Vitamin Biosynthesis by Human Gut Butyrate-Producing Bacteria and Cross-Feeding in Synthetic Microbial Communities

Abstract

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.

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria

“…A recent in vitro study highlighted the auxotrophy of F. prausnitzii for multiple B-vitamins. However, while several auxotrophic butyrate producers for folate or thiamine could benefit from the presence of prototrophic strains, vitamin-independent growth stimulation was observed for F. prausnitzii A2-165, suggesting that it used other growth factors from other bacterial members [ 29 ].…”

“…Lactic acid bacteria/bifidobacteria consumption have been shown to modulate gut microbiota [ 24 ]). In vitro models have allowed to identify cross-feeding between lactic acid bacteria/bifidobacteria and gut microbiota through short-chain fatty acids (SCFAs) [ 25 , 26 ], cell wall-derived polysaccharides [ 27 , 28 ], and vitamins [ 29 ]. Many studies have reported then capacity of lactic acid bacteria to inhibit pathogen growth [ 30 , 31 ] through the production antimicrobial compounds such as bacteriocins [ 32 ].…”

Role of Dietary Micronutrients on Gut Microbial Dysbiosis and Modulation in Inflammatory Bowel Disease

“…Recently, multiple B vitamin auxotrophies in a panel of the most abundant butyrate‐producing Firmicutes species from the healthy human gut were demonstrated in vitro. [ 231 ] Also, lower butyrate production was observed in low Ca, low Se, and low vitamin A conditions. Certain micronutrients may have similar anti‐inflammatory effects as butyrate as reported for vitamin B3, which makes in situ B3 delivery or stimulation of in situ bacterial B3 production a promising target for further investigation, for example, by including B3‐producing taxa in LBP.…”

Prevalent Human Gut Bacteria Hydrolyse and Metabolise Important Food-Derived Mycotoxins and Masked Mycotoxins

“…At the end of the experiment, growth data were captured using Gen 5 software [version 3.02.1]. Growth rates were determined as described by Soto-Martin et al [ 70 ]. The exponential phase of growth (blank subtracted data) was visualised by plotting the OD reading on a logarithmic scale.…”