Arm & Hammer Animal and Food Production
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Innovative ways to improve resilience in dairy herds. 

Posted March 14, 2023 by Dr. Ben Saylor, Dairy Technical Services Manager

The most successful dairies demonstrate resilience, achieving consistent, high-level performance in the face of challenges. They do this by limiting the pressures cows face—and preparing for those beyond anyone’s control.

Feed hygiene’s role in building resilience.

Building resilience in cows requires focus in three areas: 

  • Controlling pathogens within the gastrointestinal tract
  • Optimizing rumen function
  • Establishing hindgut integrity

Often overlooked in feed management strategies, feed hygiene can directly affect all three areas. Hygienic feed is free of pathogens and toxins that could prove detrimental to health and performance.

Unfortunately, poor feed hygiene is not an isolated challenge. Pathogens and toxins within feed can interact with other stressors to cause digestive disorders and productivity losses. For example, common challenges like heat stress (Koch et al., 2019), feed restriction (Kvidera et al., 2017), or sub-acute ruminal acidosis (SARA; Emmanuel et al., 2007) have all been shown to increase the permeability of the intestinal epithelium. When the intestinal epithelium is unable to protect the host from the environment, pathogens and toxins enter systemic circulation.

Since the gastrointestinal tract is home to approximately 75% of the immune system (van der Heijden et al., 1987), this insult can cause an inflammatory response in the host. In addition to the negative effects of pathogens and toxins in the cow, systemic inflammation is known to have a profound energetic cost, >2 kg of glucose per day (Horst et al.; 2021), competing with more beneficial processes such as milk production and reproduction.

Bad actors threatening feed hygiene.

The total mixed ration (TMR) is the primary source of pathogens and toxins threatening cow health and productivity. These bad actors can be introduced in the field, during storage and feed-out, or throughout the course of feed mixing and delivery.


Clostridia are present everywhere in the environment. These gram-positive, spore-forming anaerobes can have numerous effects on the digestive health of dairy cattle. We surveyed dairies across the country, analyzing 30,000 fecal samples and 7,000 feed samples, and found that 98.6% of fecal samples and 84.7% of feed samples contained clostridia (Bretl et al., 2022). It was also observed that 78.5% and 33.6% of fecal and feed samples, respectively, contained C. perfringens, a pathogenic species of clostridia known to contribute to hemorrhagic bowel syndrome (HBS) in cattle.

Clostridia found in dairy systems are generally classified into one of two groups:

  1. Toxin-producers: The most common toxin-producer is C. perfringens, which is a known contributor to hemorrhagic bowel syndrome (HBS) in dairy cattle. C. perfringens proliferates in the lumen of the intestine to the point that it overwhelms the normal gut microflora (Goossens et al., 2017). It then produces enzymes that cause the breakdown of the mucus layer protecting the intestinal epithelium. Without a functional mucus layer, toxins produced by C. perfringens can bind to the intestinal epithelium, inducing an immune response. The subsequent inflammation leads to sloughing of the epithelium, allowing toxins present in the gastrointestinal tract to enter systemic circulation, ultimately leading to intestinal hemorrhaging and death.
  2. Solvent-producers: Clostridium beijerinckii and C. bifermentans are the most common solvent-producing clostridia found in dairy systems. These organisms produce solvents like acetone, ethanol and butanol which could negatively impact ruminal fibrolytic bacterial populations and rumen function. Our research has found that inhibiting solvent-producing clostridia in the gastrointestinal tract of dairy cows leads to greater abundance of Ruminococcus and Fibrobacter spp. in the rumen (Maylem et al., 2013 – Article under review). 

Salmonella and E. coli

Salmonella and E. coli are found in a cow’s digestive tract and should not be present in feed. Their presence in silages suggests a poor fermentation or potential manure contamination. If found in the TMR, contamination has likely occurred during feed mixing or delivery. Salmonella and pathogenic strains of E. coli can cause many health and performance challenges (Peek et al., 2018).

