While it is well-known that the rumen has a complex microbiome (primarily bacteria and protozoa), the diversity of microorganisms found in the lower gut is less appreciated. However, the maintenance of a well-balanced microbiome in the lower gut may be as important to animal health and feed utilization as is the maintenance of a stable rumen microflora.

The concept that lower gut microflora play a role in health began about 100 years ago, but has only in the last quarter century received much study. Initially, it was thought that a major role of beneficial bacteria was due to their role in blocking pathogenic bacteria from occupying sites on the gut wall, the “competitive exclusion theory.” Work done by Bruce Watkins when he was a graduate student at Colorado State was one of the first studies demonstrating the concept.

Young chicks were raised in a sterile environment and fed Lactobacillus acidophilus and a pathogenic strain of Escherichia coli or E. coli alone. Morbidity and mortality were dramatically reduced when L. acidophilus was included in the feed. More recently, it has been shown that gene expression by enterohemmorhagic E. coli is modified depending on the microbiome present in the gut.

Since the gut is relatively sterile at birth, how do these organisms colonize the lower gut? The birth canal provides for early inoculation of the lower gut and, according to C. Yeoman et al, “is of critical importance to the morphological and immunological development of the gastrointestinal tract … providing neonatal resistance to pathogenic challenge.”

Appropriate inoculation of the hindgut appears to play a critical role in preventing some of the scouring seen in young calves. In addition to the provision of beneficial bacteria in feed (probiotic), it may also be necessary to provide “feed” for the bacteria. This can be either a fibrous or non-fibrous substrate (prebiotic), which bacteria may use as an energy source for growth.

Fermentation, which in the hindgut is anaerobic as it is in the rumen, produces the same volatile fatty acids as are found in the rumen. Butyric acid, or butyrate, is the preferred fuel of the cells lining the gut (colonocytes) and plays a role in maintaining gut health.

Poor nutrition may induce a cascade, ultimately leading to poor performance. In some species this has been attributed to a lack of butyrate-producing bacteria; addition of butyrate or butyrate-producing species has been shown to improve animal performance. Ruminal development may also be aided when butyrate concentrations are increased.

While most studies examine organisms and their effects (probiotics), it may not be necessary to provide organisms to see results, but the substrate on which they grow (prebiotics). It should be noted that, while some of these studies are in non-ruminants, results are especially applicable to pre-ruminant calves and are valid as well in animals with a functioning rumen.

Starch, either digestible or resistant to intestinal degradation, was fed to pigs. Pigs fed resistant starch had fewer pathogenic E. coli and pseudomonas species present and gene expression was altered as well when compared to those animals fed digestible starch.

Increasing evidence exists that not only can probiotics modulate host immunity and reduce the incidence and severity of disease, but prebiotics as well. A study in which mannobiose (a prebiotic) was fed indicated that the immune response was up-regulated (increased Immunoglobulin A) when animals were challenged and were less likely to become septic.

There are a number of reasons as to why the latter may occur; the presence of a stable non-pathogenic gut microflora may present a molecular pattern to the immune system that, by creating a low level of inflammation, prevents colonization by pathogenic bacteria. At the same time, because the immune response is always functioning, it may not overreact, reducing problems associated with sepsis.

Ultimately, the feeding of probiotics, prebiotics or a combination of the two (synbiotics) must result in increased efficiency; more feed energy will wind up in milk. According to Kirk Klasing (personal communication), the actual amount of energy required by the immune response is minimal; in fact, most of the drop in performance seen in sick animals is due to reductions in feed intake, rather than an increase in the cost of mounting a defense against an invading microbe.

If supplying beneficial bacteria in feed or providing substrate that allows for enhanced growth of beneficial bacteria keeps animals utilizing feed better, then it’s an area worth examining for your operation. PD