Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection

Abstract

Perturbations in the gastrointestinal microbiome caused by antibiotics are a major risk factor for Clostridium difficile infection (CDI). Probiotics are often recommended to mitigate CDI symptoms; however, there exists only limited evidence showing probiotic efficacy for CDI. Here, we examined changes to the GI microbiota in a study population where probiotic treatment was associated with significantly reduced duration of CDI diarrhea. Subjects being treated with standard of care antibiotics for a primary episode of CDI were randomized to probiotic treatment or placebo for 4 weeks. Probiotic treatment consisted of a daily multi-strain capsule (Lactobacillus acidophilus NCFM, ATCC 700396; Lactobacillus paracasei Lpc-37, ATCC SD5275; Bifidobacterium lactis Bi-07, ATCC SC5220; Bifidobacterium lactis B1-04, ATCC SD5219) containing 1.7 x 1010 CFUs. Stool was collected and analyzed using 16S rRNA sequencing. Microbiome analysis revealed apparent taxonomic differences between treatments and timepoints. Subjects administered probiotics had reduced Verrucomicrobiaceae at week 8 compared to controls. Bacteroides were significantly reduced between weeks 0 to 4 in probiotic treated subjects. Ruminococcus (family Lachnospiraceae), tended to be more abundant at week 8 than week 4 within the placebo group and at week 8 than week 0 within the probiotic group. Similar to these results, previous studies have associated these taxa with probiotic use and with mitigation of CDI symptoms. Compositional prediction of microbial community function revealed that subjects in the placebo group had microbiomes enriched with the iron complex transport system, while probiotic treated subjects had microbiomes enriched with the antibiotic transport system. Results indicate that probiotic use may impact the microbiome function in the face of a CDI; yet, more sensitive methods with higher resolution are warranted to better elucidate the roles associated with these changes. Continuing studies are needed to better understand probiotic effects on microbiome structure and function and the resulting impacts on CDI.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1. Microbial α-diversity as measured by the Shannon diversity index.

The Shannon diversity index, which is a heterogeneity measure that combines richness and evenness components of microbial diversity does not significantly differ when subjects take probiotics.

Fig 2. Taxa were found to be differentially abundant depending on treatment and time point.

(A) Subjects in the probiotic group had a significantly lower abundance of the bacterial family Verrucomicrobiaceae at week 8 than placebo treated subjects; (B) Members of the bacterial genus Bacteroides were significantly reduced in abundance between weeks 0 to 4 in probiotic treated subjects; (C) Ruminococcus (family Lachnospiraceae) tended to be more abundant at week 8 than week 4 within the placebo group and at week 8 than week 0 within the probiotic group; * 0.05 < p < 0.1 and **p ≤ 0.05.

Fig 3. Predicted functional profiling of the GI microbiome in placebo or probiotic treated subjects undergoing CDI.

Profiling of KEGG modules was based on 16S rRNA marker gene sequences from week 4 using PICRUSt. The α parameter for pairwise tests was set to 0.05 for class normality and the threshold on the logarithmic score of LDA analysis was set to 2.0. Modules that differed significantly in abundance between the treatment groups are displayed with the respective LDA score.