered log-ratio
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of 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 2024-12-20
Source: Figure 4e
Description: Boxplots of significant differentially abundant species (using ALDEX) in the distal colon of mouse microbiota between FMT-C and FMT-ABX, with at least a 0.1% mean relative abundance in either group.
Abundance in Group 1: increased abundance in FMT- ABX (antibiotic transplant mice)
Revision editor(s): YokoC
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-20
Source: Figure 4e
Description: Boxplots of significant differentially abundant species (using ALDEX) in the distal colon of mouse microbiota between FMT-C and FMT-ABX, with at least a 0.1% mean relative abundance in either group.
Abundance in Group 1: decreased abundance in FMT- ABX (antibiotic transplant mice)
Revision editor(s): YokoC
