Abstract
Background: Bifidobacterium represents an important early life microbiota member. Specific bifidobacterial components, exopolysaccharides (EPS), positively modulate host responses, with purified EPS also suggested to impact microbe–microbe interactions by acting as a nutrient substrate. Thus, we determined the longitudinal effects of bifidobacterial EPS on microbial communities and metabolite profiles using an infant model colon system.
Methods: Differential gene expression and growth characteristics were determined for each strain; Bifidobacterium breve UCC2003 and corresponding isogenic EPS-deletion mutant (B. breve UCC2003del). Model colon vessels were inoculated with B. breve and microbiome dynamics monitored using 16S rRNA sequencing and metabolomics (NMR).
Results: Transcriptomics of EPS mutant vs. B. breve UCC2003 highlighted discrete differential gene expression (e.g., eps biosynthetic cluster), though overall growth dynamics between strains were unaffected. The EPS-positive vessel had significant shifts in microbiome and metabolite profiles until study end (405 h); with increases of Tyzzerella and Faecalibacterium, and short-chain fatty acids, with further correlations between taxa and metabolites which were not observed within the EPS-negative vessel.
Conclusions: These data indicate that B. breve UCC2003 EPS is potentially metabolized by infant microbiota members, leading to differential microbial metabolism and altered metabolite by-products. Overall, these findings may allow development of EPS-specific strategies to promote infant health.
Original language | English |
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Article number | 948 |
Number of pages | 17 |
Journal | Nutrients |
Volume | 12 |
Issue number | 4 |
DOIs | |
Publication status | Published - 29 Mar 2020 |
Bibliographical note
Funding Information:Author Contributions: M.A.E.L. and L.J.H. designed the study. D.P. and M.A.E.L. performed the model colon studies. D.P. performed growth curves, prepared samples for 16S rRNA sequencing, metabolomics, TEM, and graphed figures. J.K. performed the growth curves and prepared samples for RNASeq. A.T. analysed and visualized the RNASeq data. S.C. performed QC and taxonomic profiling of the 16S rRNA amplicon data. M.J.D. analyzed and visualized the 16S rRNA, metabolomics data, and performed the co-occurrence analysis (also with S.C.). I.J.C. performed the NMR metabolomics and identified metabolites. C.B. performed the TEM. D.P., A.T., M.J.D., MAEL and L.J.H. analyzed the data and co-wrote the manuscript along with D.v.S., and T.K. All authors read and approved the final manuscript Funding: This work was part funded by an Erasmus studentship to D.P. M.A.E.L. was funded by the Marie Skłodowska-Curie Individual Fellowship (Project 661594). L.J.H. is funded by a Wellcome Trust Investigator award (100974/C/13/Z) and together with T.K. by a BBSRC ISP grant for Gut Microbes and Health BB/R012490/1 and its constituent project(s), BBS/E/F/000PR10353 and BBS/E/F/000PR10355. T.K. is also funded by the Genomics for Food security CSP grant from the BBSRC (BB/CSP17270/1). A.T. is supported by the BBSRC Norwich Research Park Biosciences Doctoral Training Partnership (grant BB/M011216/1). D.v.S. is supported by Science Foundation Ireland (SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2). The funding bodies did contribute to the design of the study, collection, analysis, and interpretation of data or in writing the manuscript.
Funding Information:
Acknowledgments: We would like to thank the parents for donating their infants’ stool samples for these experiments, the sequencing team at Wellcome Trust Sanger Institute for performing the 16S rRNA and RNA sequencing and Drs Emma Allen-Vercoe and Julie McDonald for their technical support. This research was supported in part by the NBI Computing infrastructure for Science (CiS) group through the provision of a High-Performance Computing (HPC) Cluster.
Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.
Keywords
- 16S rRNA profiling
- Bifidobacterium
- Cross-feeding
- Diet
- Early life
- Exopolysaccharides
- Metabolomics
- Model colon
ASJC Scopus subject areas
- Food Science
- Nutrition and Dietetics