Short-term effect of antibiotics on human gut microbiota

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    • Uncontrolled confounding suspected
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study design
time series / longitudinal observational
Citation
PMID PubMed identifier for scientific articles.
24748167
DOI Digital object identifier for electronic documents.
10.1371/journal.pone.0095476
URI
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


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Subjects

Location of subjects
Spain
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
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

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Curated date: 2021/01/10

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Source: Text-Results

Description: Human gut microbiota before and after antibiotics exposure

Abundance in Group 1: increased abundance in patients that took amoxiclav

NCBI Quality ControlLinks
Bacteroidia   
Bacteroides   
Bacteroidota   

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Signature 2

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Source: Text-Results

Description: Human gut microbiota before and after antibiotics exposure

Abundance in Group 1: decreased abundance in patients that took amoxiclav

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): WikiWorks

Experiment 2


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Differences from previous experiment shown

Subjects

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

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
decreased

Signature 1

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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 Quality ControlLinks
Bacteroides   
Phocaeicola plebeius   

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Signature 2

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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 Quality ControlLinks
Bacillota   

Revision editor(s): WikiWorks

Experiment 3


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Differences from previous experiment shown

Subjects

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

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
decreased

Signature 1

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Your review change was submitted
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Curated date: 2021/01/10

Curator: Gina Celentano

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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 Quality ControlLinks
Bacteroides   

Revision editor(s): WikiWorks

Signature 2

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Curated date: 2021/01/10

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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 Quality ControlLinks
Bacillota   

Revision editor(s): WikiWorks

Experiment 4


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Differences from previous experiment shown

Subjects

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

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
decreased

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
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Curated date: 2021/01/10

Curator: Gina Celentano

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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 Quality ControlLinks
Bacteroides   
Bacteroidota   

Revision editor(s): WikiWorks

Signature 2

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Mark reviewed
Your review change was submitted
Needs review

Curated date: 2021/01/10

Curator: Gina Celentano

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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 Quality ControlLinks
Bacillota   

Revision editor(s): WikiWorks

Experiment 5


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Differences from previous experiment shown

Subjects

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

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
decreased

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2021/01/10

Curator: Gina Celentano

Revision editor(s): WikiWorks

Source: Text-Results

Description: Human gut microbiota before and after antibiotics exposure

Abundance in Group 1: increased abundance in patients that took Ciprofloxacin

NCBI Quality ControlLinks
Bacteroides   
Bacteroidota   

Revision editor(s): WikiWorks

Signature 2

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2021/01/10

Curator: Gina Celentano

Revision editor(s): WikiWorks

Source: Text-Results

Description: Human gut microbiota before and after antibiotics exposure

Abundance in Group 1: decreased abundance in patients that took Ciprofloxacin

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): WikiWorks

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