Role of fungi in digestive systems of herbivores

By Corey Chin


Many people hear the word “fungi” and want to run the opposite direction – associating it with some nasty, toxic mess to stay far away from. I know because of the way people’s faces cringe to express their disgust when I tell them about the program I am enrolled in at my college titled “The Fungal Kingdom”. At this point I can just smile to myself knowing that there is so much these people don’t know about the fungi they are writing off as gross – that without them the world would look a whole lot different. Ever seen that cheesy film “A Day Without a Mexican” that shows how important immigrants from Mexico with actual work ethic are to this country, even though many complain about their presence? Well imagine what “A Day without Fungi” would look like – plants would die, delicious food sources would disappear, forest ecosystems would completely fall apart without any organisms capable of degrading wood, and many animals would have a much harder time digesting their food without the help of fungi in their gut – which is I’m going to talk about.

Chytridiomycota is a phylum of fungi that is widely dispersed globally, occurring in a diverse range of habitats “from the tropics to the arctic regions”. Chytrids can be found in aquatic systems, as plant parasites as well as vertebrate parasites like the infamous Batrachocytrium dendrobatidis responsible for the rapid decline of amphibian populations, but mostly occur in terrestrial habitats. The chytrid body – called the thallus – contains a sac-like structure called a sporangium that produces and stores zoospores (James et al., 2006). Zoospores can swim through aquatic environments using a posteriorly attached flagellum – similar to the sperm of a man that fertilizes an egg to impregnate a woman, zoospores are responsible for giving birth to new chytrids. Zoospores are capable of entering dormant states allowing them to stay alive in droughts and other harsh environments. There are five orders within the Chytridiomycota based on reproductive methods and the structure of zoospores. An especially interesting order, Neocallimastigales, occur as “anaerobic symbionts of the rumen” (James et al., 2006) as well as in intestines of other non-ruminant herbivores.

More often than not, when reading or learning about digestion in herbivores and specifically in ruminants, fungi are never mentioned – since mycology is a relatively new field of study, fungi are routinely left out of equations in which they are key players. As more and more people dive into the world of mycology, we are figuring out just how important fungi are, and finding them in places you might never think to look. All herbivores contain a spread of microflora in their gut to aid in their digestion, since high-fiber diets are very difficult to break down. Included in this gut microflora are the chytrids of Neocallimastigales. All herbivores ferment their food along their digestive tract. In ruminants – which include cows, sheep, goats, ox, deer, and more, fermentation takes place in the rumen – these animals are foregut fermenters, meaning their food is fermented before reaching the “true” stomach, allowing for more efficient digestion. To further explain, Merchen, Elizalde, and Drackly, 1997, write that “digestion by ruminants is the net result of a sequence of processes that occur in different segments of the gastrointestinal tract”. Primary fermentation of food takes place in the reticulo-rumen, then enzymes of host assist in acid hydrolysis and degreadation in the abomasums and small intestine, and lastly secondary fermentation is carried out in the cecum and large intestine (Merchen, et al., 1997).


In order to understand digestion in ruminants it is essential to also understand the microbial communities within these digestion sites. Anaerobic fungi live in areas of the digestive tract to aid in fermentation in ruminants as well as in the gut of non-ruminant herbivores along with bacteria and other microflora.

It’s hard to imagine how microorganisms such as these chytrids were discovered within the gut of animals considering they are tiny creatures living inside long, slimy, complex digestive tracts of select animals. DNA sequences were taken from feces of wild and domestic herbivores using a process called polymerase chain reaction to amplify specific gene strands. Through this sequencing, six genera were found within the Neocallimastigales – Neocallimastix, Piromyces, Orpinomyces, Anaeromyces, Caecomyces, and Cyllamyces – the most recently described genus (Nicholson, McSweeny, Mackie, Brookman, Theodorou, 2010). Species within Neocallimastigales have even been found in landfill sites, further enforcing their role as cellulose degraders (Lockhart et al., 2006). Without this technology it would be impossible to isolate these organisms or phylogenetically relate them to each other and other groups of fungi.

So we know that fungi are present in the gut of herbivores, but how do they actually help the animal? Like all members of Chytridiomycota, chytrids within the Neocallimastigales order reproduce asexually through motile zoospores with flagella, as mentioned earlier. These zoospores allow for “rapid colonisation of freshly ingested plant material” (p. 66 Nicholson et al., 2010) that enter the digestive tract of herbivores. The fungi then excrete fibrolytic enzymes – including cellulases, hemicellulases, proteases, and esterases, to help break down the plant material into three fatty acids – acetic acid, proprionic acid, and butyric acid – which are then used by the animal for energy. Don’t forget that bacteria and some protozoa are also important for this process!

So the next time you see some mold on your tangerine or are served some mushrooms you might think of as dirty and unappealing, remember how diverse fungi are and the key roles they serve in not only ecosystems around the world, but even in the digestive systems of many animals we know and love!


Brookman, J., Mackie, R., Mcsweeny, C., Nicholson, M., Theodorou, M. (2010). Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores. ScienceDirect, Volume 16, issue 2. Retrieved from

James, T., Griffith, G., Letcher, P., Longcore, J., Mozley-Standridge, S., Porter, D., Powell, M, Vilgalys, R. (2006). A molecular phylogeny of flagellated fungi (Chtridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia, 98. Retrieved from

Lockhart, R., Van Dyke, M., Beadle, I., Humphreys, P., McCarthy, A. (2006). Molecular Biological Detection of Anaerobic Gut Fungi from Landfill Sites. Applied and Environmental Microbiology, 72. Retrieved from

Merchen, N. R., Elizalde, J. C., Drackley, J. K., (1997). Journal of Animal Science. Current perspective on assessing site of digestion in ruminants, 75, 2223-2234.