Yeasts and Molds

Spoilage often results from high levels of yeasts and molds in silages and TMR. Counts greater than 100,000 CFU/g indicate spoiled feed (Kung et al., 2018). Yeasts and molds can contribute to poor aerobic stability of silages and TMR, and represent a loss of nutrients that can lead to inconsistent intakes and performance. Santos et al. (2014) demonstrated that high counts of yeasts isolated from high-moisture corn can reduce 24 h in-vitro NDF digestibility of a TMR.


Mycotoxins are secondary metabolites produced in feeds by various species of molds. A 2012 survey found that 81% of livestock feed samples collected from the Americas, Europe and Asia tested positive for at least one mycotoxin (Rodrigues and Naehrer, 2012). Many are degraded or inactivated by the rumen microbiota (Gallo et al., 2015). However, high ruminal passage rates of modern dairy cows may reduce microbial detoxification (Pantaya et al., 2016).

Taking action to build more resilient herds.

Dairy farmers and nutritionists have two options for protecting their herds from pathogens: limit the cow’s exposure to pathogens and toxins, and control those that still find their way into the gastrointestinal tract.

  • Strategy #1: Limit exposure to pathogens. As shared above, improving feed hygiene can significantly limit exposure. To achieve it, consider adopting all 10 recommendations for improving feed hygiene in our feed hygiene checklist.
  • Strategy #2: Control pathogens and toxins inside the cow. CERTILLUS™ Perform features beneficial strains of Bacillus to reduce clostridial loads in the gastrointestinal tract and improve hindgut integrity. And the Refined Functional Carbohydrates™ (RFCs™) in CELMANAX™ have been shown to bind pathogens and mycotoxins in the gut.

The proof is in the research.

Our research with 77 dairies and 230,000 cows across 18 states looked at the shift in risk for total clostridia and C. perfringens challenges before and after feeding CERTILLUS Perform. On average, an 89% increase in the number of fecal samples classified as low risk for total clostridia, and a 13% decrease in the number of fecal samples classified as high-risk for total clostridia was observed following CERTILLUS supplementation. This study also found that CERTILLUS Perform supplementation contributed to a 20% increase in the number of fecal samples classified as low risk for C. perfringens, and a 26% decrease in the number of fecal samples classified as high-risk for C. perfringens. Other research from ARM & HAMMER has shown that Bacillus in CERTILLUS Perform increase the expression of tight junction proteins in the small intestine and can increase gut barrier integrity (as measured by transepithelial electrical resistance).

Research has also documented the effect of feeding RFCs on agglutination of Salmonella and E. coli. In one study, the number of unbound S. Newport, S. enteritidis, S. Dublin and S. cholerasius was reduced in the presence of CELMANAX (Jalukar et al., 2009). In the same study, the number of unbound E. coli F18 was reduced in the presence of CELMANAX. Refined functional carbohydrates have also been shown to reduce epithelial cell damage (as measured by cytotoxicity score) caused by aflatoxin, T-2, DON, zearalenone, and fumonisin B1 (Baines et al., 2014).

With improved feed hygiene and innovations like CERTILLUS and CELMANAX, dairy farmers can better prepare their herds for the challenges that silently steal productivity.




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Baines, D., S. Erb, R. Lowe, K. Turkington, E. Sabau, G. Kuldau, J. Juba, L. Masson, A. Mazza, and A. Roberts. A prebiotic, CELMANAX, decreases Escherichia coli O157:H7 colonization of bovine cells and feed-associated cytotoxicity in vitro. BMC Research Notes, 2011, 4:110.

Bretl, V. G., J. S. Thompson, A. H. Smith, and T. G. Rehberger. 2022. Survey of Clostridia levels in dairy cows and feed across the United States. J. Dairy Sci. 105(Suppl. 1):336. (Abstr.)

Emmanuel, D. G., K. L. Madsen, T. A. Churchill, S. M. Dunn, and B. N. Ametaj. 2007. Acidosis and lipopolysaccharide from Escherichia coli B:055 cause hyperpermeability of rumen and colon tissues. J. Dairy Sci. 90:5552–5557.

