Vitamin biosynthesis by human gut butyrate-producing bacteria and cross-feeding in synthetic microbial communities

Eva Soto Martin, Ines Warnke, Freda Farquharson, Marilena Christodoulou, Graham Horgan, Muriel Derrien, Jean-Michel Faurie, Harry J. Flint, Sylvia Duncan, Petra Louis* (Corresponding Author)

*Corresponding author for this work

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We investigated the requirement of 15 human butyrate-producing gut bacterial strains for eight B vitamins and the proteinogenic amino acids by a combination of genome sequence analysis and in vitro growth experiments. The Ruminococcaceae species Faecalibacterium prausnitzii and Subdoligranulum variabile were auxotrophic for most of the vitamins and the amino acid tryptophan. Within the Lachnospiraceae, most species were prototrophic for all amino acids and several vitamins, but biotin auxotrophy was widespread. In addition, most of the strains belonging to Eubacterium rectale and Roseburia spp., but few of the other Lachnospiraceae strains, were auxotrophic for thiamine and folate. Synthetic coculture experiments of five thiamine or folate auxotrophic strains with different prototrophic bacteria in the absence and presence of different vitamin concentrations were carried out. This demonstrated that cross-feeding between bacteria does take place and revealed differences in cross-feeding efficiency between prototrophic strains. Vitamin-independent growth stimulation in coculture compared to monococulture was also observed, in particular for F. prausnitzii A2-165, suggesting that it benefits from the provision of other growth factors from community members. The presence of multiple vitamin auxotrophies in the most abundant butyrate-producing Firmicutes species found in the healthy human colon indicates that these bacteria depend upon vitamins supplied from the diet or via cross-feeding from other members of the microbial community.
IMPORTANCE: Microbes in the intestinal tract have a strong influence on human health. Their fermentation of dietary nondigestible carbohydrates leads to the formation of health-promoting short-chain fatty acids, including butyrate, which is the main fuel for the colonic wall and has anticarcinogenic and anti-inflammatory properties. A good understanding of the growth requirements of butyrate-producing bacteria is important for the development of efficient strategies to promote these microbes in the gut, especially in cases where their abundance is altered. The demonstration of the inability of several dominant butyrate producers to grow in the absence of certain vitamins confirms the results of previous in silico analyses. Furthermore, establishing that strains prototrophic for thiamine or folate (butyrate producers and non-butyrate producers) were able to stimulate growth and affect the composition of auxotrophic synthetic communities suggests that the provision of prototrophic bacteria that are efficient cross feeders may stimulate butyrate-producing bacteria under certain in vivo conditions.
Original languageEnglish
Article number e00886-20
Number of pages18
Issue number4
Early online date14 Jul 2020
Publication statusPublished - Jul 2020

Bibliographical note

This project was funded by Danone Nutricia Research. F.M.F., G.H., H.J.F., S.H.D., and P.L. receive support from the Scottish Government Rural and Environment Sciences and Analytical Services. Method development for coculture microbial analysis was partially supported by European 7th Framework grant (289517) “Dietary fibres supporting gut and immune function; from polysaccharide compound to health claim (Fibebiotics).” We thank Timo Kramer for his technical support with the in silico analyses. M.D., J.-M.F., H.J.F., S.H.D., and P.L. conceived and designed the study. E.C.S.-M., I.W., F.M.F., and M.C. acquired data and contributed to interpreting the results. G.H. performed statistical analysis. E.C.S.-M. and P.L. drafted the manuscript. All authors contributed to revising the manuscript and approved the final version.


  • amino acid biosynthesis
  • butyrate
  • cross-feeding
  • human gut microbiota
  • vitamin biosynthesis
  • Vitamin biosynthesis
  • Amino acid biosynthesis
  • Human gut microbiota
  • Cross-feeding
  • Butyrate


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