Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

28561276

DOI Digital object identifier for electronic documents.

10.1111/liv.13485

URI Uniform resource identifier for web resources.

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

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

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Curated date: 2021/01/10

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Subjects

Location of subjects: Germany

Host species Species from which microbiome was sampled (if applicable): 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

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

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: heatitis C patients without 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

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

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

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Curated date: 2020-03-25

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

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	Links
Alloprevotella
Lactobacillus
Streptococcus
Veillonella
Akkermansia
Escherichia
Shigella
Haemophilus
Micrococcus
Weissella

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Signature 2

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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	Links
Butyricimonas
Victivallis
Bilophila
k__Bacteria, p__Firmicutes, c__Clostridia, o__Clostridiales, f__Clostridiaceae, g__Clostridium IVg__Clostridium IV
k__Bacteria, p__Firmicutes, c__Clostridia, o__Clostridiales, f__Clostridiaceae, g__Clostridium XIVbg__Clostridium XIVb
Mitsuokella
Vampirovibrio

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Experiment 2

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Subjects

Location of subjects: Germany

Host species Species from which microbiome was sampled (if applicable): 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

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: no cirrhosis
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: heatitis C patients with cirrhosis
Group 0 sample size Number of subjects in the control (unexposed) group: 38
Group 1 sample size Number of subjects in the case (exposed) group: 57
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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

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

Signature 1

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Mark reviewed

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Needs review

Curated date: 2020-03-25

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

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	Links
Citrobacter
Clostridium
Pediococcus

Revision editor(s): WikiWorks743

Experiment 3

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects: Germany

Host species Species from which microbiome was sampled (if applicable): 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

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

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: hepatitis C patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: hepatitic C patients
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: 95
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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