The oxygen-gut dysbiosis connection

What causes gut health to go downhill, and how to break the cycle of gut inflammation, dysbiosis, and epithelial energy starvation.
November 14th, 2019

Virtually every cell in the human body requires oxygen. That is – every human cell. Most of our microbial cells on the other hand, thrive in an environment devoid of oxygen. If oxygen leaks into the gut, it can promote bacterial imbalances and inflammation. Read on to learn more about the oxygen-gut dysbiosis connection, and how we might use this knowledge to improve gut health.

The human body requires oxygen for survival. But we’re only about 43 percent human.1 The other 57 percent are microbes – most of which do not tolerate oxygen very well. Fortunately, these microbes reside in the colon, which in a healthy state is a low-oxygen environment.

If the state of the gut is perturbed, however, oxygen can start to leak into the gut, beginning a vicious cycle of gut dysbiosis, cellular energy starvation, and inflammation. In this article, I’ll break down the oxygen-gut dysbiosis connection and discuss its potential implications in shaping gut treatment.

Fair warning: this one is going to be dense, as this is the culmination of several months of independent research, but it is probably one of the most important articles I’ve ever written. As always, I’ll provide a succinct summary & takeaways section at the end for anyone who just wants the actionable insights.

The healthy colon: a low oxygen environment rich in microbes

The human gut is home to a dense community of microbes. The healthy human colon contains an estimated 38 trillion bacterial cells, which are predominantly obligate anaerobes. These are bacteria that can only grow and reproduce in an environment largely devoid of oxygen. Many of these bacteria are crucial to breaking down complex carbohydrates to produce important gut metabolites like short-chain fatty acids.

The healthy colon may also contain a small number of facultative anaerobes, which are capable of growing and reproducing in an environment with or without oxygen. Facultative anaerobes include many gut pathogens. The low oxygen concentration of a healthy gut and the abundance of obligate anaerobes both suppress the growth of these facultative anaerobes.

Butyrate helps maintain “physiologic hypoxia” in the colon

One of the metabolites produced by obligate anaerobes is butyrate. Butyrate is a short-chain fatty acid (SCFA) produced when these bacteria metabolize dietary fiber in the colon. I’ve written before about the benefits of butyrate for health, including its ability to attenuate neuroinflammation, protect against colon cancer, and help maintain gut barrier function. It wasn’t until recently, however, that I learned about the role of butyrate in maintaining low gut oxygen levels.

In the healthy gut, butyrate supplies about 70 percent of the energy required by colonocytes. These are the cells that line the colon and form the gut barrier. After uptake by colonocytes, butyrate and other SCFAs are broken down in the mitochondria through a process called beta oxidation. This process utilizes large amounts of oxygen. As it turns out, this colonocyte oxygen consumption is very important to maintaining gut homeostasis.

In 2015, a research group led by Dr. Sean Colgan at the University of Colorado demonstrated that gut metabolism of butyrate was required for maintaining “physiologic hypoxia” in the colon.2 Through a series of experiments, they demonstrated that butyrate, and to a lesser extent, the SCFAs propionate and acetate, deplete oxygen levels in colonocytes. This leads to the stabilization of a protein called hypoxia-inducible factor (HIF), which acts as a sort of “oxygen sensor” in the cell. When oxygen levels are low, HIF promotes the expression of genes that help coordinate gut barrier protection. If oxygen levels rise, HIF is no longer stabilized, and these gut-protective genes are no longer expressed.

The researchers wondered whether antibiotics could affect this state of hypoxia. After just three days of broad-spectrum antibiotics, butyrate levels had dropped dramatically, gut oxygen levels had risen, and the state of epithelial hypoxia was lost. The oxygen-sensor HIF was no longer stabilized, and the gut-protective genes were no longer expressed, leading to a loss of gut barrier function.

And it wasn’t just a lack of fiber, the substrate for butyrate production. The gut microbiota of the antibiotic-treated mice had completely lost its ability to produce butyrate or other SCFAs from dietary fermentable fibers! Fortunately, they went on to find that the administration of supplemental butyrate was able to rescue the “physiologic hypoxia” and gut barrier function. But more on that later.

A microbial signature of gut dysbiosis: low abundance of butyrate producers and an expansion of facultative anaerobes

For now, we’re going to switch gears a bit. The term “gut dysbiosis” generally refers to an altered state of the gut microbiota, often associated with disease. In the last decade, advanced sequencing techniques have allowed us to characterize gut dysbiosis in hundreds of different diseases. While there are virtually infinite states of the gut microbiota that could be considered dysbiosis, there do seem to be a few patterns that are most frequently associated with disease.

