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The Role of the Microbiota in Animals


Ian Rodney Tizard

, BVMS, BSc, PhD, DSc (Hons), DACVM, Department of Veterinary Pathobiology, College of Veterinary and Biomedical Sciences, Texas A&M University

Reviewed/Revised May 2020 | Modified Oct 2022

Modifying the Intestinal Microbiota in Animals

The presence of a massive resident bacterial population within the GI tract of animals has been recognized since the dawn of microbiology. It was not until comparatively recently that advances in microbiology and microbial genetics have provided a significant understanding of its importance. It is now recognized that signals from the intestinal microbiota regulate diverse body functions. Most notably, the microbiota increase energy yield from foods, provide us with essential micronutrients, and provide signals that optimize immune function.

Veterinarians have long been aware of the importance of microbiota because they work with ruminants, mammals that exploit microbial digestion as a way to obtain additional nutrients from otherwise indigestible plant material. The microbiota protect against colonization by pathogens and the overgrowth of endogenous pathobionts. They also influence the development of obesity, allergic diseases, inflammatory diseases, and some forms of autoimmune diseases. It is increasingly clear that the microbiota directly influence an animal’s tendency to mount cell-mediated immune reactions and thus allergies.

In healthy animals, the gram-negative Proteobacteria and Bacteroidetes and the gram-positive Firmicutes are the major bacterial phyla inhabiting the large and small intestines. The Firmicutes include Clostridiales and Lactobacillales. All of these organisms are well adapted to the intraintestinal environment and generally form very stable and complex populations.

The composition of the microbiota differs between individuals, between families, and most significantly between carnivores, omnivores, and herbivores. Because of their complex interactions and their stability, it may be very difficult to induce longterm changes in the composition of the microbiota.

The microbiota control pathogens by direct interactions. They release bacteriocins that kill competitors, they compete for essential nutrients, and they alter the conditions required for bacterial growth. They also control pathogens by stimulating host immunity and mucosal barrier function. Three factors—diet, microbiota, and the immune system—all interact to affect intestinal and immune function. It is increasingly recognized that disruptions in the microbiota (dysbiosis) can have adverse effects on health and disease resistance. This raises the question: can microbiota be modified to counter dysbiosis, optimize its functions, and improve animal health?

Dysbiosis and intestinal inflammation are interrelated. Dysbiosis may be a result of inflammation or a cause of it. Dysbiosis in dogs is reflected in decreased diversity and a reduction in the bacterial species used to generate short-chain fatty acids. These fatty acids protect the mucosa and stimulate the immune system. Dysbiosis also includes the term "small intestinal bacterial overgrowth" and the changes induced by oral antibiotic treatment. Dysbiosis is a common feature of many GI diseases. So, can the microbiota be manipulated to fight microbial infection, reduce allergies, or stimulate immunity?

Little is known about how the microbiota regulates colonization resistance. Feeding of commensals that are metabolically related to enteropathogens may enable them to outcompete the pathogens. Feeding prebiotics to boost the growth of natural competitors may also help. Can these prevent the overgrowth of pathogens such as enterotoxic Escherichia coli or Clostridium difficile? Can changes be induced by transplanting the large intestinal microbiota using fecal transplants?

The microbiota may be modified by five possible approaches:

  • changes in diet

  • administration of:

    • prebiotics

    • probiotics

    • antibiotics

  • microbiota transplants

Thus, an animal’s diet can be altered to permit the growth of beneficial bacteria through the use of prebiotics. Alternatively, specific beneficial bacteria (probiotics) can be fed to an animal in an effort to change the composition of the microbiota. Finally, antibiotics can destroy some components of the microbiota. These interventions often have an unclear or nonspecific goal, so it is difficult to determine their efficacy.

Microbiome Transplantation (Transfaunation) in Animals

One way to change the microbiota is to transfer intestinal contents from an animal with a healthy gut to an animal with dysbiosis. The variability of the donor microbiota and the potential presence of pathogens is, however, a cause for concern. It is more desirable to identify and characterize the specific bacteria that can constrain the growth of organisms such as C difficile.

It is believed that the mechanism by which fecal transplants act is by restoring the normal microbiota and increasing their diversity. In animals, the most common and longest established form of such a transplant is the use of fresh ruminal contents to restore ruminal function in cattle that have had a ruminal impaction or other event that has destroyed the ruminal microbiota. In these cases, it is unclear whether the beneficial results are due to the bacteria or to the many other organisms such as protozoa or viruses or to the provision of bile acids, vitamins, or proteins. Fecal transplants have proven successful in treating C difficile infections in humans.

