Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Subjects
- Location of subjects
- Belgium
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Sus scrofa domesticus
- 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
- Ascariasis Ascariasis,ascariasis,Ascariasis - roundworm,ascariasis - roundworm,Ascaris lumbricoides caused disease or disorder,Ascaris lumbricoides disease or disorder,Ascaris lumbricoides infection,Ascaris lumbricoides infectious disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Uninfected piglets
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High worm burden ascaris suum infected piglets
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples from high worm burden ascariasis infected piglets
- 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
- 5
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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).
- relative abundances
- Statistical test
- Kruskall-Wallis
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Source: Table 2
Description: Differences in taxonomic units in the colon of high worm burden ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: decreased abundance in High worm burden ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovibrio | ||
| Erysipelotrichaceae | ||
| Lachnospiraceae | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Parabacteroides | ||
| Prevotella | ||
| Segatella copri |
Revision editor(s): JimFlashy, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Source: Table 2
Description: Differences in taxonomic units in the colon of high worm burden ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: increased abundance in High worm burden ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Segatella copri |
Revision editor(s): JimFlashy, Scholastica
