Due to the growing human population and increased demand for animal food products, animal breeding became unsustainable in terms of climate change, available resources and deforestation, as well as a health problem both for humans and animals because of increasing antibiotic resistance and rise in new microbial infections.
Poultry industry is well known for massive breeding of animals in small and confined spaces and their susceptibility for spread of dangerous human pathogens, such as Salmonella species. Swine breeding is a potential risk area for zoonotic diseases such as Trichinellosis. Microbiome-based product development in this area is mostly focused on probiotics, phage therapy or microbial engineering. Some of these products are already in the pipelines.
Ruminant animals (e.g. cattle, sheep, goats and others) are all very important for dairy industry as well as production of meat and wool. These animals are also well known for having a special digestive system, which houses an extremely large number of microbial species (up to 50 billion of bacteria per 1ml!). Besides helping them to digest plant fibers, many of these bacterial species are producers of methane, a very potent greenhouse gas. Improvements in microbiomes of the ruminants, can therefore not only improve farming productivity but also contribute to the decrease of their environmental footprint.
In aquacultures, fishes, shrimps or shells are typically grown in very large densities. Therefore, a single parasite or other microbial pathogen can cause massive economic losses. Use of antibiotics, leads to increasing antibiotic resistance, susceptibility to the other microbial pathogens and is also an environmental hazard. Several bacterial species and food supplements have been already shown as effective alternatives to antibiotics in aquacultures, either as probiotics or for their bactericidal effects.
More collaboration between research and industry is urgently needed in this sector.