Organic ingredient sourcing for optimal nutrition in dogs and cats

A look at the intestinal microbiome and why fresh organic food is the healthiest choice for your animal patients.

Many holistic or alternative veterinarians still express some angst regarding their recommendations on the type of food clients should feed their pets. Confusion about what constitutes the appropriate diet for dogs and cats comes from an interesting convergence of food production and labeling politics; marketing strategies in OTC pet foods and veterinary prescription diets; food journalism as it applies to animal and human health; and the science of nutrition. The science of nutrition, rather than adding clarity to the discussion, has obscured our understanding of food with its emphasis on the material contents of food and the internal metabolic machinery of each species.1,2

The microbiome, the biosphere and Qi

The missing link in our education involves what exactly happens to food as it passes through our patients’ guts. We are only now beginning to understand that the miraculous transformation of food into tissue could not take place without the contribution of an enriched broth of bacteria and fungi we call the intestinal microbiome (each individual’s microbiome outnumbers their own cells by ten to one). Only a few pathogens negatively impact animal health.3 All plants and animals share their functional life with a nurturing and supportive microbiome from birth (or sprout) to decomposition.4 Likewise, the earth could not support plant or animal life if not for the rich mat of organic material that inhabits its crust.5

The TCVM concept of Qi, the vital life force that encompasses all living things, is remarkably similar to our current understanding of the planet’s robust biosphere, and its continuous cycle of promotion and decay – a cycle that has been taking place in the deepest, farthest, and most extreme places on the planet for billions of years.6

Veterinarians learn that healthy ruminant digestion relies on a partnership with microbial inhabitants. A similar discussion of the microbiome in dogs and cats was largely overlooked in small animal nutritional textbooks, as if it was only marginally involved in digestion and overall health.1,2 In fact, each pet’s microbiome is establishing residence within one hour after birth, and hastily begins directing the development of the structure of the host’s intestines, immune system and neurologic system.4,7 The resident microbiome, in concert with the host’s cells, is responsible for an elaborate communication system that influences nutrient assimilation, tissue growth and repair, body composition, inflammation, neurological development and mental health. At weaning, the microbiome population alters as the food substrate changes. In carnivores, this means that microbes and enzymes associated with carbohydrate digestion begin to naturally diminish, while microbes, intestinal cells, and organs that assist in amino acid and fat digestion flourish and develop.7 The host’s hormonal state during puberty, estrus, pregnancy and lactation influences the bacterial population in the intestines by promoting a shift towards microbes that are more efficient at harvesting energy from the diet.

The external environment also influences the microbiome. Research shows that animals and people who spend time outdoors have more robust microbiomes, as do humans that live in multi-generational households, or share their living space with pets.8

Bio-availability and dry extruded diets

What is it about the overcooked dry extruded diets, fed to pets since the 1950s, that are contributing to the marginal health and diminished lifespan of dogs and cats? Perhaps an example concerning the discovery in the 1980s that taurine was deficient in commercial cat foods answers that question (clinical symptoms cats presented with were CHF and blindness). It seems taurine was present in the cat food (according to the guaranteed analysis), but the high cooking temperatures made this essential amino acid unavailable to feline intestinal microbes. This interesting finding illustrates how dynamic the science of nutrition is as it applies to industrialized pet foods. The paradigm of essential nutrients depends on the recognition that a particular disease can be associated with a specific nutrient. As more diseases or clinical conditions are reported and investigated, more nutrients may be defined as essential.2

The paradigm of bio-availability currently compares the concentration of a nutrient or drug before it is ingested, to the blood levels achieved at post-ingestion intervals. We now know that the health and composition of the microbiome influences what crosses from the lumen of the gut into the bloodstream and impacts the analysis of the bio-availability. Currently, fresh food diets (commercial or home-prepared) are being scrutinized by veterinary nutritionists as they compare their guaranteed analyses to industrial processed preparations. This work ignores the concept of microbial-assisted bioavailability which favors amino acids, fats and minerals from fresh uncooked meat, fat and bone diets for carnivores. It is true that processing and cooking improves the digestibility of plants (by making their contents more bio-available to microbial digestion), but one could argue that amplifying the energy content of pet food will not benefit the health of our largely overweight and obese pets. Dry extruded diets (even grain-free) are deficient in essential amino acids and fatty acids, and excess in plant sugars, because of the high temperatures associated with their cooking and composition.

