Research by Dr. Carol Hughes, Biome4Pets and Equibiome
Everybody is talking about the importance of the microbiome these days, and good that they are. The gut axis is critical to health and well-being, and a healthy gut needs microbes in the right balance. So let’s have a look into how we can support our dogs microbiome, the APA way. But before we can talk about healing an imbalanced microbiome, it helps to understand what we are aiming for. What does a healthy gut actually look like, in numbers and in function?
What Does a Healthy Microbiome Actually Look Like?
The microbiome is the community of trillions of microorganisms living primarily in the large intestine. In a healthy dog, this community is dominated by five bacterial phyla, each with its own distinct job. Think of them as different departments in a well-run organisation. When all the departments are functioning, and none has taken over, the whole system runs smoothly. When one collapses, or one dominates, everything built on top of it begins to fail.
Firmicutes are the largest and most diverse group, making up roughly 40% to 45% of a healthy dog’s microbiome. Within Firmicutes, the Clostridia family is particularly important: these are the bacteria responsible for fermenting dietary fibre into short-chain fatty acids, including butyrate, which is the primary energy source for the cells lining the gut wall. They are also responsible for digesting bones. When Clostridia drop, you will often see dogs that can no longer comfortably digest raw bones the way they once could. Firmicutes are not antibiotic-resistant, which means they are the first casualty of antibiotic treatment or antibiotic-resistant bacterial overgrowth.
Bacteroidetes make up around 25% to 30% of a healthy gut and include genera like Prevotella and Bacteroides. Their primary roles are fermenting a wide range of carbohydrates and proteins, supporting immune function, and helping to maintain the anaerobic environment that the rest of the microbiome depends on. They are highly variable between individual dogs. When antibiotic-resistant Bacteroidetes species overgrow and dominate. Dr Carol Hughes’s lab tests thousands of dogs and she has observed in the post-COVID dog population that they crowd out the Firmicutes and collapse diversity.
Fusobacteria are unique to carnivores. In humans, Fusobacterium is associated with gastrointestinal disease, but in dogs, it is associated with health. These bacteria specialise in breaking down proteins into amino acids and peptides, making them essential in a carnivore’s gut. They are found in higher numbers in dogs with access to the outdoors and are severely impacted by antibiotic treatment, recovering more slowly than any other phylum after disruption.
Proteobacteria encode functions across protein, carbohydrate, and vitamin metabolism, and help maintain the anaerobic gut environment that the rest of the microbiome needs to function. Their levels need to be in balance: elevated Proteobacteria is one of the recognised markers of dysbiosis.
Actinobacteria are the smallest of the five main groups and include Bifidobacterium, which plays a role in producing B vitamins, supporting immune development, and maintaining the gut barrier.
Beyond which bacteria are present, what matters most is how many different species are present and how balanced they are. This is what researchers call diversity, and it is the single most important indicator of a healthy microbiome. Before 2020, a healthy domestic dog in the UK could be expected to carry around 800 bacterial species. Wild street dogs carry upward of 1,100. Today, the average domestic dog in Carol Hughes testing population carries around 131 species, and many score below that.
A diversity score of 3.2 or above was previously considered a healthy baseline. Today, 2.2 is average. Many dogs score 1.5 or lower, and at that level, the microbiome is essentially just managing to digest food. The support systems built on top of a diverse bacterial community, immune regulation, stress chemistry, neurotransmitter production, and anti-inflammatory capacity are barely functioning.
That is the gap we are trying to close, not by adding one thing in, but by understanding the whole system, removing what is blocking it, and creating the conditions for diversity to return.
Step 1: Recognise the Signs of a Microbiome Imbalance
An out-of-balance microbiome in one animal can look completely different from an out-of-balance microbiome in another, even when the symptoms are the same. What works for one will not necessarily work for the other. That said, there is a clear sequence of intervention that applies broadly, and understanding it changes everything about how you approach the problem.