In a 2017 review paper, Litvak et al. wrote:

Perhaps the most consistent and robust ecological pattern observed during gut dysbiosis is an expansion of facultative anaerobic bacteria belonging to the phylum Proteobacteria.” 3

Proteobacteria is one of five major bacterial phyla that are commonly found in the human gut. It includes a wide variety of genera, including Escherichia, Shigella, Salmonella, Helicobacter, Vibrio, Yersinia, Pseudomonas, Campylobacter, and Desulfovibrio. Most of these are considered opportunistic pathogens – microbes that are harmless at low abundance, in the context of a balanced ecosystem, but quickly expand and cause issues when the environment becomes particularly suitable for their growth.

One environmental factor that leads to a rapid expansion of Proteobacteria is – you guessed it – oxygen. Most Proteobacteria are facultative anaerobes, meaning they can survive and reproduce in the presence of oxygen. This gives them a significant competitive advantage over beneficial obligate anaerobes in an environment that contains oxygen.

Notably, the expansion of Proteobacteria is almost always accompanied by a reduction in the abundance of butyrate-producing bacteria. This pattern – high Proteobacteria and low butyrate-producers – is a microbial signature of dysbiosis and has been associated with a number of chronic diseases, including:

  • Inflammatory bowel disease4
  • Irritable bowel syndrome5
  • Colorectal cancer6
  • Diverticulitis7
  • Histamine intolerance8
  • Type 2 diabetes9
  • Obesity10

As we’ll learn in the next few sections, this signature also suggests an underlying epithelial dysfunction.

Epithelial cell metabolism drives gut dysbiosis

Epithelial cells are the cells that line the wall of the gut and are the primary interface for host-microbe communication. Recall from earlier that when the gut is healthy and in a state of homeostasis, colonocytes primarily metabolize fatty acids like butyrate through processes that utilize large amounts of oxygen. The resulting hypoxia (lack of oxygen) in the gut mucosa helps to maintain a gut microbiota dominated by obligate anaerobes. These obligate anaerobic bacteria in turn promote health by fermenting fiber into SCFAs like butyrate, which are absorbed by colonic epithelial cells. This positive feedback loop maintains a state of gut health.

However, when a disturbance shifts the metabolism of colonic epithelial cells away from beta oxidation of fatty acids, the system breaks down. Energy-starved colonocytes must look for other sources of energy. They end up pulling glucose from the bloodstream and fermenting it to lactate, a process that does not utilize oxygen.11 The resulting inflammation also leads to increased production of nitrate. Without anywhere else to go, oxygen, lactate, and nitrate “leak” into the gut mucosa.

This environmental change favors pathogens in the Proteobacteria phylum, such as Salmonella, Klebsiella, Citrobacter, and E. coli, which can tolerate oxygen and thrive on lactate and nitrate. At the same time, the oxygenation of the colon inhibits the growth of obligate anaerobes, including the ever-important butyrate-producers. In other words, the metabolism of colonocytes functions as a control switch of the gut microbiota, mediating a shift between homeostatic and dysbiotic communities.” 11

So, what causes epithelial cells to make this switch that ultimately leads to gut dysbiosis? In the next few sections, I’ll discuss a few known inducers of this epithelial switch: antibiotics, infections, and a low fiber diet.

Antibiotics deplete colonic butyrate and drive oxygen leakage into the gut

Last spring, I had the pleasure of meeting Dr. Sebastian Winter, a professor of microbiology and immunology at UT Southwestern and one of the few prominent researchers trying to understand this control switch and its impact on host health.

In an animal model, Dr. Winter’s lab demonstrated in 2016 that a single dose of the antibiotic streptomycin resulted in a four-fold reduction in gut butyrate concentrations.12 This was primarily attributed to depletion of populations of Clostridia, a class of bacteria that consists of many known butyrate-producers, including Eubacterium, Roseburia, Butyrivibrio, Clostridium, Coprococcus, and Ruminococcus species.

Using a special staining technique, they went on to demonstrate that the antibiotic treatment had increased colonocyte oxygenation and resulted in a loss of hypoxia in the gut mucosa. This loss of hypoxia allowed for the oxygen-driven expansion of Salmonella and other facultative anaerobes.

Of course, Dr. Winter’s lab chose streptomycin specifically because it is particularly effective at depleting Clostridia, so that they could examine the effects of butyrate depletion on colonic metabolism. Streptomycin is not typically used orally in humans; however, many other broad-spectrum antibiotics are known to impact butyrate-producing bacteria, so it’s likely that a 1-2 week course of other antibiotics would also drive oxygen leakage into the gut via this same mechanism.

