Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H, Pieper DH
Journal
Liver international : official journal of the International Association for the Study of the Liver
Year
2018
Keywords:
alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity
BACKGROUND & AIMS: The importance of the intestinal microbiota for the onset and clinical course of many diseases, including liver diseases like non-alcoholic steatohepatitis and cirrhosis, is increasingly recognized. However, the role of intestinal microbiota in chronic hepatitis C virus (HCV) infection remains unclear. METHODS: In a cross-sectional approach, the intestinal microbiota of 95 patients chronically infected with HCV (n=57 without cirrhosis [NO-CIR]; n=38 with cirrhosis [CIR]) and 50 healthy controls (HC) without documented liver diseases was analysed. RESULTS: Alpha diversity, measured by number of phylotypes (S) and Shannon diversity index (H'), decreased significantly from HC to NO-CIR to CIR. S and H' correlated negatively with liver elastography. Analysis of similarities revealed highly statistically significant differences in the microbial communities between HC, NO-CIR and CIR (R=.090; P<1.0×10-6 ). Stratifying for HCV genotypes even increased the differences. In addition, we observed distinct patterns in the relative abundance of genera being either positive or negative correlated with diseases status. CONCLUSIONS: This study shows that not only the stage of liver disease but also HCV infection is associated with a reduced alpha diversity and different microbial community patterns. These differences might be caused by direct interactions between HCV and the microbiota or indirect interactions facilitated by the immune system.
Experiment 1
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 |
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- no cirrhosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- heatitis C patients with cirrhosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
Lab analysis
Statistical Analysis
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
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-14
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 |
|---|---|---|
| Lactobacillus | ||
| Veillonella | ||
| Bifidobacterium | ||
| Akkermansia | ||
| Haemophilus | ||
| Micrococcus | ||
| Weissella |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-14
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 |
|---|---|---|
| Vampirovibrio |
Revision editor(s): Atrayees
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Differences from previous experiment shown
Subjects
- 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
- No cirrhosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hepatitis C patients with no 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
- 57
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-14
Source: Table 3
Description: Genera with distinct patterns and their mean abundance in predefinded groups
Abundance in Group 1: decreased abundance in No cirrhosis
| NCBI | Quality Control | Links |
|---|---|---|
| Mitsuokella | ||
| Flavonifractor | ||
| Megasphaera | ||
| Acetivibrio |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Source: Table 3
Description: Genera with distinct patterns and their differential mean abundance between healthy control and hepatitis C patients with no cirrhosis
Abundance in Group 1: increased abundance in No cirrhosis
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Lactobacillus | ||
| Streptococcus | ||
| Veillonella | ||
| Clostridium |
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