Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F, Manichanh C
Journal
PloS one
Year
2014
From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002). At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016). Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04). The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.
Experiment 1
Subjects
- Location of subjects
- Spain
- 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 antibiotic exposure
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients that took amoxiclav
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- took amoxiclav for 7 days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
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
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: increased abundance in patients that took amoxiclav
| NCBI | Links |
|---|---|
| Bacteroidia | |
| Bacteroides | |
| Bacteroidota |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: decreased abundance in patients that took amoxiclav
| NCBI | Links |
|---|---|
| Bacillota |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Location of subjects
- Spain
- 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 antibiotic exposure
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients that took levofloxacin/Metronidazole
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- took levofloxacin/Metronidazole for 7 days
- 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
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
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
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: increased abundance in patients that took levofloxacin/Metronidazole
| NCBI | Links |
|---|---|
| Bacteroides | |
| Phocaeicola plebeius |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: decreased abundance in patients that took levofloxacin/Metronidazole
| NCBI | Links |
|---|---|
| Bacillota |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Location of subjects
- Spain
- 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 antibiotic exposure
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients that took Piperacilin/Tazobactam
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- took Piperacilin/Tazobactam for 7 days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1
- Group 1 sample size Number of subjects in the case (exposed) group
- 1
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
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
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: increased abundance in patients that took Piperacilin/Tazobactam
| NCBI | Links |
|---|---|
| Bacteroides |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: decreased abundance in patients that took Piperacilin/Tazobactam
| NCBI | Links |
|---|---|
| Bacillota |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Location of subjects
- Spain
- 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 antibiotic exposure
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients that took Ceftriaxone/Azithromycin
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- took Ceftriaxone/Azithromycin for 7 days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
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
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: increased abundance in patients that took Ceftriaxone/Azithromycin
| NCBI | Links |
|---|---|
| Bacteroides | |
| Bacteroidota |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: decreased abundance in patients that took Ceftriaxone/Azithromycin
| NCBI | Links |
|---|---|
| Bacillota |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Location of subjects
- Spain
- 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 antibiotic exposure
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients that took Ciprofloxacin
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- took Ciprofloxacin for 7 days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1
- Group 1 sample size Number of subjects in the case (exposed) group
- 1
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
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
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: increased abundance in patients that took Ciprofloxacin
| NCBI | Links |
|---|---|
| Bacteroides | |
| Bacteroidota |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Text-Results
Description: Human gut microbiota before and after antibiotics exposure
Abundance in Group 1: decreased abundance in patients that took Ciprofloxacin
| NCBI | Links |
|---|---|
| Bacillota |
Revision editor(s): WikiWorks
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