Pathogenic bacteria can hack colonocyte metabolism to promote gut dysbiosis

Certain pathogens may also exploit this colonocyte switch to gain a competitive advantage in the gut. If you’ve ever come down with an acute case of food poisoning and had trouble with your gut health afterwards, this could explain why.

In the same paper highlighted in the previous section, Byndloss et al. further demonstrated that certain strains of Salmonella (specifically Salmonella enterica serotype Typhimurium, hereafter abbreviated S. Tm) can manipulate the host epithelium to promote gut dysbiosis.12

S. Tm is a particularly virulent bacterium that invades the host mucosa, causing severe inflammation. This inflammation led to a depletion of butyrate-producing Clostridia, which further enhanced the ability of S. Tm to proliferate in the gut. In other words, this suggests that certain pathogens may “hack” gut metabolism to increase their own fitness, to the detriment of healthy bacteria.

Notably, the depletion of butyrate-producers appeared to be more gradual than with antibiotic treatment, occurring over about 1-3 weeks, but was also much slower to recover. At four weeks post-infection, the abundance of Clostridia was still two and a half orders of magnitude below baseline levels.

The inflammation induced by S. Tm also resulted in the release of reactive oxygen and nitrogen species into the gut, which reacted with simple sugars to form substrates that selectively fed S. Tm and other microbes within the Enterobacteriaceae family (Proteobacteria phylum).

This is not just true of S. Tm. In 2007, Lupp et al. demonstrated in a mouse model that Citrobacter rodentium and Campylobacter jejuni infection are also capable of causing host intestinal inflammation and driving overgrowth of Enterobacteriaceae.13

Overall, this suggests that gut infections may contribute to oxygenation of the colon and promote a prolonged state of gut dysbiosis. Thus, clearing existing infections may be a key step to restoring the normal metabolism of the gut epithelium and a healthy gut microbiota.

A low fiber diet may drive oxygen leakage and Proteobacteria expansion

So far, we’ve seen two examples where butyrate depletion led to gut oxygenation and dysbiosis. Given that the #1 source of butyrate is from dietary fiber, it’s likely that a low fiber diet could, in theory, promote the expansion of Proteobacteria via the same mechanism. If dietary fiber intake is low, butyrate and other SCFAs will not be produced at sufficient levels to provide for the energy needs of colonocytes. Colonocytes will turn to anaerobic glucose metabolism. Anaerobic metabolism will consume less oxygen and result in increased oxygen leakage into the gut.

While all of the steps in this mechanism have yet to be as elegantly demonstrated with a low fiber diet as they have for antibiotics and gut infections, several studies have indeed linked low fiber intake with higher levels of Proteobacteria:

  • A large-scale comparative study among children from urban areas in Europe and children from a rural African village in Burkina Faso found that European children had higher levels of Enterobacteriaceae.14 The researchers speculated that this was due to the low fiber content in the Western diet.
  • A 2009 study found that individuals on a gluten-free diet had lower relative abundance of Bifidobacterium and Lactobacillus, and higher amounts of Enterobacteriaceae. The gluten-free diet had significantly reduced the participants’ intake of polysaccharides.

What about a low carb, ketogenic diet? As I’ve discussed before, the ketone bodies acetoacetate and beta-hydroxybutyrate can supplement butyrate as a fuel source for gut epithelial cells. Thus, it’s unlikely that a low-fiber, ketogenic diet would activate this mechanism to drive gut dysbiosis. In fact, ketones might be beneficial in helping to restore epithelial hypoxia. We’ll come back to that later.

Other agents that contribute to gut inflammation may also drive gut dysbiosis

Intriguingly, all of these drivers of gut dysbiosis – antibiotics, gut infections, and a low fiber, processed diet – are associated with intestinal inflammation.

In 2007, Lupp et al. demonstrated in animal models that gut inflammation itself is enough to disrupt the gut microbiota and promote overgrowth of Enterobacteriaceae. Both exposure to dextran sodium sulfate, a chemical that disrupts gut barrier integrity, or severe genetic predisposition, via knocking out IL-10, were  able to drive gut dysbiosis.13

Other, more mild inflammatory agents could also promote the expansion of these inflammatory bacteria. Chassaing et al. (2015) demonstrated that feeding mice carboxymethylcellulose and polysorbate-80, two emulsifiers commonly used in processed foods, for 12 weeks reduced microbial diversity and resulted in increased mucosa-associated Proteobacteria.15 Similarly, Palmnas et al. found that feeding rats the non-caloric sweetener Aspartame for 8 weeks resulted in increased Enterobacteriaceae.16

Stress can also promote inflammation and gut dysbiosis. Langgartner et al. reported an expansion of Proteobacteria in a mouse model for chronic psychosocial stress.17

Unrecognized food intolerances may also contribute to gut inflammation, altered colonocyte metabolism, and gut dysbiosis, though more research is needed to confirm this.

