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

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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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Reviewed Marked as Reviewed by Atrayees on 2023-7-14

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Atrayees

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 ControlLinks
Alloprevotella
Lactobacillus
Streptococcus
Veillonella
Akkermansia
Escherichia
Shigella
Haemophilus
Micrococcus
Weissella
Citricoccus
Pediococcus

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-14

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Merit, Atrayees

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 ControlLinks
Bilophila
Butyricimonas
Mitsuokella
Vampirovibrio
Victivallis
Clostridium
Pseudoflavonifractor
Acetivibrio

Revision editor(s): WikiWorks, Merit, Atrayees

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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
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

Reviewed Marked as Reviewed by Atrayees on 2023-7-14

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks, Atrayees

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 ControlLinks
Lactobacillus
Veillonella
Bifidobacterium
Akkermansia
Haemophilus
Micrococcus
Weissella

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-14

Curated date: 2023/07/14

Curator: Atrayees

Revision editor(s): Atrayees

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 ControlLinks
Vampirovibrio

Revision editor(s): Atrayees

Experiment 3


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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
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

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-14

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Table 3

Description: Genera with distinct patterns and their mean abundance in predefinded groups

Abundance in Group 1: decreased abundance in hepatitis C patients

NCBI Quality ControlLinks
Flavonifractor
Megasphaera
Pseudoflavonifractor
Acetivibrio

Revision editor(s): WikiWorks