Gut microbiome alterations in patients with stage 4 hepatitis C

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

27625705

DOI Digital object identifier for electronic documents.

10.1186/s13099-016-0124-2

URI

Authors

Aly AM, Adel A, El-Gendy AO, Essam TM, Aziz RK

Journal

Gut pathogens

Year

2016

Keywords:

Gastro-intestinal tract, High-throughput sequencing, Infectious diseases, Liver disease, Microbiome, Next-generation sequencing, Virology

BACKGROUND: Hepatitis C virus (HCV) causes debilitating liver diseases, which may progress to cirrhosis and cancer, and claims 500,000 annual lives worldwide. While HCV epidemiology, pathophysiology, and therapy are being deeply studied, rare attention is given to reciprocal interactions between HCV infection , HCV-induced chronic liver diseases, and the human gut microbiome. As Egypt has the world's highest prevalence of HCV infections, we launched this study to monitor differences in the gut microbial community composition of Egyptian HCV patients that may affect, or result from, the patients' liver state. RESULTS: To this end, we analyzed stool samples from six stage 4-HCV patients and eight healthy individuals by high-throughput 16S rRNA gene sequencing using Illumina MiSeq. Overall, the alpha-diversity of the healthy persons' gut microbiomes was higher than those of the HCV patients. Whereas members of phylum Bacteroidetes were more abundant in HCV patients, healthy individuals had higher abundance of Firmicutes, Proteobacteria, and Actinobacteria. Genus-level analysis showed differential abundance of Prevotella and Faecalibacterium (higher in HCV patients) vs. Ruminococcus and Clostridium (healthy group), indicating that the higher abundance of Bacteroidetes in HCV patients is most likely due to Prevotella overabundance. The probiotic genus, Bifidobacterium, was only observed in the microbiotas of healthy individuals. CONCLUSIONS: To the best of our knowledge, this study provides a first overview of major phyla and genera differentiating stage 4-HCV patients from healthy individuals and suggests possible microbiome remodeling in chronic hepatitis C, possibly shaped by bacterial translocation as well as the liver's impaired role in digestion and protein synthesis. Future studies will investigate the microbiome composition and functional capabilities in more patients while tracing some potential biomarker taxa (e.g., Prevotella, Faecalibacterium vs. Bifidobacterium).

Experiment 1

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Curated date: 2021/01/10

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Subjects

Location of subjects: Egypt

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: male healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: HCV stage 4 male patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Not stated

Group 0 sample size Number of subjects in the control (unexposed) group: 8

Group 1 sample size Number of subjects in the case (exposed) group: 6

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: 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).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Chao1 Abundance-based estimator of species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Signature 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Table 2 and Fig 5

Description: Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants (non-parametric t test). All participants were male.

Abundance in Group 1: increased abundance in HCV stage 4 male patients

NCBI	Quality Control	Links
Acinetobacter
Prevotella
Veillonella
Phascolarctobacterium
Pseudomonadales
Moraxellaceae
Bacteroidales
Bacteroidia
Bacteroidota

Revision editor(s): WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

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Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Table 2 and Fig 5

Description: Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants (non-parametric t test). All participants were male.

Abundance in Group 1: decreased abundance in HCV stage 4 male patients

NCBI	Quality Control	Links
Parabacteroides
Ruminococcus
Butyricimonas
Actinomycetota
Actinomycetes
Bifidobacterium
Bifidobacteriales
Bifidobacteriaceae
Porphyromonadaceae
Mollicutes
Mycoplasmatota
Pseudoalteromonas
Pseudoalteromonadaceae
Vibrionales
Dialister
Victivallaceae
Victivallales
Lentisphaerota

Revision editor(s): WikiWorks