Short-term effect of antibiotics on human gut microbiota

Study information

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-20

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

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

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,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: 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

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months

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: Roche454, RT-qPCR

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: ANOVA

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

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18

Curated date: 2021/01/10

Curator: Gina Celentano

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results within text- Page 3, 2nd paragraph under sub-heading "Effect of B-lactams"

Description: Microbial taxa affected by amoxiclav, before and after exposure

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

NCBI	Quality Control	Links
Bacteroidales
Bacteroides
Bacteroidota

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18

Curated date: 2021/01/10

Curator: Gina Celentano

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results within text- Page 3, 2nd paragraph under sub-heading "Effect of B-lactams"

Description: Microbial taxa affected by amoxiclav, before and after exposure

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

NCBI	Quality Control	Links
Bacillota

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-19

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: patients that took levofloxacin

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: took levofloxacin for 7 days