A history of repeated antibiotic usage leads to microbiota-dependent mucus defects/Experiment 1
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.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- hCTRL (No antibiotic use humans)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- hABX (Repeated antibiotic use humans)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Human adults who had not taken any antibiotics in the 6 months prior to stool sample collection but had used antibiotics at least 5 times within the last 5 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Control group (hCTRL) = 10 years. Repeated antibiotics use (hABX) = 6 months.
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
- Statistical test
- ANCOM
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, diet, sex, Matched on: "Bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Bristol stool scale
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-20
Source: Supplementary table 4
Description: ANCOM-BC differential analysis of gut microbial composition at genus level between hABX and hCTRL samples including those with a mean relative abundance below 1%.
Abundance in Group 1: increased abundance in hABX (Repeated antibiotic use humans)
Revision editor(s): YokoC
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-20
Source: Supplementary table 4
Description: ANCOM-BC differential analysis of gut microbial composition at genus level between hABX and hCTRL samples including those with a mean relative abundance below 1%.
Abundance in Group 1: decreased abundance in hABX (Repeated antibiotic use humans)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Escherichia | ||
| unclassified Bacillati | ||
| unclassified Clostridiaceae | ||
| unclassified Mycoplasmatota | ||
| unclassified Oscillospiraceae | ||
| unclassified Sphingomonadaceae |
Revision editor(s): YokoC
