From fecal microbiota transplantation toward next-generation beneficial microbes: The case of Anaerobutyricum soehngenii

Abstract

The commensal gut microbiota is important for human health and well-being whereas deviations of the gut microbiota have been associated with a multitude of diseases. Restoration of a balanced and diverse microbiota by fecal microbiota transplantation (FMT) has emerged as a potential treatment strategy and promising tool to study causality of the microbiota in disease pathogenesis. However, FMT comes with logistical challenges and potential safety risks, such as the transfer of pathogenic microorganisms, undesired phenotypes or an increased risk of developing disease later in life. Therefore, a more controlled, personalized mixture of cultured beneficial microbes might prove a better alternative. Most of these beneficial microbes will be endogenous commensals to the host without a long history of safe and beneficial use and are therefore commonly referred to as next-generation probiotics (NGP) or live biotherapeutic products (LBP). Following a previous FMT study within our group, the commensal butyrate producer Anaerobutyricum spp. (previously named Eubacterium hallii) was found to be associated with improved insulin-sensitivity in subjects with the metabolic syndrome. After the preclinical testing with Anaerobutyricum soehngenii in mice models was completed, the strain was produced under controlled conditions and several clinical studies evaluating its safety and efficacy in humans were performed. Here, we describe and reflect on the development of A. soehngenii for clinical use, providing practical guidance for the development and testing of NGPs and reflecting on the current regulatory framework.

Keywords: Anaerobutyricum soehngenii; Eubacterium hallii; fecal microbiota transplantation; live biotherapeutic product; next-generation probiotic.

FIGURE 1

Definitions of probiotics, next-generation probiotics, and live biotherapeutic products. The different “biotics” are colored orange, here denoted as the active substance. The final products are colored green, with the darker green corresponding with products that are considered drugs, while the lighter green falls within the food and food supplements regulation.

FIGURE 2

Roadmap for the development of NGP. Important points to consider for the development of NGPs are summarized from the identification to the regulatory assessment. BLA, Biologics License Application; EC, European Commission; EFSA, European Food Safety Authority; EMA, European Medicines Agency; EU, European Union; FDA, Food and Drug Administration; GI, gastrointestinal; GMP, Good Manufacturing Practices; HACCP, Hazard Analysis and Critical Control Points; HTA, Health Technology Assessment; IB, Investigators Brochure; IMPD, Investigational Medicinal Product Dossier; IND, Investigational New Drug; SCoPAFF, Standing Committee on Plants, Animals, Food and Feed, and US, United States.

FIGURE 3

Preparation of Anaerobutyricum soehngenii. Production started with the production of a sterile anoxic growth medium (1), which was used for the seeding (2 and 3) and fermentations (4 and 5) of A. soehngenii. The fermentations were well controlled for temperature, presence of oxygen and pH amongst others. After the final fermentation, cells were cooled (6), concentrated (7) and washed by diafiltration (8). Cells were harvested from the fermenter (9), diluted with glycerol (10% final concentration) to 10¹⁰ CFU/ml and dispensed over 10 ml vials that were labeled and directly frozen. The highest concentration was used to make dilutions for the lower doses.