Alright, so we’ve reviewed a number of things that can cause gut hypoxia and drive gut dysbiosis. For the remainder of this article, I want to focus on things we can do to potentially interrupt this cycle and restore gut homeostasis. First up: butyrate!

Butyrate helps maintain gut hypoxia and protects against pathogen expansion after antibiotics

Ever since publishing my article on why probiotics might not be the best choice after antibiotics, I have received a lot of questions about what we can do to protect our gut health when we do have to take antibiotics.

At the time, I didn’t have a great answer. Now, having dug deeper into the research, I think there is enough evidence to suggest that butyrate supplementation might be particularly helpful! Over the next few sections, I’ll lay out the research that supports this hypothesis, and close with my recommendations for putting this into action.

In Dr. Winter’s studies mentioned above, streptomycin treatment depleted butyrate-producers and caused oxygenation of the mucosa – that is, unless the mice were treated with oral tributyrin, a form of butyrate that is targeted for release in the gut: “Remarkably, tributyrin supplementation restored epithelial hypoxia in streptomycin-treated mice and significantly increased the concentration of cecal butyrate.” 12

In the experimental infection model, tributyrin supplementation also reduced the fitness advantage of pathogenic bacteria! After streptomycin treatment alone, S. Tm had a significant competitive advantage in the gut, expanding to fill a greater percentage of the overall ecosystem. However, when tributyrin was provided orally three hours post-infection, the competitive advantage was lost.

Butyrate restores hypoxia and protects against C. difficile-induced colitis

In 2019, Fachi et al. demonstrated in a mouse model that administering butyrate alongside antibiotics could attenuate C. difficile-induced colitis.18 Clostridioides difficile (previously classified as Clostridium difficile and commonly abbreviated C. diff) is a gram-positive, spore-forming bacterium that is a common cause of intestinal infection after antibiotic use.

Supplemental butyrate was started one day before antibiotics and continued throughout the antibiotic course and 5-day infection challenge. Interestingly, butyrate had no effects on C. difficile colonization or toxin production, but through stabilizing HIF-1 and increasing gut barrier integrity, butyrate reduced intestinal inflammation and the movement of bacteria across the gut barrier.

The researchers went on to test two additional strategies for providing butyrate. High dose tributyrin administered in the three days surrounding infection was equally as protective as butyrate, as was feeding a high-fiber diet (containing a whopping 25 percent inulin) after antibiotics but prior to infection.

So clearly, butyrate protects against pathogen expansion after antibiotics. But can butyrate prevent the full spectrum of dysbiosis associated with antibiotics, by supporting colonocyte metabolism? This remains to be determined in controlled studies, but as we’ll see in the next section, the pieces certainly seem to fit together nicely.

PPAR-gamma as the control switch for colonocyte metabolism

So far, I’ve been talking rather abstractly about a “switch” in colonocyte metabolism that leads to gut dysbiosis. But it turns out that researchers have identified a particular gene, PPAR-gamma, that appears to mediate this switch. PPARs (which is short for peroxisome proliferator-activated receptors) are a group of proteins that bind to DNA to directly influence gene expression. PPAR-gamma is expressed in a number of cells but is most highly expressed in the adipose (fat) tissue and colon.

In a healthy gut, butyrate not only provides energy for colon cells, but also enhances PPAR-gamma activation. This acts a positive feedback loop: PPAR-gamma activates genes that increase metabolism of butyrate and other fatty acids. This reduces the oxygen concentration in the epithelium and gut mucosa, which inhibits the growth of pathogenic Proteobacteria and promotes the growth of beneficial, butyrate-producing bacteria.

In a dysbiotic gut, however, there is not enough butyrate or other substrates to activate PPAR-gamma. Lower PPAR-gamma expression results in increased expression of Nos2, the gene encoding inducible nitric oxide synthase (iNOS) and increased nitrate release into the gut. This, along with the lactate and oxygen from anaerobic glycolysis, fuels the growth of pathogenic bacteria.

PPAR-gamma activation is also crucial for the maintenance of gut innate immunity. A study published in the journal PNAS in 2010 demonstrated through a series of experiments that PPAR-gamma helps to maintain constant expression of the antimicrobial peptide β-defensin, which regulates microbial colonization of the colon.19 Mice that were deficient in PPAR-gamma showed defective immune defenses against Candida albicans, Bacteroides fragilis, Enterococcus faecalis, and E. coli. PPAR-gamma is also required for the production of secretory IgA.20

Could stimulating the PPAR-gamma pathway prevent or reverse gut dysbiosis?