Before intervening, it helps to know what a microbiome imbalance looks like in practice. In dogs and cats can manifest as:
Diarrhoea, vomiting, acid reflux, bloating or excessive gas
Itchy skin, hot spots, or chronic skin conditions
Chronic inflammation
Anxiety, stress reactivity, aggression, or unusual behaviour
Difficulty maintaining a healthy weight
Poor coat condition
Low energy or vitality
Research shows that dogs with anxiety and poor behaviour consistently show a microbiome dominated by three or fewer species, with the support systems around immunity, stress chemistry, and neurotransmitter production barely functioning.
Step 2: Identify the Most Likely Cause
Understanding what caused the microbiome to become out of balance helps determine the best approach. The most common causes are:
Antibiotics: These kill both harmful and beneficial bacteria. Following antibiotic treatment, some bacterial species recover but many do not, and a return to pretreatment status is rarely achieved without intervention.
The post-COVID environment: data shows a clear population-level shift from around the second lockdown period, with antibiotic-resistant bacteria rising significantly across the dog population, even in dogs that had never received antibiotics.
Highly processed food: highly processed food is a direct contributor to microbiome damage, as it provides high levels of carbohydrates that promote the growth of bacteria linked to inflammation, while failing to provide the whole fibre content that beneficial gut bacteria need.
Long-term medication, including antibiotics, NSAIDs, and over-vaccination, all cause a reduction in the numbers of good gut bacteria.
Factory-farmed meat in pet food: factory-farmed fish in particular carries Shewanella, an antibiotic-resistant pathogen that survives the rendering process and can make up as much as 10% of a dog’s microbiome when consumed regularly.
Previous Giardia infection: Dogs who had Giardia as puppies often retain elevated levels of spirochaetes in the gut wall long after the Giardia itself has cleared, with levels in affected dogs reaching 40% of the total microbiome compared to an average of 0.5% in healthy dogs.
Step 3: Consider a Microbiome Test
If the animal has complex or persistent problems, testing changes the quality of every decision that follows. Without knowing what is actually in the gut, interventions are informed guesswork at best. We recommend using Biome4Pets as they use long-read, deep-sequencing 16S rRNA methodology at Aberystwyth Laboratory, comparing results against a database of over 10,000 dogs and cats.
If testing is not immediately accessible, the steps below can still be followed in sequence. They will not cause harm. But testing before and after intervention gives you the data to know what has changed and what has not. It is recommended to retest after six months. Most of the issues encountered in the microbiome can be managed in six months with careful monitoring.
Step 4: Clear Before You Build
This is the most important practical shift from conventional thinking. When the gut is dominated by antibiotic-resistant bacteria or pathogenic overgrowths, adding good things in before reducing the dominant bacteria is unlikely to work. The beneficial bacteria cannot gain a foothold, and in some cases, adding probiotics into this environment can create new inflammation by introducing species the gut is not ready to support. The tool for this clearing work is the plant antimicrobial.
For general antibiotic-resistant bacterial dominance, gentle aromatic plant antimicrobials are the starting point. Thyme (Thymus vulgaris), oregano (Origanum vulgare), and rosemary (Salvia rosmarinus) are reliable fallbacks with genuine antimicrobial activity that work through pathways the resistant bacteria have not pre-adapted to resist. These are best offered through self-selection in the APA way: allow the animal to choose rather than adding to the food.
For spirochaete overgrowth specifically, Acacia catechu at 1g per day and Smilax sarsaparilla at 2g per day are the best active compounds to reduce spirochaete overgrowth. Antibiotics are not recommended for spirochaetes because they would severely disrupt the beneficial members of the microbiome, and spirochaetes are noted as often being antibiotic-resistant.
For serious pathogenic overgrowth, stronger bark-based plant antimicrobials are needed. Specifically, Acacia catechu for a more serious pathogenic load.
Important: until the dominant resistant or pathogenic bacteria are reduced, other interventions, including FMT will not work effectively. The clearing step is not optional.
Step 5: Remove the Sources of Ongoing Damage
Clearing the microbiome will not hold if the inputs causing the imbalance are still present.
Review the diet: Remove or significantly reduce highly processed food. Highly processed feeds provide high carbohydrate levels that feed inflammatory bacteria. Factory-farmed fish products specifically may be carrying Shewanella.
Reduce overfeeding: Overfeeding overwhelms a compromised microbiome. Feeding less overall and fasting occasionally gives the gut space to stabilise. Reducing from twice daily to once daily feeding can reduce protein load without removing protein from the diet.
