Role of dietary fiber in the recovery of the human gut microbiome and its metabolome/Experiment 1
Curated date: 2021/11/11
Curator: Lorakasselman
Revision editor(s): WikiWorks, Chloe, Lorakasselman, Atrayees, Victoria
Subjects
- Location of subjects
- United States of America
- 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
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- regular fiber omnivore diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- no fiber liquid omnivore diet
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- 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).
- raw counts
- Statistical test
- Linear Regression
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 2B
Description: The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong
Abundance in Group 1: increased abundance in no fiber liquid omnivore diet
| NCBI | Quality Control | Links |
|---|---|---|
| Mediterraneibacter gnavus | ||
| [Ruminococcus] torques |
Revision editor(s): Chloe, Lorakasselman
Signature 2
Source: Figure 2B
Description: The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong.
Abundance in Group 1: decreased abundance in no fiber liquid omnivore diet
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides ovatus | ||
| Faecalibacterium prausnitzii | ||
| Parabacteroides merdae | ||
| Segatella copri | ||
| Streptococcus thermophilus | ||
| Agathobacter rectalis |
Revision editor(s): Chloe, Lorakasselman
