Win the Microbial War

Diversity in microbial populations, and the specific strains present or absent, can influence cattle health and overall performance.
Diversity in microbial populations, and the specific strains present or absent, can influence cattle health and overall performance.
(Ascus Biosciences)

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, and others 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 last 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 may 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, PhD, 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 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, where some cause enteric disease and others can influence 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.

Tests in a variety of animals show that low microbial diversity can limit an animal’s ability to utilize complex carbohydrates, growth and resistance to respiratory disease. Scientists 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. Research in pigs has shown that a single antibiotic treatment in a young pig can affect its microbiome for 25 weeks – 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.

Attack the Source of Acidosis


The use of microbial products in rumen microbiome management offers tremendous potential for improving animal health and performance, and a growing number of well-established companies are investing in research to develop products and processes that provide measurable benefits.


Kansas-based MS Biotec began marketing its Lactipro advance® probiotic containing Megasphaera elsdenii bacteria in 2010.  The company continues to invest in field trials to measure outcomes at multiple production stages.  MS Biotec Chief Commercial Officer Carl Guthrie, DVM, and Celine Aperce, PhD, the company’s Director of Research & Development and Quality, say the product fits in several production segments or stages.


The organism was first isolated from the rumen of a dairy cow in South Africa 25 years ago. On the market since 2010, the mode of action of Megasphaera elsdenii is well-known, Aperce says. It aggressively metabolizes lactic acid, making it effective in regulating rumen pH and preventing digestive disorders.


Lactic acid is produced in the rumen when cattle consume highly-fermentable feedstuffs.  It can become problematic when feedlot cattle are transitioned to high-energy feeds, or when cows are turned out onto crop residue fields.


Accumulation of lactic acid decreases rumen pH and leads to disorders such as acidosis and founder. Drenching cattle with live M. elsdenii introduces a bacterial population capable of utilizing lactic acid and preventing its accumulation.


The bacteria is anaerobic though, meaning it must be handled properly from fermentation through packaging, shipping and administration, Guthrie says. The product is administered through an oral drench, as the live culture would lose viability if exposed to oxygen. The company packages the liquid product in flexible, poly-foil pouches contained in a box – similar to a boxed wine – to allow animal application without exposing remaining product to air.


The feedlot receiving period serves as a prime example of a time where gut health can make or break long-term health and performance, Guthrie says. Research and field experience have shown that administering M. elsdenii at initial processing can help calves transition to higher-energy rations with fewer disruptions in feed intake or cases of ruminal acidosis. Using the product at receiving can help shorten the step-up period from 20 to 30 days down to 10 to 15 days. Some research indicates the product could reduce respiratory morbidity by helping control acidosis in newly received high risk calves.


Cattle feeders also find that administering the probiotic at re-implant time can help prevent the drop in feed intake cattle often experience, which can lead to digestive disorders when they subsequently overeat. In addition to its existing portfolio of research study results, MS Biotec is currently developing large-pen commercial feedlot trials to quantify the effect at re-implant.  The studies are scheduled to take place this summer and fall.


Likewise, in feedlots that hold cattle in hospital pens, where they typically consume a high-roughage diet, the probiotic can prevent digestive problems when the animals return to their home pens.


Guthrie also notes the product has seen considerable use in cattle moving to harvested grain fields in the fall and winter. That transition can result in digestive problems when larger-than-usual amounts of grain remain on the ground. While trial data remains sparse, Guthrie says producers have seen good success when administering the probiotic prior to turnout on stubble, especially when they see excess grain in the field.

Selecting the best bugs

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,” said 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 that 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 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 and select a core set of common microbial rumen strains distinguishing high performing animals from their lesser performing peers for both dairy and feedlot applications

Product development involves isolating and culturing the selected native bacterial and fungal strains from rumen content of healthy animals. After isolation, scientists stabilize and preserve microbes for inclusion in new microbial products.

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

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 roles of specific microorganisms, their management will become increasingly effective as a tool for improving health and performance.

For more information on the cattle microbiome and uses of microbial management for cattle health and performance, see these articles on

Endomicrobial Ecology Could Harness Diversity of Cattle Microbiome

USDA Funds Study of Plant and Animal Phenomics and Microbiomes

Dissecting the Microbiome

Probiotic Research Could Address Nitrite Poisoning and Methane



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