Ketones, Butyrate & the Microbiome: Understanding Fibre-Free Trade-Offs

Carnivore and ketogenic diets are increasingly used to reduce inflammation, improve energy, and provide symptom relief - particularly in clients with gut dysfunction, SIBO or IBS. Much of this benefit is attributed to ketone bodies like β-hydroxybutyrate (BHB), which inhibit the NLRP3 inflammasome and modulate immune signalling (Youm et al., 2015).

But ketones and butyrate are not functionally interchangeable.

Ketones are systemically produced and act as metabolic signals. Butyrate is locally produced in the colon via fermentation of dietary fibre by gut microbes. It is a primary fuel source for colonocytes, regulates tight junctions, maintains epithelial barrier integrity, modulates T-reg activity, and preserves an acidic colonic pH - all of which support Bifidobacterium and Akkermansia muciniphila (Canani et al., 2011; Smith et al., 2013; Zhang et al., 2015).

When fibre is absent, these bacteria starve. Colonic pH rises. Proteolytic bacteria begin to dominate - organisms that ferment protein instead of fibre. 

This shift increases production of ammonia, phenols, indoles, hydrogen sulfide, and secondary bile acids - all of which are associated with epithelial damage, increased permeability, and mucosal inflammation (Windey et al., 2012; Zhu et al., 2014). These are not inert metabolic leftovers - they are bioactive and cytotoxic to colonocytes when unbuffered by fibre fermentation.

Clients often feel better on carnivore because they’ve removed fermentable carbohydrates that feed overgrown or dysbiotic microbes. 

But absence of symptoms is not evidence of functional restoration. 

When microbial fermentation halts, so does SCFA production. 

Over time, this can lead to:

 • Thinning of the gut lining

 • Loss of microbial diversity

 • Reduced gut motility and ENS signalling

 • Impaired immune modulation

 • Downstream metabolic dysfunction

Importantly, no study has shown ketones can replicate the trophic effects of butyrate. Their anti-inflammatory pathways overlap, but their mechanisms differ. Butyrate’s local roles - pH regulation, HDAC inhibition in epithelial cells, and mucosal energy support are not replaced by circulating ketones.

Fibre may not be “essential” by RDA standards. But it is essential for feeding the microbes that maintain gut structure, immunity, and resilience.

Carnivore can be a valuable short-term tool for calming inflammation. But long-term, the exit strategy matters. If we fail to reintroduce fermentable substrates, we risk trading symptomatic relief for microbial collapse.

Lauren Wallis BSc MSc DipCLN FNTP IFMCA

Functional Nutritionist | Certified IFM Health Coach

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