Several studies have demonstrated that PPAR-gamma activation could potentially prevent or reverse gut dysbiosis and tissue injury associated with immune activation. For instance, PPAR-gamma expression is significantly reduced in inflammatory bowel disease (IBD).21 Rosiglitazone, a drug that binds to PPAR-gamma and increases its activity, has been shown to prevent dysbiosis and reduce symptoms of colitis in animal models, when given acutely.22 While this drug is still sometimes used in the U.S. as an antidiabetic drug, it has several unwanted side effects, and is not ideal for long-term use. Nonetheless, it demonstrates the ability of this pathway to exert significant changes on the gut microbiota.

Researchers kept looking for other options to stimulate this pathway. Another drug, mesalamine, can also activate PPAR-gamma, but to a moderate extent. It has more localized action in the gut and therefore has fewer systemic side effects. This drug is now used as the first-line treatment of IBD. Notably, the anti-inflammatory effects of this drug are mediated through its ability to upregulate PPAR-gamma.23 Moreover, controlled studies have demonstrated that mesalamine treatment reduces Proteobacteria abundance and increases the abundance of Faecalibacterium and Bifidobacterium species!24

A group of researchers in Beijing have also identified Danshensu Bingpian Zhi (DBZ) as a PPAR-gamma agonist with potential for preventing or reversing gut dysbiosis. DBZ is a synthetic version of two compounds that are naturally found in the traditional Chinese medicinal formula Fufang Danshen. DBZ was found to activate PPAR-gamma to a lesser extent than rosiglitazone and other classic thiazolidinedione drugs, yet was still able to confer significant protection against the gut dysbiosis, intestinal barrier dysfunction, insulin resistance, and body weight gain in a mouse model of diet-induced obesity.25

Butyrate supplementation has also been shown to shift the gut ecosystem in humans. A prospective, randomized, placebo-controlled study of 49 patients with IBD found that 1800 milligrams per day of butyrate not only reduced inflammation and improved quality of life, but also increased the number of butyrate-producing bacteria! After two months of supplementation, individuals with Crohn’s disease had increased abundance of Butyricoccus and Subdoligranulum, while those with ulcerative colitis had a major increase in Lachnospiraceae.26 While the researchers did not directly measure PPAR-gamma, the involvement of this pathway is likely given such a dramatic change in the abundance of butyrate producers and inflammatory markers.

Altogether, this is an incredibly intriguing area of study that will no doubt get more attention in the years to come. As Litvak et al. wrote in their recent review published in the journal Science:

“Metabolic reprogramming of colonocytes to restore epithelial hypoxia represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.” 11

In other words, if we can target the metabolism of colonocytes, we can restore the low oxygen environment in the gut and potentially reverse dysbiosis. I am actively pursuing research collaborations to determine whether butyrate and other PPAR-gamma agonists can prevent the full spectrum of antibiotic-induced dysbiosis.

Strategies to target PPAR-gamma and support gut hypoxia

Below is a summary of interventions that can potentially increase PPAR-gamma activity in the gut to support gut hypoxia. I believe that a combination of the following may be helpful for difficult cases of gut dysbiosis that do not respond to other treatments, particularly those characterized by high Proteobacteria and a low abundance of butyrate-producers.

Disclaimer: I write about a lot of these detailed mechanisms and pathways to help people who have tried almost everything and are still struggling with their gut health. If you don’t already have the major health behaviors in place — eating a healthy/ancestral-type diet, getting regular exercise, adequate sleep, sunlight, and healthy social interaction – this is where your focus should be. 

Furthermore, the following information should NOT be taken as medical advice. Always be sure to consult with your physician or gastroenterologist about whether a particular treatment is appropriate for you.

