Encourage the “Good Bugs”

As scientists learn more about the hundreds of species of microorganisms that thrive in and on animals, microbiome management could become the next giant leap in improving animal health and performance efficiency, along with food safety and quality.

We know that cattle, as well as humans and all animals, support huge populations of bacteria and other microorganisms in their digestive tracts, mouths, airways, skin and other tissues. Some are known to be beneficial and some are pathogenic. Some pathogens are benign in certain locations but cause sickness when they reach other tissues. Many of these microbes though, are either benign or perform functions we do not yet understand.

“The microbiome is a collection of different microorganisms that we find in the intestinal tract of animals, and we know these microorganisms are essential to immune development,” says Christopher Chase, DVM, Ph.D., at South Dakota State University. “Understanding how they interact with the gut, and particularly the epithelium of the gut, is really important.”

In the past five to 10 years, Chase says, researchers have shown the epithelial cells of the gut and respiratory tract act as an immune organ. “This means the cells are not just there to absorb and secrete, but also pick up signals—particularly signals from the microbiome.” Some types of probiotics and prebiotics can help support gut health. In addition, these additives might also help send signals to the epithelium to maintain the anti-inflammatory response.

“As we look at managing immunity,” Chase adds, “it’s important that we think about feeding probiotics and prebiotics that will help us with health, managing hydration and having good intakes. If we do all those things, we’re going to help manage disease and the inflammatory response.”

Megan C. Niederwerder, DVM, Ph.D., conducts research on swine disease and the role of the microbiome at Kansas State University. Scientists have just begun to tap the potential of understanding and manipulating the microbiome in cattle, she says. Researchers have published about 700 microbiome studies in cattle, compared with thousands of studies on the human microbiome, which still is not well understood. Studies in livestock have examined the role of various microbes in the digestive tract, oral, nasal and lung tissues and skin.

Much of the study has focused on organisms colonizing the gastrointestinal tract, and while some cause enteric disease, some others can be involved in diseases in other tissues, such as in the lungs, Niederwerder says. Many, of course, are beneficial and necessary for normal digestion, absorption of nutrients and immune function.

Diversity in the microbiome generally is positive. Tests in animals have shown low diversity can limit an animal’s ability to use complex carbohydrates. Low diversity in the gut microbiome in cattle appears to be associated with lower weight gains and a higher incidence of respiratory disease, and feeding probiotics can, in some cases, improve gains and overall health.

Scientists also have found they can, with fecal transplants from obese mice, make skinny mice obese, all with the same diet, suggesting the obese mice carry populations of microbes that increase their capacity to harvest energy from their feed.

On the other end of the scale, scientists have raised “germ-free” mice lacking the normal gut microbiome and found multiple negative effects on immunity. Research in pigs has shown as little as one antibiotic treatment in a young pig can affect its microbiome for 25 weeks or virtually its entire life.

To explore the relationship between the microbiome and disease in pigs, Niederwerder and her team designed a series of experiments generating results showing correlation between microbiome and performance. They also identified one strain of E. coli that was particularly high in the best-performing groups.

Selecting the Best Bugs

Several reputable companies now market microbial feed additives for various applications in cattle, with a growing pool of research data to support their claims of benefits. One relatively new company, Ascus Biosciences, has focused on “endomicrobial ecology,” an emerging science harnessing the natural diversity within an animal’s microbiome to improve animal health and performance.

“There is a tremendous demand for more natural products that help solve some of the most important problems within animal systems,” says Mike Seely, CEO and co-founder of Ascus; “We believe that identifying the right microbes from the ground up represents the next wave of innovation for our industry.”

Seely explains producers use genetic information and breeding to select cattle for better performance, so his company saw an opportunity to do the same with the cattle microbiome. Toward that goal, Ascus has generated the largest rumen microbiome dataset in the world, identifying more than 50,000 unique rumen microbial strains from more than 6,500 dairy cow rumen samples and 2,000 feedlot cattle rumen samples. Ascus computer scientists then analyzed the relationships between these microbes and how they affect animal function and health. Further analysis of these samples enabled researchers to identify a core set of common microbial rumen strains distinguishing high-performing animals from their lesser-performing peers for both dairy and feedlot applications. Despite the variability in lifestyle and animal genetics, a core microbiome common to all cattle exists. Potential product strains were selected from the core microbiome to ensure ubiquitous efficacy across all breeds, geographies, management styles and diets.

“In this process, we select and use naturally occurring strains of microbes, without any genetic modification,” Seely says. With the science being based on the animal’s microbiome, the innovations developed using endomicrobial ecology provide a naturally safe and effective approach to supporting animal health and performance. Once the desired microbes are selected computationally, the final product development process involves isolating and culturing the selected native bacterial and fungal strains from rumen content of healthy animals. After isolation, the microbes are stabilized, preserved and then formulated into new microbial products that are shelf stable and drop directly into existing farm management practices.

When talking about feedlot cattle, Seely says that although diet and lifestyle result in severe rumen microbiome shifts as the animals move from grazing (a more cellulolytic-rich diet) to a feedlot environment, the populations of microbes are relatively consistent within each feedlot production system despite breed differences and environmental variation between operations. In feedlot cattle, Ascus is looking closely at the ability of target microbial strains to metabolize waste byproducts of microbial fermentation into energy sources the animal can use. Beyond the performance benefits to the animal that they have seen in field trials, they suspect that these novel microbes compete directly against methanogens for methanogenic precursors, which in turn would reduce methane production. A win-win for the animal, the producer and the environment.

Ascus currently offers a microbial feed additive for lactating dairy cows and is planning to introduce its microbial product for cattle feeders to use during the step-up process to high-energy diets soon.

Ongoing research suggest that as we learn more about the microbiome and the positive or negative roles of specific icroorganisms, management of the microbiome will become increasingly effective as a method for improving health and performance.