Read the Progressive Dairyman Canada digital edition

Troubleshooting feed hygiene challenges

John P. Goeser for Progressive Dairyman Published on 31 January 2019
it’s the feed hygiene (or rather lack thereof) that triggers the issue

In 2007, my career path was somewhat redirected after working with a high-profile dairy herd’s health and performance challenge.

My memory is like a goldfish in that I often do not remember fine details, yet this specific situation and details are tattooed within my mind forever forward due to our inability to identify the causative factors behind the dairy recognizing digestive upsets and hemorrhagic bowel symptoms.



Unfortunately, the dairy lost a few of the herd’s “family” following gastroenteritis (intestinal hemorrhaging).

Generally, we should be driven to advance our understanding of that which isn’t immediately clear. We should strive to learn, and then hopefully make better decisions going forward.

I went to graduate school with the aim of learning how to approach issues that don’t have clear answers. Coming out of the situation described above, we came away with far more questions than answers. I also came out of the situation with a desire to better understand feedborne factors that could impact animal health (beyond mycotoxins, mold or yeast).

Dairy farm management, feed quality and nutrition formulation have advanced considerably the past decade; however, gut health challenges seem to persist.

In fact, I wonder at times if the frequency is increasing due to dairy cattle eating greater intakes, producing greater levels, potentially stressed in different ways and then also recognizing that microbial counts (mold and yeast in this case) have increased over the past several years across much of North America.


My perceptions may also be biased in that I’ve had increasing opportunity to provide technical support in this area, working with nutritionists, veterinarians and key technical support staff throughout the world. We recognize there is a massive amount to learn, yet have developed troubleshooting paths to work through when confronted with unexplained digestive upsets and gut health challenges.

Historically, we investigated feed (i.e., corn silage, haylage or high-moisture corn) mold and yeast counts when suspecting feedborne hygiene challenges. Then, the next step has been to assess an indicator mycotoxin (i.e., vomitoxin) or a mycotoxin panel in hopes we’d find answers.

There are numerous situations, though, where this approach hasn’t provided clear direction, and with the continued learning aim in mind, my impression now is that we should go about the troubleshooting process differently.

During troubleshooting, I now recommend starting with the TMR and then working backward to identify contamination points or feeds. TMR sampling comes with known issues that Bill Weiss, professor in the department of animal sciences at Ohio State University, and others have described; however, resulting TMR hygiene challenges aren’t always feedborne (i.e., from haylage or corn silage). Thus, sampling individual feeds can miss critical contamination points.

Feed delivery equipment (i.e., tires, buckets or mixer wagon), birds or other pests, or rotten feed not cleaned out of the feedbunk are all contamination points that can negatively affect animals beyond forages or grains from the silo.

Then with a TMR sample in hand, we need to open our minds beyond the typical fungal contamination points (mold, yeast and mycotoxin) we’ve focused on to this point.


Years of research in both veterinary and animal science journals has demonstrated that opportunistic or pathogenic bacterial contaminants can have detrimental effects on animal health and performance.

When troubleshooting feed hygiene challenges, we need to merge veterinary and nutritional sciences and work together to also consider negative bacterial loads in feed.

Clostridia spp. loads in feed have gained recent attention as a number of nutrition solutions are coming to market to help combat clostridia spp. challenges. Yet these species represent just a fraction of the potentially harmful bacterial challenges farms can experience.

Salmonella, enterococcus, E. coli, listeria, shigell and klebsiella spp. are other exemplary bacterial genera that one could also look at in the TMR. An enterobacteriaceae count, much like a mold and yeast count, will quantify the total sum of these organisms (and more genera from within this family).

Future research will better help us understand TMR bacterial load variation, but generally, in my mind, a clean TMR shouldn’t have any of these bacterial species present, much like we don’t want any salmonella or E. coli on our food.

Reflecting back to the story that kick-started my interest in this area, as well as the start of this article, we must continue looking to answer questions to which we don’t yet have clear answers. Our industry has an immense amount to learn about feed hygiene.

I expect feed hygiene and cleanliness will be a rapidly evolving area to consider and then manage on-farm for improved health and efficiencies in performance the next five to 10 years. Bring your veterinarian, nutritionist and other key industry technical service representatives to the table and jump-start the conversation.  end mark

PHOTO: When dairies have a herd health issue, often the investigation begins with the TMR – and for good reason. But often, it’s not the nutritional ingredients at fault; it’s the feed hygiene (or rather lack thereof) that triggers the issue. When herd health issues arise, include the veterinarian, the nutritionist and other technical advisers in the investigation to get to the heart of the matter. Staff photo.

References omitted but are available upon request. Click here to email an editor.

John Goeser earned a Ph.D. in animal nutrition from the University of Wisconsin – Madison where he currently serves as an adjunct professor in the dairy science department. He also directs animal nutrition, research and innovation efforts at Rock River Lab Inc. based in Watertown, Wisconsin.

John P. Goeser
  • John P. Goeser

  • Director of Nutrition, Research and Innovation
  • Rock River Laboratory Inc.
  • Email John P. Goeser