The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model/Experiment 1
From BugSigDB
Needs review Marked as Needs review by Svetlana up on 2024-3-11
Subjects
- Location of subjects
- Republic of Korea
- 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
- Cachexia Wasting syndrome,Cachexia,cachexia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cachexia-induced mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All mice that were induced with cancer cachexia (Lewis lung cancer cells).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
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).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16
Source: Fig 3
Description: Differential abundance analysis of gut microbiota by DESeq2. (B) Microbes of significantly different abundance in genus level by DESeq2 analysis between groups expressed in log2 fold change.
Abundance in Group 1: increased abundance in cachexia-induced mice
| NCBI | Quality Control | Links |
|---|---|---|
| rumen bacterium NK4A214 | ||
| Marvinbryantia | ||
| Erysipelotrichaceae | ||
| Candidatus Arthromitus | ||
| Streptococcus | ||
| Clostridium | ||
| Raoultibacter |
Revision editor(s): Grace og, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-16
Source: Fig 3
Description: Differential abundance analysis of gut microbiota by DESeq2. (B) Microbes of significantly different abundance in genus level by DESeq2 analysis between groups expressed in log2 fold change.
Abundance in Group 1: decreased abundance in cachexia-induced mice
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia | ||
| Lactococcus | ||
| Turicibacter | ||
| Bifidobacterium | ||
| Ruminococcus | ||
| Colidextribacter |
Revision editor(s): Grace og, Hodan Issah, Peace Sandy
