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Is manure spreading disease-causing pathogens on your dairy?

John O’Neill for Progressive Dairy Published on 31 July 2020

The components of manure reflect the components of the cow’s internal and external environment, including a variety of potential disease-causing microorganisms.

Proper manure management and attention to detail as part of a whole-farm approach to pathogen control can help limit your herd’s exposure to these harmful pathogens.



Common pathogens in manure

The primary pathogens excreted by animals through manure include clostridial and coliform bacteria.

Clostridia are commonly found in soil, feed and the digestive tract and are shed into the environment through the cow’s manure. Since clostridial organisms produce spores, they can survive anywhere on the farm.

Clostridial bacteria shed by cows into manure include both toxigenic and non-toxigenic strains. One toxigenic strain, C. perfringens type A, is the major culprit in deadly hemorrhagic bowel syndrome (HBS) in cattle. Even at subclinical levels, C. perfringens type A and other clostridial strains can cause off-feed problems and digestive upsets that reduce animal performance and herd productivity.

Research shows C. perfringens is highly prevalent in manure from both calves and cows. Data from sampling of U.S. dairy herds by Arm & Hammer Animal and Food Production revealed 83% of cow manure samples and 72% of calf manure samples tested positive for C. perfringens.

Another common strain, C. butyricum, is non-toxigenic but can harm animals’ feed intake through its butyric acid byproduct that forms under poor silage fermentation conditions, reducing feed palatability and consumption. Other non-toxigenic strains, including C. beijerinckii and C. bifermentans, can impact rumen efficiency and gastrointestinal function.


Manure and bedding often contain high levels of coliform bacteria, including E. coli and Klebsiella spp. shed by infected cows. Most E. coli strains reside in dairy cattle without harmful effects, but some can infect the udder and cause mastitis. Klebsiella bacteria can also be shed in high concentrations in manure. Klebsiella pneumoniae is a common cause of clinical mastitis in dairy cattle.

Controlling the disease-causing organisms that may lurk in manure begins with an understanding of the pathogen cycle. Pathogens that exist in animals’ systems are excreted along with undigested nutrients. These organisms often stay alive in the manure pit or lagoon. When manure is applied to fields, there is a risk these pathogens will contaminate the growing crop. When animals eventually consume that crop in the form of grazed or harvested forage, pathogens return to the animals’ systems, and the cycle begins anew, with potentially damaging effects on cow health and productivity.

Proper manure application and storage

Broadcasting manure on standing crops or the soil surface increases the risk of pathogens coating the plant surface and continuing this pathogen cycle when the plant is consumed. One of the best ways to break the cycle is by injecting manure into the soil. Injection application methods prevent manure from contacting the plant surface where pathogens can be consumed by cows, through grazed or harvested forage.

Unfortunately, injecting manure can be problematic when solids settle to the bottom of deep manure pits or storage units and become too heavy and viscous for pumping and injection application. When this happens, producers often end up pumping the liquid portion out and using a front-end loader to remove the remaining solids from the bottom of the storage structure.

Used properly, manure pit additives can enhance manure digestion in the pit to improve microbial decomposition and prevent manure solids separation issues during storage. Enzyme-producing bacteria in certain additives can break down the solids into smaller particles for easier removal from the storage system. Increased microbial activity during the decomposition process can also decrease the levels of potential disease-causing organisms in the manure.

Manure additive products also tend to reduce odour by reducing ammonia production and volatile fatty acids that are byproducts of anaerobic decomposition of manure solids.


Keep in mind these tips when selecting a manure additive:

  • Check for high levels of enzyme-producing Bacillus bacteria strains, such as Bacillus licheniformis and Bacillus subtilus.

  • Ensure the product is easy to handle and apply.

  • Be aware of potentially caustic products on the market.

Reduce pathogen shedding

Another way to disrupt the pathogen cycle is to reduce the level of shedding by the animal into the manure by reducing the pathogen load within the animal. Ration ingredients containing beneficial Bacillus strains in targeted microbial solutions have been shown to significantly reduce the risk of pathogenic challenges, particularly those from clostridia.

For best results, it’s important to match Bacillus strains to the specific clostridial challenges in the operation. Feeding the proper Bacillus strains can directly inhibit toxigenic clostridia, help manage the gut microbial populations to decrease harmful pathogens and encourage growth of beneficial organisms. Properly selected strains also benefit the cow directly by controlling inflammation and maintaining a healthy gut lining.

When working to reduce the spread of pathogens in manure on your operation, don’t forget the basics of a clean, dry environment. This includes keeping stalls clean and scraping alleys and holding pens frequently to prevent transmission of harmful microorganisms from manure to animals.

When it comes to pathogen control, it’s important to take a whole-farm approach. Manage the dairy environment to limit animals’ exposure to harmful pathogens at every step of the operation, including manure handling, storage and application.

For more on controlling pathogen loads on your dairy, see “Whole-farm pathogen control starts with calves” by Gene Boomer, Progressive Dairy March 1, 2020.  end mark

John O’Neill
  • John O’Neill

  • Ruminant Account Manager
  • Arm & Hammer Animal and Food Production
  • Email John O’Neill