What is the Microbiome, and Why Should Organic Dairy Producers' Care?

By 1Chris Dean, 1Felipe Pena Mosca, 1Tui Ray, 1Bradley Heins, 2Pablo Pinedo, 3Vinicius Machado, 1Luciano Caixeta, 1Noelle Noyes

November 2020 


Since the 1960s, the Five-Point Mastitis Control Plan has remained the “gold standard” for reducing mastitis incidence rates and high somatic cell counts on conventional dairy farms and continues to be revised as new information and tools become. However, despite widespread adoption of this plan, mastitis remains one of the costliest diseases affecting dairy producers, and ultimately, udder health. Organic producers are in a particularly difficult situation because they are unable to benefit from the use of some of these tools – antibiotics, for example. This simple observation implies that organic producers are most in need of new tools that can further support udder health and productivity on organic dairy farms. In partnership with scientists across the country, our group at the University of Minnesota works on the challenge of mastitis on organic dairy farms, using one of the most promising tools at our disposal -- the microbiome. You may have heard the term “microbiome” thrown around before, but what does it really mean, and why should you -- as a dairy or livestock producer -- really care? 

History of the Microbiome

By far, most of our knowledge about the microbiome and health stems from research done in humans; hence, we will begin our journey into the microbiome starting from there. Though it may be somewhat unpleasant to think about, the human body is home to trillions of microorganisms. These range from single-celled organisms like bacteria and protozoa, to more complex organisms like fungi or even viruses. Collectively, these microorganisms make up what is often referred to as the “human microbiome” and they are ubiquitous within and on the human body. Herein lies an important question: why are these microorganisms present and what are they doing? We can admit that what we know and understand about the function of these microorganisms is limited, but what we do know is that they play a critical role in human health. Perturbations to the microbiome can contribute to a number of diseases, such as obesity, inflammatory bowel disease and diabetes. 

Applications of the Microbiome

Interestingly, the human microbiome can play a dual role in human health, acting as the root of disease, or acting as a “helper” to rid the body of disease. Let’s illustrate this idea with a real-life example. Clostridium difficile infection (CDI) is a major cause of hospital-acquired infections in the U.S. and is often preceded by the use of antibiotics, which are known to disrupt the human gut microbiome -- the microbes inhabiting the human gastrointestinal tract. In other words, the good microbes -- which normally keep the bad microbes in check -- are destroyed, giving the bad microbes the opportunity to take over. Unfortunately, treatments for CDI are limited and relapse rates can be quite high, highlighting the need for new tools -- one of which is, you guessed it, the microbiome. 

The idea is pretty simple and may be something you are already familiar with. Donor feces from a healthy individual is inserted inside the gastrointestinal tract of an individual with CDI, with the goal of restoring a healthy balance between the good and bad microbes. This simple procedure has continued to show positive results, with a majority of individuals undergoing the procedure experiencing eventual resolution of CDI after follow-up. If you’re a dairy producer or veterinarian, this may sound familiar: indeed, it is similar to something that dairy producers and veterinarians have already been doing for over a century: rumen transfaunation. This relatively simple procedure involves transferring microorganisms from the rumen of a healthy animal to a diseased animal to treat rumen-related disorders. Similar to the success of microbiome transplants in human CDI patients, the healthy rumen microbiome usually establishes itself quickly within the diseased rumen, thus promoting greatly improved health in the cow itself. 

Challenges in Microbiome Research

These success stories make it clear that the microbiome can be an extremely powerful tool for the treatment of both human and animal diseases. However, it is important to note that in both cases, the microbiome of the diseased animal or human is dramatically imbalanced. In other words, these microbiomes are nearly completely decimated -- much like a forest after a forest fire. Without much competition from other microbes, it is relatively easy for the unhealthy microbes to take root and flourish within these decimated landscapes. But what about situations when that microbiome imbalance is less intense? Unfortunately, it turns out that in these situations, it’s not quite as easy to re-establish a “healthy” microbiome. But we -- and many others -- are working hard to overcome this challenge, because doing so would open up a vast array of new microbiome-based tools for support of livestock health and performance, using bovine mastitis as a test case. 

Project Goals, Outcomes and Collaborations

Specifically, our group is trying to understand how the normal skin microbiome of a cow’s udder may protect against mastitis. To answer this important question, we have partnered with organic dairy farmers across the U.S., all of whom are committed to helping discover new ways to curb mastitis in dairy cows. Equally important is our diverse research team, with individuals at the University of Minnesota, Texas Tech University, Colorado State University, and Oregon State University. This team consists of faculty trained in veterinary epidemiology and dairy production; graduate students trained to analyze and interpret large and complex biological datasets from livestock systems; and numerous student and lab workers. One of the major lessons of microbiome research is the need for integrated yet diverse teams, with expertise that spans from on-the-ground livestock production to molecular biology and computer science. We are fortunate to have assembled such a team, all of whom are passionate about dairy cow health and welfare. This team is dedicated to ensuring that the livestock community benefits from microbiome-related advances. We hope to bring these discoveries to the livestock producer community through several channels, including upcoming webinars and YouTube videos. For now, a good place to start is our website.

If you are interested in learning more about the microbiome, check out the webinar that we presented for eOganic entitled “The microbiome: what is it, and how might it impact organic dairy production?”

1University of Minnesota, 2Colorado State University, 3Texas Tech University