Gastrointestinal Microorganisms and Other Animal Hosts

Gastrointestinal Microorganisms and Animals


Gastrointestinal microorganisms exist in symbiotic associations with animals. Microorganisms in the gut assist in the digestion of feedstuffs, help protect the animal from infections, and some microbes even synthesize and provide essential nutrients to their animal host. Therefore, understanding the complex symbiotic relationships between gastrointestinal microbes and their animal hosts can lead to the development of practices to improve animal performance and promote animal health.

Digestive Strategies

Animals are often classified according to their digestive physiology and gastrointestinal microorganisms can be examined according to gut location: foregut (before gastric stomach), midgut (small intestine) and hindgut (large intestine) (4, 5). Enzymes secreted in the mouth and stomach assist in the breakdown of foods consumed by animals. Microorganisms residing in other areas of the gastrointestinal tract can also help breakdown feedstuffs by a process called fermentation. Fermentation is the anaerobic breakdown of organic compounds.

Pre-gastric, cecal and colonic fermenters are descriptive terms used to indicate the location in the digestive tract where the majority of microbial activity occurs. Pre-gastric fermenters (before the gastric stomach), include ruminants such as cows, sheep and giraffes. When the majority of fermentative activity occurs in the cecum, animals can be described as cecal fermenters (guinea pigs, rabbits, chinchillas, rats, etc.). Colonic fermenters (gorillas, ponies, elephants, etc.) have the majority of fermentation occurring in the large intestine.

The Angert laboratory has investigated the microbial communities residing in the gastrointestinal tracts of surgeonfish, guinea pigs, cows and gorillas. Therefore, the following discussion will focus on those animals.


There are ~80 species of fish in the surgeonfish family (Acanthuridae). Most surgeonfish are herbivores (eat algae primarily), and the herbivorous species tend to have long intestinal tracts when compared with carnivorous fish of the same body size (4, 5). The lengthy intestinal tract allows for a longer retention time of digesta and permits ample fermentation. Surgeonfish host Epulopiscium spp., members of the Low G+C gram-positive bacterial lineage. Scientists have observed surgeonfish behavior in the wild, and found that juvenile surgeonfish consume the feces of adult surgeonfish (1). This behavior may help the fish develop their intestinal microbial communities.


Guinea Pigs


Guinea pigs have a large cecum, and like herbivorous surgeonfish, guinea pigs are coprophagous; they eat their own feces! In addition to obtaining intestinal microbes, ingestion of feces allows animals to recover more nutrients and vitamins (2, 4). One of the closest known relatives of Epulopiscium is a bacterium called Metabacterium polyspora. M. polyspora is also a Low G+C gram-positive bacterium and is a gastrointestinal symbiont of guinea pigs. The M. polyspora life cycle takes advantage of the coprophagous nature of the guinea pig host. This bacterium produces dormant endospores that can be found in the feces of the guinea pig. Coprophagy allows Metabacterium to reenter the host gastrointestinal tract or colonize new hosts.

A fistula (a surgical opening) can be implanted in the rumen, allowing for easy collection of ruminal contents and microbes.

Cellulose, a polymer of ß 1-4 linked glucose units, is the world·s most abundant carbohydrate. Animals often consume diets rich in cellulose. Mammals lack enzymes that breakdown cellulose, but often harbor microorganisms in their gastrointestinal tracts that have the capacity to perform this important function. As an example, fiber-degrading bacteria in the rumen can ferment cellulose. Microscopic images of three common cellulolytic ruminal bacteria are shown below: (A) Fibrobacter succinogenes, (B) Ruminococcus albus and (C) Ruminococcus flavefaciens.


Purpose of the Website

In addition to cellulose-degrading bacteria, our laboratory is interested in methanogens, a group of ruminal microorganisms belonging to the Domain Archaea. The methanogens are of great economic and environmental importance because they generate methane gas (CH4), an important greenhouse gas and contributor to global warming. When ruminants eructate (burp), CH4 formed in the rumen is released into the atmosphere. Hindgut methanogenesis also occurs. Methane produced in the hindgut of ruminants has an impact on global warming although the magnitude of this source has yet to be fully determined.



Gorillas have a large colon (5) and are likely colonic fermenters. Gorillas are herbivores, and eat a diet of leaves, bark, stems, shoots and fruit (3). Recently, we have isolated gene sequences from the feces of a wild gorilla residing in Bwindi Impenetrable National Park, Uganda. The sequences were related to the following bacterial phyla: Firmicutes (or Low G+C Gram-positive bacteria), Actinobacteria, Bacteriodetes, Lentisphaerae, Planctomycetes, Spirochetes and Verrucomicrobia (). Some of the sequences were very similar to sequences from bacteria that degrade fiber, reduce aromatic compounds (tannins), and ferment simple and non-structural carbohydrates. These bacteria probably ferment feedstuffs in the gastrointestinal tract of the gorilla. They may also help detoxify tannins, anti-nutritional compounds which bind valuable protein and decrease palatability.

The symbiotic interaction between gastrointestinal microbes and their animal host enables animals to maximize the nutrients they obtain from the foods that they consume. Of note, the Low G+C gram-positive bacteria are important microorganisms in the digestive tract, and are commonly found in large proportions in surgeonfish, guinea pigs, ruminants, pigs, humans and gorillas. Because microbes perform vital functions throughout the gut, a characterization of both the types and functions of these microorganisms would allow scientists to develop effective management strategies. Practices could then be implemented to promote animal conservation, as well as to increase animal health and performance.


  1. Clements, K. D. 1997. Fermentation and gastrointestinal microorganisms in fishes, p. 156-198. In R. I. Mackie and B. A. White (ed.), Gastrointestinal Microbiology: Gastrointestinal Ecosystems and Fermentations, vol. 1. Chapman and Hall, New York.
  2. Holtenius, K., and C. Björnhag. 1985. The colonic separation mechanism in the guinea-pig (Cavia porcellus) and the chinchilla (Chinchilla laniger). Comp. Biochem. Phys. A. 82:537-542.
  3. Rothman, J. M., A. N. Pell, E. S. Dierenfeld, D. O. Molina, A. V. Shaw, and H. F. Hintz. Nutritional chemistry of the diet of gorillas in the Bwindi Impenetrable National Park, Uganda. Am. J. Primatol., In Press.
  4. Stevens, C. E., and I. D. Hume. 1995. Comparative Physiology of the Vertebrate Digestive System, Cambridge, United Kingdom. Cambridge University Press.
  5. Stevens, C. E., and I. D. Hume. 1998. Contributions of microbes in vertebrate gastrointestinal tract to production and conservation of nutrients. Physiol. Rev. 78:393-427.
  6. Frey, J. C., J. M. Rothman, A. N. Pell,  J. Bosco Nizeyi, M. R. Cranfield and E. R. Angert. 2006.  Fecal bacterial diversity in a wild gorilla.  Appl Environ Microbiol 71: 3788-3792.

Useful links

Useful Books: Rumen Microbiology

  1. Hespell, R. B., D. E. Akin, and B. A. Dehority. 1997. Bacteria, fungi, and protozoa of the rumen, p. 59-141. In R. I. Mackie, B. A. White, and R. E. Isaacson (ed.), Gastrointestinal microbiology, vol. 2. Chapman and Hall, New York.
  2. Hobson, P. N., and C. S. Stewart (ed.). 1997. The Rumen Microbial Ecosystem, p. 719, 2 ed. Chapman & Hall, Suffolk, UK.
  3. Hungate, R. E. 1966. The Rumen and its Microbes. Academic Press, New York.