The gut mycobiome and animal health

Authors: Summers, Katie; ARFKEN, ANN - US Department Of Agriculture (USDA)

Submitted to: Springer Nature Applied Sciences
Publication Type: Book / Chapter
Publication Acceptance Date: 1/20/2021
Publication Date: 1/1/2022
Citation: Summers, K.L., Arfken, A.M. 2022. The gut mycobiome and animal health. Springer Nature Applied Sciences. https://doi.org/10.1007/978-3-030-90303-9_6.
DOI: https://doi.org/10.1007/978-3-030-90303-9_6

Interpretive Summary: The mycobiome (fungal microbiome) in the gut is a critical component in animal health despite being numerically inferior to the bacteriome (bacterial microbiome). Investigations into the gut mycobiome have been lacking due to limitations in techniques and technology, but recent advances in the field have made these studies possible. While challenges remain and there is no consensus on accepted techniques, fungi have been found to differ from gut bacteria in colonization pattern and diversity. The mycobiome is easily manipulated by environmental factors, such as diet, more readily than the bacteriome, making it an excellent candidate for dietary interventions to promote animal growth and health. In this chapter we will examine the limitations to the field, assess the current knowledge of the gut mycobiome in agricultural animals, investigate known fungal-bacterial interactions, and review what is known regarding fungal immunity promoting gut homeostasis.

Technical Abstract: The gut microbiome plays a critical role in animal health through its ability to alter nutrition, immune development, inflammation, prevent potential pathogens, and participate in fungal-bacterial-host interactions. The mycobiome (fungal microbiome) in the gut is a critical component in animal health despite being numerically inferior to the bacteriome (bacterial microbiome). Currently, studies on the gut mycobiome in agricultural animals have been lacking due to limitations in technology, but the recent use of high throughput sequencing techniques has furthered the field. While challenges remain in DNA isolation, primer design, PCR parameters, and database accuracies, fungi have been found to have complex interactions in the gut milieu. Further, fungi do not demonstrate the diversity or succession seen in the gut bacteriome, suggesting a distinct colonization pattern. Studies have also shown the ability of the mycobiome to be manipulated by environmental factors, such as diet, more readily than the bacteriome, making it an excellent candidate for dietary interventions to promote animal growth and health. In this chapter we assess the current knowledge of the gut mycobiome in agricultural animals, investigate known fungal-bacterial interactions, and review what is known regarding fungal immunity promoting gut homeostasis. We also examine limitations to the field and present unpublished data from our laboratory that demonstrates deficiencies in fungal primer design and databases.