  • Mesalamine (5-ASA): this drug is commonly used as first-line treatment of IBD. It’s anti-inflammatory effects have been shown to be mediated through its ability to upregulate PPARgamma.23
  • Danshensu Bingpian Zhi (DBZ): this compound is derived from tanshinol and borneol, found in the traditional Chinese medicinal formula Fufang Danshen. It upregulates PPAR-gamma, and has demonstrated potential for attenuating dysbiosis.25 Note: Herbals should be sourced and dosed carefully, ideally under the direction of a physician experienced in herbal medicine.
  • Butyrate: a short-chain fatty acid and potent stimulator of PPAR-gamma. Even low concentrations of butyrate have been shown to increase PPAR-gamma protein expression by 7-fold. I typically recommend ProButyrate, though ButyCaps Tributyrin may also be a viable option (no affiliations).
  • Ketones: beta-hydroxybutyrate and acetoacetate almost certainly activate PPAR-gamma in intestinal epithelial cells, just as butyrate does. A ketogenic diet has been shown to upregulate PPAR-gamma across a number of tissues and also provides substrate for beta oxidation and epithelial energy production. I am hoping to support more research in this area.
  • Fasting/caloric restriction: One study found that intestinal PPAR-gamma was required for sympathetic nervous system activation during caloric restriction.27 However, the degree to which fasting or caloric restriction induces this pathway in the gut is still unclear.
  • Exercise: one research group found that the protective effects of voluntary exercise on the gut in both a colitis model and a diet-induced obesity model were mediated by the ability of exercise to increase endogenous glucocorticoids in the gut and upregulate PPAR-gamma!28,29 Future studies in our lab will be studying the potential implications of exercise on this pathway.
  • Stress management: stress reduces PPAR-gamma expression in the gut.20
  • Cannabinoids: cannabidiol (CBD) reduced iNOS activity in rectal biopsies of patients with ulcerative colitis, an effect that was mediated through activation of PPAR-gamma.30
  • Sulforaphane: a 2008 found that this phytochemical from cruciferous vegetables enhances components of innate immunity via activation of PPAR-gamma.31
  • Curcumin: one study found that curcumin inhibited chemically-induced colitis in mice by activation of PPAR-gamma.32 The oral dosage required to achieve these effects is unknown.
  • Other herbals: chamomile, angelica, silymarin, licorice root, and lemon balm are all partial activators of PPAR-gamma. These herbs can be taken individually but are all found within the product Iberogast, which has been shown to be clinically effective for IBS and functional GI disorders.33
  • Fatty acids: Conjugated linoleic acid (CLA)34 and omega-3 fatty acids (DHA)35 both enhance expression of PPAR-gamma.
  • Probiotics: In vitro studies on colonocytes have demonstrated the ability of Saccharomyces boulardii to increase PPAR-gamma expression.
  • Prebiotics: in vitro studies on colonocytes have shown that the anti-inflammatory effects of the oligosaccharides alpha3-siallylactose and FOS are mediated through their ability to induce PPAR-gamma.36
  • Vitamin A: retinoic acid, a form of vitamin A, is required for the activation and function of PPAR-gamma.

The importance of mitochondrial health

Mitochondria are essential to butyrate metabolism and oxygen utilization, and are therefore crucial to maintaining the low-oxygen environment of the gut. PPAR-gamma activation itself helps support the formation of new mitochondria through a process called mitochondrial biogenesis. However, supplemental nutrients like L-Carnitine, CoQ10, alpha lipoic acid, and others may also be useful to optimize mitochondrial health and oxygen consumption.

Harnessing synergy for breaking the cycle

While each of these components may be helpful on their own, there is also potential for synergism between these components. For instance, mesalamine combined with curcumin or butyrate has been shown to be more effective for the treatment of IBD than mesalamine alone.37,38

The synergistic potential of more than two components together has not yet been studied, but we might imagine that an integrative approach, using a combination of mesalamine, curcumin, DHA, and CBD to activate PPAR-gamma, butyrate and ketones to provide energy for epithelial cells, and L-carnitine to ensure these substrates actually get into the mitochondria to be utilized.

I am currently trialing such approaches in my one-on-one work with clients and will post the results once I have a chance to test this out more. Please note that these individuals are working very closely with their gastroenterologists to implement this. I am not a licensed physician and do NOT recommend using the more potent PPAR-gamma agonists without the close oversight of a medical doctor.

What about dysbiosis of the small intestine?

So far, all of the research I’ve discussed has been focused on colon metabolism and colonic dysbiosis. But we now know that small intestinal dysbiosis, rather than bacterial overgrowth, is responsible for a great deal of gut symptoms, especially the abdominal discomfort and bloating that underlies irritable bowel syndrome (IBS).

As of this writing, this metabolic switch has only been shown in the colon, or large intestine. While PPAR-gamma expression is much lower in the small intestine than the colon, it’s entirely plausible that the same switch occurs in the small intestine.

Indeed, one 2016 animal study published in PNAS found that a processed high-sugar, high-fat diet downregulated PPAR-gamma in the small intestine almost two-fold, which led to altered antimicrobial gene expression and small intestinal dysbiosis.39  This was reversed when the mice were treated for one week with rosiglitazone, a PPAR-gamma agonist.

Glutamine, an amino acid that serves as the primary fuel for small intestinal epithelial cells, has also been shown to induce PPAR-gamma40,41, much like butyrate does in the large intestine.

What about mesalamine for IBS? Several research groups have explored the off-label use of this IBD drug for treating IBS. Most studies have found fairly low efficacy for IBS symptoms; however, a recent study using a higher dosage (1500 mg once per day) for 12 weeks demonstrated significant benefit in IBS-D patients.42

As in the colon, I believe that integrative, synergistic treatments may have potential for restoring small intestinal homeostasis. It’s possible that mesalamine or DBZ combined with glutamine and ketones would be more efficacious than mesalamine alone for IBS, though this remains to be tested in controlled studies.

