The gastrointestinal microbiota, that is the collection of all microorganisms found in the gastrointestinal tract, has long been recognized to play a crucial role in gastrointestinal health. It has also long been hypothesized that alterations in the intestinal microbiota can lead to gastrointestinal and systemic disease. Elie Metchnikoff was the first to hypothesize that consumption of fermented foods, such as yogurt, sauerkraut, or cheese, would elicit a beneficial effect by way of altering the gastrointestinal microbiota. However, today it is widely recognized that most of these foods do not contain sufficient numbers of bacterial colonies to successfully modify the gastrointestinal microbiota. More recently, probiotics, that is formulations of life microorganisms that are part of the normal intestinal microbiota, have become commercially available and a wide variety of studies have been undertaken to evaluate their usefulness in human patients with gastrointestinal diseases. Promising results in humans have led to the development of specific probiotics for use in dogs and cats and the study of their clinical efficacy.

The microbiota

The intestinal microbiota is made of a wide variety of microorganisms, including bacteria, viruses, and fungal organisms. Most attention has been given to the intestinal bacterial ecosystem, which is made up of a complex mixture of a wide variety of bacterial species. Traditional studies describing the intestinal bacterial ecosystem have employed traditional culture techniques. Unfortunately, such studies are associated with problems in reproducibility. For example, a variety of studies reported the physiologic bacterial ecosystem in the proximal small intestine of dogs, but different studies found a preponderance of different bacterial species. It has since been recognized that a variety of factors, such as location, breed, age, collection method, culture media, culture conditions, and others all play an important role in the results of culture-based studies. However, the true diversity of the intestinal bacterial ecosystem became evident only recently with the advent of new micromolecular technologies. These newer technologies have revealed a far greater diversity of the bacterial ecosystem in the intestinal tract than previously assumed and have also shown that fungal organisms, such as Pichia spp., Cryptococcus spp., Candida spp., and Trichosporon spp. are far more frequently present in the intestinal tract of healthy dogs than previously believed. Using these new methodologies it has now been estimated that the intestinal bacterial ecosystem is made up of more than 1000 different bacterial species. These new studies are also crucial in studying the microbiota in patients gastrointestinal diseases.

This ecosystem is initially established during birth and continues to develop during suckling. The impact of the intestinal microbiota and the bacterial ecosystem has been well established by studies in germ-free rodents. These rodents show a wide variety of morphological and physiological alterations that overall equate to a state of compromised intestinal function and immunity. In healthy animals the physiologic microbiota, and most prominently the bacterial ecosystem, has several important functions. Firstly, it protects the host against pathogenic bacteria, by competing for oxygen, luminal substrates, and space, but also by synthesizing and releasing substances that inhibit bacterial growth, so-called bacteriocins. Intestinal bacteria also produce short-chain fatty acids by metabolizing dietary components that are often non-digestible for the host. In turn, these short chain fatty acids serve as an important energy source for the intestinal mucosa, leading to epithelial cell proliferation and mucosal growth. Members of the intestinal bacterial ecosystem also synthesize a variety of vitamins, including riboflavin (vitamin B2), biotin (vitamin B7), folic acid (vitamin B9), cobalamin (vitamin B12), and vitamin K. It is important to note, however, that physiologically, the synthesis of some of these vitamins, for example cobalamin, is not of any significance to the host as the synthesis may occur distally to where the vitamin can be absorbed. Finally, intestinal bacteria also play a crucial role in the development of the intestinal immune system. They stimulate said intestinal immune system, which plays a crucial role in overall host defense throughout all stages of life.