The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Chloe on 2021/07/22

Curated date: 2021/07/21

Curator: Gina

Revision editor(s): Chloe, Gina, WikiWorks

Subjects

Location of subjects
Italy
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
Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Patients before Rifaximin treatment
Group 1 name Corresponds to the case (exposed) group for case-control studies
Patients after Rifaximin treatment
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively treated with 1,200 mg of Rifaximin daily for 10 days.
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
20
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Statistical test
metagenomeSeq
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


Signature 1

Reviewed Marked as Reviewed by Chloe on 2021/07/22

Curated date: 2021/07/21

Curator: Gina

Revision editor(s): Gina

Source: Table 2

Description: Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.

Abundance in Group 1: decreased abundance in Patients after Rifaximin treatment

NCBI Quality ControlLinks
Haemophilus
Roseburia
Veillonella

Revision editor(s): Gina

Signature 2

Reviewed Marked as Reviewed by Chloe on 2021/07/22

Curated date: 2021/07/21

Curator: Gina

Revision editor(s): Gina

Source: Table 2

Description: Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.

Abundance in Group 1: increased abundance in Patients after Rifaximin treatment

NCBI Quality ControlLinks

Revision editor(s): Gina