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

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
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
Keywords:
antibiotics, culture, intestinal microbiota, pyrosequencing
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


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

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: increased abundance in after ciprofloxacin exposure

NCBI Quality ControlLinks
Bacteroides

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 Quality ControlLinks
Alistipes
Faecalibacterium
unclassified Oscillospiraceae

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

Alpha Diversity

Richness Number of species
decreased

Signature 1

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 clindamycin exposure

NCBI Quality ControlLinks
Coprococcus
Dorea
Eubacteriales
Lachnospira
Lachnospiraceae
Roseburia
Ruminococcus

Revision editor(s): Claregrieve1, WikiWorks