Turning state-of-the-art microbiome research into commercial success in animal industry was the topic of the Animal Microbiome Congress 2021, organized by Kisaco Research. The virtual event took place on 24-25 March, and it offered panel and roundtable discussions, as well as pre-recorded keynote presentations and networking tools.

Increased understanding on the effects of gastrointestinal microbes to animal performance has contributed to the recent interest towards microbiota-modulating products. Both the meat industry and the pet healthcare sector, from start-up companies to big players, are striving to develop innovative products for the ever-increasing markets. The shared motivation in this work is to reduce the usage of medically important antimicrobial drugs for animals, in order to maintain their efficacy against human pathogens. The keynote presentations of the Animal Microbiome Congress emphasized the huge potential for product development when applying new microbiological research tools for farm animal and pet sectors.

Developing novel microbial products has its challenges. First of all, the intestinal milieu of animals is not as well studied as one might think. As professor Mark Pallen from the University of East Anglia & Quadram Institute pointed out in his keynote lecture, more is known about the far side of the Moon than the microbes that inhabit our livestock. He formulated the three key questions of microbial ecology as follows: “Who’s there?, What are they doing? and Who are they doing it with?”. Thus it is not enough to know the identity and metabolic patterns of individual microbial species, but it is equally important to understand their interactions. According to professor Pallen, all these aspects together are needed for unlocking the functional significance of the microbiome.
Another question raised on several occasions during the congress was the lack of proper definition for health or normality, when it comes to gut microbes. Sound function can be achieved through various forms of gut ecosystem, and the presence of obvious health problems is much easier to define than the lack of them. This poses a challenge to those seeking for microbial patterns that predict either good or compromised performance of animals.

Typical approaches for influencing the intestinal microbiota include applying probiotics, prebiotics, or their combination called synbiotics. As microbes act in communities of hundreds of species, the potential of single-species probiotics in affecting the microbiota has its limits, and now many scientists have turned their interest in discovering the potential of specifically designed mixtures of microbial species. In his keynote presentation, professor Thomas Clavel from the University Hospital of RWTH Aachen, emphasized the importance of host-specific microbial cultures as research tools. Culturable species from native microbiota can be purchased from strain collections for designing so-called “synthetic microbiomes”. These tailor-made minimal microbiomes allow detailed studies of bacterial interactions and interdependencies, and also allow development of biotherapeutic products. The first chicken studies in which a synthetic microbiome of nine bacterial species was applied to chickens right after hatch, indicated increased diversity of gut microbiota, and improved adaptive immune responses of the treated animals.

Another strategy was presented by Dr. Mike Kogut from USDA-ARS. He pointed out that the taxonomical identification of microbes in a given community is prone to changes while the functional activity of the microbiome may remain relatively stable. Colonization resistance limits the ability of probiotics to establish a permanent position in the microbiota. On the other hand, the targets and specificity of prebiotics are limited, because they can boost the growth of many bacterial species within a community. Instead, Dr. Kogut suggested using postbiotics, which are bioactive molecules produced by beneficial microbes: metabolites such as butyrate, vitamins or enzymes, or bacterial cell wall components with e.g. immunomodulatory activity. By using postbiotics, the targeted effects on the host are no longer dependent on the actions of live microbes in the gastrointestinal tract. Thus, according to Dr. Kogut, postbiotics open a more consistent way for beneficial modulation of host performance.

A shared concern of many companies developing second generation microbials is the difficulties associated with product registration. Getting new products through the registration jungle into markets may take years. It was pointed out that for smoothening the path of novel microbial modulators to markets, it is necessary to maintain an active and friendly discussion with the regulatory officials.