Regrettably, treatment of “SIBO” has largely focused on antibiotics, which often reduce symptoms in the short-term, but may further stress the gut epithelium, leading to relapse or even the worsening of symptoms in the long-term. Rather than quelling bacterial overgrowth, we need to shift our focus towards creating a gut environment that favors growth of healthy microbes.

Summary & takeaways: how this knowledge may inform treatment

That was a lot of information and nitty-gritty pathways, but hopefully you can see the enormous potential of this knowledge for shaping how we approach gut dysbiosis and disease! Below are the key takeaways from this body of research and potential ways to put this knowledge into practice:

1) An abundance of Proteobacteria and lack of butyrate-producers is a common signature of gut dysbiosis and typically indicates epithelial metabolic dysfunction and gut inflammation. There are several commercially available microbiome tests that will allow you to check your abundance of Proteobacteria and butyrate-producers.

2) Antibiotics, gut infections, low fiber intake, or stress can all deplete gut butyrate, lead to oxygen leakage into the gut, and promote gut dysbiosis. Avoiding antibiotics whenever possible, treating existing gut infections, eating plenty of fiber, and managing stress are key to supporting healthy gut metabolism and in turn, a healthy gut microbiota.

3) This new understanding of how oxygen drives gut dysbiosis directs future research and offers important insight as to how we might be able to reestablish a healthy ecosystem. In other words, if we can overcome the epithelial energy starvation and restore gut hypoxia, we may be able to restore a healthy gut ecosystem and reverse dysbiosis.

4) If you have to take antibiotics, take butyrate! Antibiotics wipe out butyrate producers, putting significant stress on the cells that line the large intestine. If we can support epithelial metabolism with supplemental butyrate until our butyrate-producers can recover, theoretically, we may be able to prevent an environment that favors opportunistic pathogens. (Likewise, supplementing with glutamine may prevent antibiotic-induced dysbiosis in the small intestine.)

5) If basic diet and lifestyle interventions are not enough, targeting PPAR-gamma and colonic energy starvation may be the key to breaking the cycle and reversing gut dysbiosis. This may be particularly useful for those with IBD and those with very stubborn “SIBO” or IBS symptoms.

6) There are numerous interventions with the potential to synergistically “reprogram” colonocytes, ranging from drug therapies to nutrients and lifestyle factors. I discussed many of the known interventions in this article but am hopeful that future research will further explore these therapies, both in isolation and in combination, to elucidate the best therapies to treat gut dysbiosis.

That’s all for now! Let me know what you think in the comments below, subscribe to my newsletter to be notified of any updates, and please share your experience if you use any of this information to improve your own health!

