Diet at birth is critical for healthy growth, independent of effects on the gut microbiota/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-10-17
Subjects
- Location of subjects
- Australia
- 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
- 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
- Postnatal growth retardation Growth delay as children,Growth retardation as children,Postnatal growth deceleration,Postnatal growth deficiency,Postnatal growth failure,Postnatal growth retardation,postnatal growth retardation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colostrum-deprived mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Newborn mice deprived of colostrum, fed with mature milk.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NA
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
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-17
Source: Figure 4D
Description: Differential abundance in colostrum-deprived mice compared to the control mice.
Abundance in Group 1: increased abundance in Colostrum-deprived mice
Revision editor(s): Princess Ben, Svetlana up
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-10-17
Source: Figure 4D
Description: Differential abundance in colostrum-deprived mice compared to the control mice.
Abundance in Group 1: decreased abundance in Colostrum-deprived mice
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalicatena fissicatena | ||
| Tyzzerella | ||
| unclassified Rhodospirillales | ||
| Lachnospiraceae UCG001Lachnospiraceae UCG001 |
Revision editor(s): Princess Ben, Svetlana up
