Antibiotic administration alters the community structure of the gastrointestinal micobiota

Abstract

We recently demonstrated that antibiotic administration has a reproducible effect on the community structure of the indigenous gastrointestinal microbiota of mice. In this addendum we report on additional experimentation using the antibiotic vancomycin. In accord with our previous findings, vancomycin administration results in consistent alteration of the microbiota of the cecal contents and the cecal mucosa. These alterations are largely reversed by a three-week period of recovery without antibiotics. In contrast to our previous results using other antibiotics, the alterations in community structure associated with vancomycin occured without a significant decrease in the overall bacterial biomass. These results indicate that different antibiotics have specific effects on the gut microbiota. This points the way towards targeted, therapeutic alteration of the gut bacterial community as a whole.

Figure 1

Reduction of richness in gut microbiota following vancomycin administration. Partial 16S rRNA-encoding gene sequences were obtained from the cecal mucosa (A) and cecal contents (B) from individual mice treated with 10 days of vancomycin (Vancomycin,V), animals that received 10 days of vancomycin followed by a three-week recovery period without antibiotic (Recovered, R) and animals that received no antibiotics (Control, C). Rarefaction curves were generated using mothur and OTUs were defined at the 0.03 cutoff (97% similarity).

Figure 2

Vancomycin alters community structure and recovery results in a return to near-baseline structure. UPGMA clustering of communities from the cecal mucosa (A) and cecal contents (B) from individual mice treated vancomycin (Vancomycin), vancomycin followed by a three-week recovery period without antibiotic (Recovered) and animals that received no antibiotics (Control). Dendrogram was generated using distances reflecting community structure dissimilarity (1-similarity). Community structure similarity was calculated in mothur using the Yue and Clayton (θ) index at OTU_0.03.

Figure 3

Distribution of phylogentic groups shift following vancomycin administration. Classification of partial 16S rRNA-encoding gene sequences obtained from the cecal contents and cecal mucosa from mice treated with vancomycin (vancomycin) and vancomycin followed by a three-week recovery period without antibiotic (recovered). Comparisons were made to the communities detected in untreated mice (control). Sequences were analyzed and classified to the level of phylum (outer ring) and family (inner pie chart) using the RDP Classifier.