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

Study information

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

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

27027301

DOI Digital object identifier for electronic documents.

10.1159/000443361

URI

Authors

Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M, Gasbarrini A

Journal

Digestive diseases (Basel, Switzerland)

Year

2016

Antibiotics are mainly used in clinical practice for their activity against pathogens, but they also alter the composition of commensal gut microbial community. Rifaximin is a non-absorbable antibiotic with additional effects on the gut microbiota about which very little is known. It is still not clear to what extent rifaximin can be able to modulate gut microbiota composition and diversity in different clinical settings. Studies based on culture-dependent techniques revealed that rifaximin treatment promotes the growth of beneficial bacteria, such as Bifidobacteria and Lactobacilli. Accordingly, our metagenomic analysis carried out on patients with different gastrointestinal and liver diseases highlighted a significant increase in Lactobacilli after rifaximin treatment, persisting in the short time period. This result was independent of the disease background and was not accompanied by a significant alteration of the overall gut microbial ecology. This suggests that rifaximin can exert important eubiotic effects independently of the original disease, producing a favorable gut microbiota perturbation without changing its overall composition and diversity.

Experiment 1

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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

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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 Control	Links
Haemophilus
Roseburia
Veillonella

Revision editor(s): Gina

Signature 2

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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 Control	Links

Revision editor(s): Gina

Experiment 2

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

Curated date: 2021/07/21

Curator: Gina

Revision editor(s): Gina, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Patients 1 month after Rifaximin treatment

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients 1 month after Rifaximin treatment affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively.

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month prior to Rifaximin treatment.