Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Subjects
- Location of subjects
- Germany
- 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
- Chronic hepatitis C virus infection chronic Hepatitis C,Chronic Hepatitis C infection,chronic hepatitis C infection,chronic hepatitis C virus infection,chronic hepatitis C with hepatic coma,chronic type C viral hepatitis,chronic viral hepatitis C,hepatitis C infection, chronic,Hepatitis C, Chronic,hepatitis C, chronic,Chronic hepatitis C virus infection
- 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
- cirrhosis patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- hepatitis C patients with cirrhosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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)?
- Yes
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-14
Curated date: 2021/01/10
Curator: Fatima Zohra
Source: Table 3
Description: Genera with distinct patterns and their mean abundance in predefinded groups
Abundance in Group 1: increased abundance in cirrhosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Alloprevotella | ||
| Citrobacter | ||
| Escherichia/Shigella sp. | ||
| Haemophilus | ||
| Lactobacillus | ||
| Micrococcus | ||
| Pediococcus | ||
| Streptococcus | ||
| Veillonella | ||
| Weissella | ||
| Clostridium |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-14
Curated date: 2021/01/10
Curator: Fatima Zohra
Source: Table 3
Description: Genera with distinct patterns and their mean abundance in predefinded groups
Abundance in Group 1: decreased abundance in cirrhosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acetivibrio | ||
| Bilophila | ||
| Butyricimonas | ||
| Mitsuokella | ||
| Pseudoflavonifractor | ||
| Vampirovibrio | ||
| Victivallis | ||
| Clostridium IVClostridium IV | ||
| Clostridium XIVbClostridium XIVb |
