Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls/Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

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

Revision editor(s): WikiWorks, Atrayees, Folakunmi, MyleeeA

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
Akkermansia
Alloprevotella
Citrobacter
Escherichia/Shigella sp.
Haemophilus
Lactobacillus
Micrococcus
Pediococcus
Streptococcus
Veillonella
Weissella
Clostridium

Revision editor(s): WikiWorks, Atrayees, Folakunmi, MyleeeA

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, Folakunmi

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
Acetivibrio
Bilophila
Butyricimonas
Mitsuokella
Pseudoflavonifractor
Vampirovibrio
Victivallis
Clostridium IVClostridium IV
Clostridium XIVbClostridium XIVb

Revision editor(s): WikiWorks, Merit, Atrayees, Folakunmi