Abstract
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences. We identify mucin utilizers and species inhibited by amino acids and short-chain fatty acids. Our analysis also uncovers media for in vitro studies wherein growth capacity correlates well with in vivo abundance. Further value of the underlying resource is demonstrated by correcting pathway gaps in available genome-scale metabolic models of gut microorganisms. Together, the media resource and the extracted knowledge on growth abilities widen experimental and computational access to the gut microbiota.
| Original language | English |
|---|---|
| Pages (from-to) | 514-522 |
| Number of pages | 9 |
| Journal | Nature Microbiology |
| Volume | 3 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - 1 Apr 2018 |
| MoE publication type | A1 Journal article-refereed |
Funding
We thank H. KleinJan and L. Maier for experimental assistance, O. Ponomarova for advice on media design and D. Machado for advice on metabolic modelling. Sequencing was performed at Genecore, EMBL. We thank Dupont Health and Nutrition (formerly Danisco Sweeteners OY, Finland) for providing L. acidophilus NCFM, L. paracasei ATCC SDS275, B. animalis subsp. lactis Bl-04 and BI-07, D. Clarke for Shigella sonnei 53 G and the enteropathogenic Escherichia coli strains CFT073, E2348/69, H10407, HM605 and UTI89, E. Denamur for the Escherichia coli strains ED1a and IAI1, M. Blokesch for the Vibrio cholerae strains A1552 and N16961, H. Andrews-Polymenis for the Salmonella enterica typhimurium strains CDC 6516-60 and LT2 and C. Darby for Yersinia pseudotuberculosis YPIII. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 686070. MT and MP were supported by the EMBL interdisciplinary postdoctoral program.