Reduce unnecessary medication where possible: long-term NSAID and antibiotic use are direct contributors to microbiome damage.
Review environmental toxins: household toxins are a relevant factor in microbiome health. Highly sanitised indoor environments also reduce the beneficial microbial input that supports diversity.
Step 6: Preserve What Remains with Prebiotic-Rich Plants
Once the clearing work has begun, the focus shifts to nourishing the beneficial bacteria that remain and preventing further diversity loss.
Inulin is great for this purpose. It is a sugar that feeds the bacteria you want to keep in the gut. The recommended dose is one teaspoon per day (for dogs); it can be safely added to the diet of all dogs. Inulin supplements are derived from chicory root or artichoke. Natural inulin-rich plants that can be offered through self-selection or added to food include marshmallow root (Althaea officinalis), burdock root (Arctium lappa), and couch grass root (Elymus repens).
Beet pulp is also recommended following antibiotic treatment, specifically, to increase the numbers of Firmicutes and Clostridia while reducing Erysipelotrichi and Fusobacteria. Psyllium husk is equally effective, at 10g soaked per day for a small dog and 20g for a large dog.
Step 7: Rebuild Through Environment and Lifestyle
This step does not require a product. It requires access.
Animals that are allowed to dig, forage, roll in soil, and move through varied outdoor environments maintain far more diverse microbiomes than those kept in controlled indoor settings. The gut, like any ecosystem, needs diverse microbial input from the environment to sustain and rebuild its own diversity. Practical steps that support this:
Allow access to healthy outdoor soil environments where possible
Permit natural foraging behaviours, including occasional eating of things that might seem undesirable
Reduce sanitisation of the home environment where reasonable
Allow the animal to self-select from herbs and aromatic plants
Step 8: Fermented Foods, by Self-Selection Only
Fermented foods such as kefir, with one important condition: they must be offered by self-selection, not mixed into food. The gut-brain axis in animals is a real and measurable signalling system. When a dog consistently chooses kefir, something is being served at a microbiome level, though the precise mechanism may differ from what product labels claim. Fermented food offered this way does no harm; the animal will choose and stop as they see fit. .
Step 9: Consider a Probiotic Carefully
Most commercial probiotics do not do what they claim, and some can actively cause harm by introducing species not appropriate to the individual animal’s gut. If a probiotic is to be used, a soil-based product containing Bacillus species is best, because these are ecologically appropriate to the environments dogs naturally encounter.
High-Lactobacillus probiotics are not recommended for dogs. Large amounts of Lactobacillus are detrimental to dogs, as most commercial strains are not species-specific to the dog gut and can trigger resistance inflammation.
The feline microbiome is somewhere between ten and twenty times more complex than a dog’s. It is closest in character to healthy, balanced soil. An outdoor cat that hunts, rolls in earth, and lives close to nature is, in microbiome terms, operating near its wild baseline. No commercial probiotic comes close to that complexity. Our role with cats, as with all animals, is primarily to stop removing the conditions that their microbiome depends on.
Step 10: Consider FMT for Very Low Diversity or Acute Diarrhoea
Faecal Microbial Transplant is appropriate in two specific situations:
Acute diarrhoeal infections
Cases where diversity has dropped so low that the internal ecosystem cannot rebuild without significant help.
It is not appropriate when the problem is a motility issue, gastric emptying that is too fast, or excessive protein fermentation in the large intestine. In those cases, the problem is physiological, not microbial.
Donor quality is critical. Donors should have a diversity score of 3.1 or above, a threshold that eliminates the majority of dogs in the current population. Avoid using mass-produced FMT products from suppliers who do not test to this depth.
Step 11: Retest at Six Months
After six months, retest. This is not simply a commercial recommendation: it is the only way to know whether the intervention has changed what you intended to change, and what remains to address. Most microbiome issues can be managed within six months with careful monitoring.
I hope you found this article helpful. Many thanks to Dr Carol Hughes for sharing her expertise on the subject so generously. For more information, check out our webinars The Biome, what on earth goes on in there? And The Microbiome part 2.
By Nayana Morag
