Building a Healthy Microbiome in Your New Puppy


Building a Healthy Microbiome in Your New Puppy

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by Steve Brown

Building a healthy gut is crucial for long-term healthfulness in your dog. To do this, it’s integral he’s fed a nutritious, biodiverse diet so the ecosystem, or microbiome, in his digestive tract can flourish.

The most important time for providing great nutrition for your dog and building his microbiome is when he is young, as soon as you bring him home, or sooner when possible. We recommend building a up your puppy’s microbiome while he’s still in utero, or at least when he’s still very young and nursing. Since that’s not always possible, we’ve put together a guide for puppies who’ve just gotten home with their new families.

Through feeding micronutrient-balanced, microbe-rich foods and exposing our puppies to microbe-rich environments, we help them develop healthy gut, ears, mouths, and skin and coat microbiomes. A balanced microbiome is composed of thousands of different species with no species dominating, which is ideal for optimal health. 

The microbiome as a puppy generally affects your dog for her entire life, so start to build her microbiome as soon as you pick up your puppy.

Here are some tips and guidelines for building up and balancing out your new puppy’s microbiome:

Labrador puppy building microbiome

  • Encourage puppy to eat and roll around in clean dirt and clean grass. According to Dr. Barbara Royal, DVM, CVA, “Dirt is king.” She also notes that puppy diets can be supplemented with unpasteurized goat milk or yogurt and fish stock.
    • The ideal dirt is collected from organic, polyculture farms. Farms with many types of plants and animals usually contain more biodiverse dirt and dust than do monoculture farms. Make sure the dirt has no pesticides, herbicides, including glyphosate, an active ingredient in Roundup that correlates with changes in the microbiome. Ideally, you should test your dirt for specific types of pathogens, including roundworms, whipworms, and hookworms, and heavy metals such as lead, arsenic, barium, cadmium and mercury. Start feeding your new friend a fresh, raw food diet. Start feeding your new friend a fresh, raw food diet.
  • Start feeding your new friend a fresh, raw food diet. Note: All of Darwin’s foods are suitable for puppies over 4 months in age, as well as all other life stages. If your puppy is still younger than 4 months old, gently cooked fresh food is the way to go.
  • Watch his weight. Growing puppies need more food per pound of body weight than adult dogs. But it’s still important to keep your pup lean for his long-term health. Small breed puppies may need up to 20% of their weight per day in food, especially if they are active outdoors in cold weather.  Large breed puppies may need 3-4% of their weight per day.
  • Get your puppy accustomed to a variety of foods with a variety of meat sources and fiber sources from plants to build a highly diverse microbiome.
    • Feeding the same food every day is not healthy. It is a myth perpetuated by billions of dollars in advertising. Dogs, like people, need a variety of foods, and a lack of diversity can actually cause harm.  According to my and Beth Taylor’s book, See Spot Live Longer, “The most common ingredient causing food allergy is the one that is consumed most often.”
  • Whatever you plan to feed as your dog as an adult, feed as a puppy. If you plan to travel with your dog when he is an adult, plan how you’ll be feeding his while you travel and feed some of that food now.

Additionally, here’s some information if you choose not to feed a balanced, fresh, raw diet:


If feeding kibble, which is almost sterile, add left over vegetables to feed the good microbes, and make sure your puppy eats lots of clean dirt to consume a large variety of organisms.

If feeding a high-fat raw diet, which we strongly recommend against for puppies unless dictated by your vet,  ask the manufacturer for analyses showing it is suitable for puppies. Some high fat raw diets do not contain enough protein for puppies. On the whole, a high-fat diet is difficult to balance. 

The FEDIAF (European Pet Food Industry Federation) states that the minimum amount of protein for early growth is 62.5 grams per 1000 kcal.  If you’re feeding a raw food in which the listed protein is only slightly higher than the listed fat, ask the manufacturer how many grams of protein per 1000 kcals is contained in the food.  If they can’t answer, avoid the food.

High-fat diets reduce the diversity of microbes in the guts. If you’re feeding high fat raw diets, add a variety of vegetables to increase gut biodiversity.

If feeding raw diets without vegetables, add a variety of properly-prepared vegetables, and let your puppy eat grass and dirt.

In summary, it’s easy to help build a diverse microbiome in your puppy. Feed a balanced raw puppy food or all life stages food, and let your puppy be a puppy. Puppies love to eat and roll in all sorts of microbe-rich organic matter. Just make sure that it’s clean and that no lawn chemicals were applied.

For more information on transitioning your pup to his new Darwin’s diet, check out our Transition Center.

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