Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

study design

randomized controlled trial

Citation

PMID PubMed identifier for scientific articles.

25922405

DOI Digital object identifier for electronic documents.

10.1093/cid/civ137

URI Uniform resource identifier for web resources.

Authors

Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE, Weintraub A

Journal

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Year

2015

The purpose of the study was to assess the effect of ciprofloxacin (500 mg twice daily for 10 days) or clindamycin (150 mg 4 times daily for 10 days) on the fecal microbiota of healthy humans for a period of 1 year as compared to placebo. Two different methods, culture and microbiome analysis, were used. Fecal samples were collected for analyses at 6 time-points. The interval needed for the normal microbiota to be normalized after ciprofloxacin or clindamycin treatment differed for various bacterial species. It took 1-12 months to normalize the human microbiota after antibiotic administration, with the most pronounced effect on day 11. Exposure to ciprofloxacin or clindamycin had a strong effect on the diversity of the microbiome, and changes in microbial composition were observed until the 12th month, with the most pronounced microbial shift at month 1. No Clostridium difficile colonization or C. difficile infections were reported. Based on the pyrosequencing results, it appears that clindamycin has more impact than ciprofloxacin on the intestinal microbiota.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: Sweden

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: antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,antimicrobial agent

Group 0 name Corresponds to the control (unexposed) group for case-control studies: before ciprofloxacin exposure
Group 1 name Corresponds to the case (exposed) group for case-control studies: after ciprofloxacin exposure
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: "healthy" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were given ciprofloxacin
Group 0 sample size Number of subjects in the control (unexposed) group: 9
Group 1 sample size Number of subjects in the case (exposed) group: 9
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: V5-V7

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon)

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

Richness Number of species: decreased

Signature 1

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Curated date: 2021/01/10

Curator: Gina Celentano

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Source: Text (results)

Description: Human normal intestinal microbiota before versus after antibiotic administration

Abundance in Group 1: increased abundance in after ciprofloxacin exposure

NCBI	Links
Bacteroides

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Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Gina Celentano

Revision editor(s): Claregrieve1, WikiWorks

Source: Text (results)

Description: Human normal intestinal microbiota before versus after antibiotic administration

Abundance in Group 1: decreased abundance in after ciprofloxacin exposure

NCBI	Links
Alistipes
Faecalibacterium
unclassified Oscillospiraceae

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: Sweden

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: antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,antimicrobial agent

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Before clindamycin exposure
Group 1 name Corresponds to the case (exposed) group for case-control studies: after clindamycin exposure
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: "healthy" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were exporsed to clindamycin
Group 0 sample size Number of subjects in the control (unexposed) group: 9
Group 1 sample size Number of subjects in the case (exposed) group: 9
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon)

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