High-fiber, plant-based processed diets designed to reduce a pet’s energy harvest from food (and theoretically help reduce weight) further amplify these deficiencies. These diets increase the volume of indigestible fiber and dilute not only the caloric content of the food, but also its essential amino acid and fatty acid content, leaving pets extremely deficient in both.

Ancestral diets, the biosphere and industrial farming

The current trend towards “ancestral diets” represents an effort to correctly feed the ancestral microbiome of our carnivorous pets. This is not an attempt to take our canine pets back to wolves, or turn apartment-dwelling felines into lynx. It recognizes that the evolution of domestic dogs and cats from carnivorous hunting partners, varmint managers and scavengers to house-dwelling couch potatoes spans just 150 years – a short period when compared to the approximately 20,000 years of domestication. Many variations of ancestral diets are now commercially available, and most are approximately 75% to 80% meat, fat and bone with variable plant material and supplements added. Most are designed to be fed raw or gently cooked; either is biologically appropriate.

Many animal owners, with little support from their veterinarians, use the information from books, other publications and the internet to feed their pets combinations of raw meat by-products from human food distributors, such as chicken backs and necks, tripe and various organ meats. Typically, some type of vegetable material is added along with many variations of commercially available supplements. These animal owners are motivated to improve their pets’ health and longevity with fresh species-appropriate food, and most report favorable results. But are these industrially-produced food animals and plants really “ancestral”?

After WWII, agriculture used scientific innovations to develop a war on insects, weeds and plant pathogens. The war on famine justified the overproduction of cereal grains, and government subsidies for politically-important crops influenced the development and use of agro-chemicals to maximize production. This focus on the health benefits to plants of being grown in a world free of pathogenic bacteria, fungi and insects now seems unrealistic and short-sighted. The increased yields and profits realized through these farming methods are celebrated, while the costs to beneficial microbes and the environment are largely ignored. The non-target effects of agricultural technological development continue to be realized only as they play out in the laboratory of our world, our pets’ health and our own lives.

Authors David Montgomery and Anne Bikle (The Hidden Half of Nature) write about the remarkable similarity between the relationships human and animal hosts develop with their microbiome, and the relationships plants develop with the earth’s biosphere. They note the functional similarities between the roots of plants and the cells of our gut as they interact with a healthy, robust microbiome. These beneficial soil microbes function much like the microbiome of our colons, enhancing the plant’s ability to uptake minerals and additional nutrients. Plants evolved by providing exudates to soil bacteria and fungi through their roots, in exchange for nitrogen the microbes fix from the soil and atmosphere and make available to the plant.

The theoretically-benign herbicide glyphosate is toxic to these critical nitrogen-fixing bacteria and mycorrhizal fungi in the soil. Additional chemical fertilizers are needed to supply nitrogen, phosphorous and potassium to enhance plant growth. Chemically-fertilized plants get lazy and fail to develop robust root systems, which starves soil microbes. The result of 70+ years of chemical fertilization and soil microbe starvation is a substantial decrease in the plant content of most soil micronutrients (vitamins and minerals). One study that looked at changes in the micronutrient content of fruits and vegetables from 1940 to 1992 documented decreases in all micronutrients, with the exception of phosphorous. These decreases ranged from 2% to 97%, depending on the plant type.

Studies have shown that magnesium, for example, is necessary for the development of several digestive enzymes. A dietary deficiency of magnesium is related to many human health problems such as ADHD, schizophrenia, bipolar disorder, depression, and not surprisingly, chronic gut inflammation. It is estimated that most Americans now only get 10% to 20% of the magnesium they need through their diets. Many GMO plants (corn, soybeans) were genetically designed to resist the effects of glyphosate, which means they can be exposed to and uptake this chemical without dying. The toxicity of glyphosate residues to the beneficial microbiota of animals and humans is currently being explored. Researchers have found alterations in the beneficial gut microbiome of poultry and cattle fed GMO corn and soybeans, which leaves the animals vulnerable to pathogenic bacteria.

