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Cultivating Gut Anaerobes with Yeast-Based Nutrients for Live Biotherapeutic Products

Cultivating gut microorganisms for Live Biotherapeutic Products (LBP) at an industrial scale can be challenging as many of these microorganisms are sensitive to a variety of factors such as oxygen. Furthermore, many potentially useful microorganisms are difficult to cultivate due to unknown nutritional requirements.

Determining the right culture conditions and nutrient combination is crucial for each strain to cultivate them effectively for use in LBP. Let’s take a look into the challenging and fascinating world of Faecalibacterium duncaniae production, a promising gut microbial species!

Faecalibacterium duncaniae: a promising but tough-to-cultivate microbe

Several gut microbial species from the Faecalibacterium genus are encouraging candidates for pharmaceutical applications due to their versatile protective effects against gastrointestinal and systemic disorders.

Faecalibacterium’s abundance in the human gut has been demonstrated to have a negative correlation with diseases, such as:

  • Cancer
  • Atopic diseases
  • Disorders related to the intestines and gut-metabolism


These microbes are further being explored for other treatments against:

  • Inflammation
  • Colitis
  • Diabetes
  • Obesity


Cultivating microbial species within the Faecalibacterium genus can be especially challenging due to their extreme oxygen sensitivity and relatively unknown nutritional requirements.

Nonetheless, to enable clinical studies and broader applications, there is a pressing need to refine cultivation methods for Faecalibacterium following the current Good Manufacturing Practice regulations.

Scientific research on cultivating F. duncaniae

ETH Zurich researchers recently explored ways to cultivate F. duncaniae with animal-free ingredients.

The first step comprised screening six distinct yeast-based nutrients by first evaluating F. duncaniae’s growth in microtiter plates under various settings. Then scientists tested the three yeas-based nutrients that showed the best growth performance in bioreactors.

In the second step, the growth-promoting effect of eight B vitamins at different dosages was tested on F. duncaniae.

Lastly, researchers tested which mix of yeast-based nutrients and B vitamins was most effective for the growth of F. duncaniae.

Figure 1. Steps for testing the best combination of yeast-based nutrients and B vitamins for cultivating F. duncaniae.1

Benefits of using yeast-based nutrients to cultivate F. duncaniae

Scientists noticed that the growth-promoting effect of yeast extracts for cultivating F. duncaniae is dependent on the dosage. Yeast extracts effectively supported the growth thanks to their richness in nitrogen nutrients (proteins, peptides, amino acids, etc.) and growth factors (vitamins, trace elements, etc.).

In another hand, they also showed that yeast peptones act as a crucial source of macronutrients but are deficient in the micronutrients necessary for F. duncaniae growth. Therefore, yeast peptones should only be integrated into a medium formulation that is enriched with proper amounts of essential growth factors or used in conjunction with yeast extract naturally rich in these growth factors.

Whereas multiple B-vitamin auxotrophies were reported for F. duncaniae in the literature, researchers found that vitamin B5 (Pantothenic acid) was the primary nutritional factor responsible for promoting growth out of all the B vitamins tested (B1, B2, B3, B5, B6, B7, B12). Vitamin B5 is indeed known as an essential precursor for the biosynthesis of coenzyme A which is involved in a multitude of metabolic reactions and is a key factor for cell growth.

Metabolite analysis also confirmed the stimulating properties of vitamin B5 with increased substrate consumption and acetate and formate production. Researchers observed variations in butyrate production depending on the yeast extracts tested. Formation of butyrate over the acetyl-CoA pathway relies on cofactors such as thiamine (vitamin B1) and Riboflavine (vitamin B2) Both are naturally present in yeast extracts and may be key nutritional factors for directing F. ducaniae metabolism towards butyrate production.

Through the substitution of casein peptone with a combination of yeast extract and yeast peptones, the researchers successfully developed a culture medium free of all allergenic ingredients and of animal origin. Additionally, this medium was shown to be compatible with current Good Manufacturing Practice (cGMP) standards.

This research illustrates that the growth and metabolite production patterns of F. duncaniae are significantly influenced by the type of yeast-based nutrients used.

This study emphasizes the importance of comprehending the specific nutritional requirements of the cultured strain. This understanding enables the selection of the most suitable yeast-based nutrients and growth factors to support high cell-density biomass and metabolites productions.

Optimizing the composition of the culture medium through the careful selection of the most appropriate yeast-based nutrients for a specific microorganism and bioprocess has the potential to enhance cell and metabolite yields, reduce manufacturing costs, and contribute to the stability of cultures during downstream processing and preservation.

Yeast-based nutrients for cultivating gut microbes

Yeast-based nutrients contain a range of essential nutrients such as proteins, peptides of different sizes, free amino acids, and essential growth factors including vitamins, minerals, nucleic bases, and trace elements. However, their composition varies depending on the production processes.  Therefore, to meet the nutritional needs of a specific bacteria, it is necessary to carefully choose yeast-based nutrients or a combination of them that contains the optimal ratio of nutrients and growth factors.

Discover more about optimizing tough-to-grow microbial strains by using yeast-based nutrients through a collaborative 2023 study between ETH Zurich and Procelys by Lesaffre.

1 – L. Bircher, A. M. Sourabié, M. Paurevic, J. Hochuli, A. Geirnaert, C. Navas, B. Drogue, C. Lacroix. 2023. Faecalibacterium duncaniae A2-165 growth is strongly promoted by yeast extract and vitamin B5 in cGMP medium. Microbial Biotechnology. Volume 17, Issue 1, https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.14374