Another widely employed technique is to deliver a mixture of organisms that outcompete selected intestinal pathogens such as Salmonella. This involves oral administration of diluted feces or complex bacterial mixtures to outcompete Salmonellae in poultry and pigs. Competitive exclusion techniques have been used in the poultry industry for many years in an effort to minimize Salmonella enteritidis infection in birds. In initial studies it was found that the normal microbiota of adult birds could prevent Salmonella colonization in chicks. The effect was ascribed to the obligate anaerobic bacteria that can be grown in a mixed culture. Thus, adult-type resistance to Salmonella could be established by administering adult microorganisms. This is called the Nurmi or competitive exclusion technique. It is believed that the effect is mediated by competition for nutrients and attachment sites as well as the production of antibacterial substances. A similar phenomenon is also seen by the observation that an established Salmonella serovar in a bird’s intestine can prevent subsequent colonization by other Salmonella serovars.

Prebiotics in Animals

Prebiotics are nondigestible compounds that, through microbial metabolism, modulate the composition or activity of the gut microbiota. Examples include wheat starch, beet pulp, inulin, nonstarch polysaccharides, fructo-oligosaccharides, and galacto-oligosaccharides. The same principle is involved in the feeding of high-fiber diets. These provide bulk, and when metabolized by the colonic microbiota, generate large amounts of immunostimulatory short-chain fatty acids. They also induce anti-inflammatory cells such as regulatory T cells. Prebiotics also serve to protect the gut epithelium and increase the mucus layer. They may increase numbers of lactobacilli and bifidobacteria in dogs and cats while reducing the numbers of potential pathogens such as E coli and C perfringens. The nutritional composition of feed is known to influence the composition of the microbiota as well as their metabolic products. For example, feeding high carbohydrate diets to dogs increases their fecal ammonia levels.

Probiotics in Animals

Probiotics are cultures of living bacteria that, when fed in sufficient amounts, may improve host health. Probiotics are widely used in people because the underlying rationale for their use is clear. They are also generally regarded as safe. It has been suggested that they reduce intestinal permeability, increase mucin production, increase production of defensins, generate short-chain fatty acids, stimulate IgA production, alter intestinal pH, and possibly even act as immunostimulants. Unfortunately, there is very little scientific data to substantiate many of these claims. Many claims have been exaggerated, and the regulatory authorities in the USA and Europe have had to act to control misleading labelling regarding unsubstantiated health claims.

Feeding probiotics is designed to provide large numbers of a single bacterium or a mixture of bacteria, in anticipation that these will colonize the intestine and improve or restore the microbiota in some manner. There are two major problems with this approach. First, the probiotic must contain sufficient living bacteria to cause a significant change, and second, the duration of any induced changes is totally unknown. The intestinal microbiota are generally very stable and resistant to major changes in their composition. Even if temporarily altered they will often revert to an original state.

Lactobacilli and Bifidobacteria are commonly used in commercial probiotics and appear to reduce susceptibility to diarrhea and respiratory tract infections. Others may also contain Bacilli and Streptococci. The effects of probiotics depend not only on the dose but also the precise strain and composition of the mixture fed. If these organisms are to be delivered to the intestine, they must also survive exposure to the stomach and bile acids. Although they may not survive long, some consider that transient colonization may be beneficial. Several probiotic mixtures have been shown to benefit mice and people, especially in reducing bacterial diarrhea.

Several small clinical trials have been undertaken in dogs. An example is the use of cultures of lactobacilli to reduce intestinal pH and thus reduce coliform populations. Ideally, this will also decrease inflammation and reduce inflammatory cytokine levels. Lactobacilli are, however, only a small component of the canine microbiota.

Some probiotics may reduce the severity of allergic diseases. For example, it is possible that some lactobacilli such as Lactobacillus rhamnosus may alter the Th1/Th2 balance in an animal and thus reduce the severity of canine atopic dermatitis by reducing specific IgE production.

Encouraging results have also been obtained in using probiotics to treat inflammatory bowel disease, protein losing enteropathy, and chronic diarrhea. In general, however, the microbiota contain a very complex mixture of both immunostimulatory and immunosuppressive bacteria, and although these can be carefully studied in mice, it is important not to extrapolate too generally to companion animal and livestock species. In general, improving animal health by modifying the gut microbiota is probably best effected by longterm dietary changes.

Antibiotics in Animals

Huge quantities of antibiotics are incorporated in livestock feed, where they act as growth promoters. It is claimed that they reduce pathogen load and subclinical disease, decrease growth-reducing metabolites (eg, NH3), and may decrease competition for nutrients and reduce inflammation, making more energy available. Their use, however, is controversial because of their potential to transfer antibiotic resistance to human pathogens.

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