Gallo, A., G. Giuberti, J. C. Frisvad, T. Bertuzzi, and K. F. Nielsen. 2015. Review on mycotoxin issues in ruminants: Occurrence in forages, effects of mycotoxin ingestion on health status and animal performance and practical strategies to counteract their negative effects. Toxins (Basel) 7:3057–3111.

Goossens, E., B. R. Valgaeren, B. Pardon, F. Haesebrouck, R. Ducatelle, P. R. Deprez, and F. Van Immerseel. 2017. Rethinking the role of alpha toxin in Clostridium perfringens-associated enteric diseases: a review on bovine necro-haemorrhagic enteritis. Vet Res. 48:9.

Horst, E. A., S. K. Kvidera, and L. H. Baumgard. 2021. Invited review: The influence of immune activation on transition cow health and performance—A critical evaluation of traditional dogmas. J. Dairy Sci. 104:8380–8410.  

Jalukar, S., J. Oppy, and M. Holt. In-vitro assay to evaluate ability of enzymatically hydrolyzed yeast containing MOS to bind enteropathogenic bacteria. Presented as an abstract at the Midwest Animal Science Meeting, Des Moines, Iowa, March 2009, Abstract #228.

Koch, F., U. Thom, E. Albrecht, R. Weikard, W. Nolte, B. Kuhla, and C. Kuehn. 2019. Heat stress directly impairs gut integrity and recruits distinct immune cell populations into the bovine intestine. Proc. Natl. Acad. Sci. USA 116:10333–10338.

Kung, L., R. D. Shaver, R. J. Grant, and R. J. Schmidt. 2018. Silage review: Interpretation of chemical, microbial, and organoleptic components of silages. J. Dairy Sci. 101:4020–4033.  

Kvidera, S. K., E. A. Horst, M. V. Sanz Fernandez, M. Abuajamieh, S. Ganesan, P. J. Gorden, H. B. Green, K. M. Schoenberg, W. E. Trout, A. F. Keating, and L. H. Baumgard. 2017d. Characterizing effects of feed restriction and glucagon-like peptide 2 administration on biomarkers of inflammation and intestinal morphology. J. Dairy Sci. 100:9402–9417.  

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Pantaya, D., D. P. Morgavi, M. Silberberg, F. Chaucheyras-Durand, C. Martin, K. G. Wiryawan, and H. Boudra. 2016. Bioavailability of aflatoxin B1 and ochratoxin A, but not fumonisin B1 or deoxynivalenol, is increased in starch-induced low ruminal pH in nonlactating dairy cows. J. Dairy Sci. 99:9759–9767.  

Peek, S. F., S. M. Mcguirk, R. W. Sweeney, and K. J. Cummings. 2018. Infectious diseases of the gastrointestinal tract. Pages 249-356 in Rebhun’s Diseases of Dairy Cattle. 3rd Edition. S. F. Peek and T. J Divers, ed. Saunders, Philadelphia, PA.  

Rodrigues, I., and K. Naehrer. 2012. A three-year survey on the worldwide occurrence of mycotoxins in feedstuffs and feed. Toxins (Basel) 4:663–675.  

Santos, M. C., A. L. Lock, G. D. Mechor, and L. Kung Jr. 2014. Effects of a spoilage yeast from silage on in vitro ruminal fermentation. J. Dairy Sci. 98 :2603–2610.  

van der Heijden, P. J., W. Stok, and A. T. J. Bianchi. 1987. Contribution of immunoglobulin secreting cells in the murine small intestine to the total “background” immunoglobulin production. Immunology 62:551–555.  



About Dr. Ben Saylor

Dr. Saylor  has extensive experience in ruminant nutrition including his current role as a dairy technical services manager at Arm & Hammer Animal and Food Production. Dr. Saylor earned his bachelor’s degree in animal sciences from the University of Arizona, a master’s degree in ruminant nutrition from Kansas State University and a Ph.D. in ruminant nutrition from the University of Wisconsin-Madison.



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