Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants

Katri Korpela, Anne Salonen, Outi Vepsäläinen, Marjo Suomalainen, Carolin Kolmeder, Markku Varjosalo, Sini Miettinen, Kaarina Kukkonen, Erkki Savilahti, Mikael Kuitunen, Willem M de Vos, Katri Korpela, Anne Salonen, Outi Vepsäläinen, Marjo Suomalainen, Carolin Kolmeder, Markku Varjosalo, Sini Miettinen, Kaarina Kukkonen, Erkki Savilahti, Mikael Kuitunen, Willem M de Vos

Abstract

Background: Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches.

Results: The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced.

Conclusions: The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding.

Trial registration: clinicaltrials.gov NCT00298337 . Registered March 2, 2006.

Keywords: Bifidobacteria; Early-life microbiota; Lactobacilli; Metagenomics; Metaproteomics.

Conflict of interest statement

Ethics approval and consent to participate

The Ethics Committee of the Hospital for Children and Adolescents of Helsinki University approved the study. Parents provided written informed consent.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Effect of supplement treatment and feeding mode on the microbiota composition in the vaginally born, non-antibiotic-treated infants. a–b Relative abundance of the species in the probiotic mixture in 16S rRNA gene amplicon sequences derived from faecal samples. c–e Relative abundance of the probiotic species in whole metagenome sequences of breastfed infants. The number of infants per group is noted on the bottom of each panel (a–e). f Principal coordinates analysis (Bray-Curtis dissimilarities) on the species-level 16S rRNA gene data. g Composition of the Bifidobacterium population by treatment group and feeding type
Fig. 2
Fig. 2
Effect of supplement treatment in the vaginally born, non-antibiotic-treated breastfed infants and formula-fed infants. The fold changes represent the difference in the relative abundance of the taxon between the supplement-treated group and the control group. The asterisks indicate the significance of the difference (based on GLM or GLS, see Additional file 1: Tables S1 and S2): *p < 0.05, **p < 0.01, ***p < 0.001
Fig. 3
Fig. 3
Effects of supplement and birth mode on the microbiota. Overall average composition of the microbiota at class level in the different groups, based on the 16S rRNA amplicon data (a). Significant family-level group differences compared to the vaginally born control group (b). Effect of supplement treatment and birth mode on the metaproteome (c) and metagenome (d) in principal coordinates analysis (Bray-Curtis dissimilarities)
Fig. 4
Fig. 4
Effects of supplement treatment and antibiotic use on the microbiota composition in 16S rRNA amplicon data. Overall average composition of the microbiota at class level in the different groups (a). Significant family-level group differences compared to the non-antibiotic-treated control group (b)

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