Short-term effect of antibiotics on human gut microbiota

Abstract

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.

Figure 1. Global effect of antibiotic treatment on fecal microbiota.

Communities clustered using PCoA of the unweighted (on the left) and weighted (on the right) UniFrac distance matrix. Only the two first principal components are shown. Each dot represents the whole microbiota of a fecal sample. BF_ATB  =  Before antibiotic treatment and AF_ATB  =  After antibiotic treatment (N = 21).

Figure 2. Microbial composition at the phylum level based on 16S rRNA gene sequences.

BF  =  Before treatment; AF  =  After treatment; ATB  =  Antibiotics. For all antibiotics N = 21; for β-lactams N = 11; for fluoroquinolones N = 10.

Figure 3. Microbial load as assessed by quantitative real-time PCR (qPCR) of the 16S rRNA gene.

(A) Comparison of the microbial load between samples before (BF) and after (AF) treatment by both type of antibiotics (All_ATB). Data were compared using Wilcoxon matched-pairs test. (B) Comparison of the microbial load between before and after β-lactams treatment. Data were compared using Wilcoxon matched-pairs test. (C) Comparison of the microbial load before and after fluoroquinolone treatment. Data were compared using paired t-test. In all tests p<0.05 is considered significant. For all antibiotics N = 21; for β-lactams N = 11; for fluoroquinolones N = 10.