Industrialized agriculture and the use of glyphosate create the same deficiencies in the plants and animals it produces and in the soil that contributes to their growth. Humans and pets, as predators, are at the top of this deficient food chain. The health of our pets is definitely improved when fresh food is substituted for dry extruded diets, but “ancestral” diets can only begin to restore integrity and balance to the system when the meat, plants and supplements included in these diets are derived from organically-farmed sources.

Veterinarians interested in finding a path to health for their clients’ pets can also promote a path to health for the planet when they advocate fresh organic diets for animals. When consumers pay for the actual environmental costs associated with production of the food we and our pets consume, we begin to bring balance to our relationship with the planet.

Veterinarians are trained to provide clients with a risk benefit analysis for each medical directive or treatment protocol that we recommend. Informed veterinarians can now give clients a risk benefit analysis for organic and fresh food diets versus industrially farmed processed kibble diets by also encouraging them to consider the costs to the health of the planet.

Talking points for fresh food feeding consults with clients

  1. Always get a complete health history (TCVM or CWM) and perform any necessary diagnostics (CBC, chemistry, U/A) on new patients before you start them on a fresh diet, to avoid the potential that chronic health problems (pancreatitis, food allergies, IBD) may cause a healing crisis.
  2. Discuss stool quality and its relationship to digestion so that clients realize how important it is to daily monitor their pets’ stools.
  3. Discuss food prep and storage hygiene as well as kitchen management to educate clients on the risks of handling raw meat. Due to enzymatic activity in raw meat, amino acids can be lost during prolonged storage in refrigerators.
  4. Raw meat should not be fed to animals that have recently been on courses of antibiotics; the disruption this causes to their beneficial microbes leaves them susceptible to pathogenic bacterial invasion. A one- to four-month waiting period on gently-cooked food should be protective.
  5. Senior patients with compromised GI function may never be able to properly digest raw food.
  6. All pets on fresh food diets should receive animal-sourced Omega 3 fatty acid supplementation; even grass-fed and free-range livestock aren’t able to consume the variety of plants necessary to ensure they are incorporating these fatty acids into their own fat.
  7. All pets should be on a well-rounded mineral supplement to compensate for deficiencies in soil and harvested plants. (Even organic farms are still in the process of building good soil, and mineral deficiencies occur across the US).
  8. All pets should be on a daily pre- and probiotic to provide a source of beneficial bacteria and stabilize and promote GI function and motility.
  9. Whenever possible, clients should purchase pet foods or ingredients that are organic, non-GMO, free-range or grass-fed, and free of hormones and antibiotics.
  10. Clients should also be encouraged to establish relationships with local food producers. As more farmers become aware that consumers are willing to pay more for healthy organic food, more will begin farming that way.


1Schenk PA and Strombeck DR. Home-prepared dog and cat diets, 2nd Ed. Ames, Iowa: Wiley-Blackwell, 2010.

2Gross KL, Yamka RM, Khoo C, Freisen KG, Jewell DE, Schoener WD, Debraekeleer J, Zicker SC. “Macronutrients, micronutrients: minerals and vitamins”. In: Hand MS, ed. Small Animal Clinical Nutrition, 5th Ed. Topeka, Kan: Mark Morris Institute, 2010. 49-148.

3Freeman L, Chandler M, Hamper B, Weeth L. “Current knowledge about the risks and benefits of raw meat-based diets for dogs and cats”. JAVMA 2013; 243: 1549-1558.

4Buddington R. “Postnatal changes in bacterial populations in the gastrointestinal tract of dogs”. AJVR 2003; 64:646-51.

5Montgomery, David R and Bikle, Anne. The hidden half of nature, the microbial roots of life and health. New York: W.W. Norton & Company, Inc., 2016.

6Legget D. Helping ourselves, our guide to traditional Chinese food energetics, 2nd Ed. Devon, England: Meridian Press, 2005.

7Hamper BA. “Nutritional adequacy and performance of raw food diets in kittens”. Doctoral Dissertation, University of Tennessee (2012):14-24.

8Blaser, Martin J. Missing microbes: How the overuse of antibiotics is fueling our modern plagues. New York: Henry Holt and Co., 2014.