Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-4-8
Subjects
- Location of subjects
- Canada
- 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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 3 months
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 12 months
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infants when they are 12 months of age
- Group 0 sample size Number of subjects in the control (unexposed) group
- 99
- Group 1 sample size Number of subjects in the case (exposed) group
- 99
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- exposure prior to 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-4-8
Source: Fig 3C
Description: Comparison of bacterial growth at 3 and 12 months
Abundance in Group 1: increased abundance in 12 months
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Bacteroides caccae | ||
| Bacteroides uniformis | ||
| Segatella copri | ||
| unclassified Rikenellaceae |
Revision editor(s): Tayk26, Svetlana up
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-4-8
Source: Fig 3C
Description: Comparison of bacterial growth at 3 and 12 months
Abundance in Group 1: decreased abundance in 12 months
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides ovatus | ||
| unclassified Bacteroides |
Revision editor(s): Tayk26, Svetlana up