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  12. Rivera-Chávez, F. et al. Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella. Cell Host & Microbe 19, 443–454 (2016).
  13. Lupp, C. et al. Host-Mediated Inflammation Disrupts the Intestinal Microbiota and Promotes the Overgrowth of Enterobacteriaceae. Cell Host & Microbe 2, 119–129 (2007).
  14. De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U.S.A. 107, 14691–14696 (2010).
  15. Chassaing, B. et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 519, 92–96 (2015).
  16. Palmnäs, M. S. A. et al. Low-dose aspartame consumption differentially affects gut microbiota-host metabolic interactions in the diet-induced obese rat. PLoS ONE 9, e109841 (2014).
  17. Langgartner, D. et al. Individual differences in stress vulnerability: The role of gut pathobionts in stress-induced colitis. Brain Behav. Immun. 64, 23–32 (2017).
  18. Fachi, J. L. et al. Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism. Cell Reports 27, 750-761.e7 (2019).
  19. Peyrin-Biroulet, L. et al. Peroxisome proliferator-activated receptor gamma activation is required for maintenance of innate antimicrobial immunity in the colon. Proc. Natl. Acad. Sci. U.S.A. 107, 8772–8777 (2010).
  20. Ponferrada, Á. et al. The Role of PPARγ on Restoration of Colonic Homeostasis After Experimental Stress-Induced Inflammation and Dysfunction. Gastroenterology 132, 1791–1803 (2007).
  21. Peroxisome proliferator-activated receptor-gamma (PPAR-γ) expression is downregulated in patients with active ulcerative colitis. – PubMed – NCBI. https://www.ncbi.nlm.nih.gov/pubmed/20848495.
  22. Sánchez-Hidalgo, M., Martín, A. R., Villegas, I. & Alarcón de la Lastra, C. Rosiglitazone, a PPARγ ligand, modulates signal transduction pathways during the development of acute TNBS-induced colitis in rats. European Journal of Pharmacology 562, 247–258 (2007).
  23. Rousseaux, C. et al. Intestinal antiinflammatory effect of 5-aminosalicylic acid is dependent on peroxisome proliferator-activated receptor-gamma. J. Exp. Med. 201, 1205–1215 (2005).
  24. Xu, J. et al. 5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis. Front Microbiol 9, (2018).
  25. Xu, P. et al. DBZ is a putative PPARγ agonist that prevents high fat diet-induced obesity, insulin resistance and gut dysbiosis. Biochim Biophys Acta Gen Subj 1861, 2690–2701 (2017).
  26. Facchin, S. et al. P655 Microencapsulated Sodium Butyrate significantly modifies the microbiota in patients with inflammatory bowel disease mimicking prebiotic activity and proving effects on the treatment of the disease. in (2019). doi:10.1093/ecco-jcc/jjy222.779.
  27. Duszka, K. et al. Intestinal PPARγ signalling is required for sympathetic nervous system activation in response to caloric restriction. Scientific Reports 6, 36937 (2016).
  28. Liu, W.-X. et al. Voluntary exercise protects against ulcerative colitis by up-regulating glucocorticoid-mediated PPAR-γ activity in the colon in mice. Acta Physiologica 215, 24–36 (2015).
  29. Liu, W.-X. et al. Voluntary exercise prevents colonic inflammation in high-fat diet-induced obese mice by up-regulating PPAR-γ activity. Biochemical and Biophysical Research Communications 459, 475–480 (2015).
  30. Filippis, D. D. et al. Cannabidiol Reduces Intestinal Inflammation through the Control of Neuroimmune Axis. PLOS ONE 6, e28159 (2011).
  31. Schwab, M. et al. The dietary histone deacetylase inhibitor sulforaphane induces human β-defensin-2 in intestinal epithelial cells. Immunology 125, 241–251 (2008).
  32. Zhang, M., Deng, C., Zheng, J., Xia, J. & Sheng, D. Curcumin inhibits trinitrobenzene sulphonic acid-induced colitis in rats by activation of peroxisome proliferator-activated receptor gamma. International Immunopharmacology 6, 1233–1242 (2006).
  33. Malfertheiner, P. STW 5 (Iberogast) Therapy in Gastrointestinal Functional Disorders. Dig Dis 35 Suppl 1, 25–29 (2017).
  34. Bassaganya-Riera, J. et al. Activation of PPAR γ and δ by conjugated linoleic acid mediates protection from experimental inflammatory bowel disease. Gastroenterology 127, 777–791 (2004).
  35. Yamamoto, K. et al. 4-Hydroxydocosahexaenoic acid, a potent peroxisome proliferator-activated receptor γ agonist alleviates the symptoms of DSS-induced colitis. Biochemical and Biophysical Research Communications 367, 566–572 (2008).
  36. Zenhom, M. et al. Prebiotic Oligosaccharides Reduce Proinflammatory Cytokines in Intestinal Caco-2 Cells via Activation of PPARγ and Peptidoglycan Recognition Protein 3. J Nutr 141, 971–977 (2011).
  37. Vernia, P. et al. Combined oral sodium butyrate and mesalazine treatment compared to oral mesalazine alone in ulcerative colitis: randomized, double-blind, placebo-controlled pilot study. Dig. Dis. Sci. 45, 976–981 (2000).
  38. Lang, A. et al. Curcumin in Combination With Mesalamine Induces Remission in Patients With Mild-to-Moderate Ulcerative Colitis in a Randomized Controlled Trial. Clin. Gastroenterol. Hepatol. 13, 1444-1449.e1 (2015).
  39. Tomas, J. et al. High-fat diet modifies the PPAR-γ pathway leading to disruption of microbial and physiological ecosystem in murine small intestine. Proc. Natl. Acad. Sci. U.S.A. 113, E5934–E5943 (2016).
  40. Peng, Z., Ban, K., Wawrose, R. A., Gover, A. G. & Kozar, R. A. Protection by enteral glutamine is mediated by intestinal epithelial cell peroxisome proliferator-activated receptor-γ during intestinal ischemia/reperfusion. Shock 43, 327–333 (2015).
  41. Sato, N. et al. Differential induction of PPAR-γ by luminal glutamine and iNOS by luminal arginine in the rodent postischemic small bowel. American Journal of Physiology-Gastrointestinal and Liver Physiology 290, G616–G623 (2006).
  42. Possible overlap of IBS symptoms and inflammatory bowel disease. ScienceDaily https://www.sciencedaily.com/releases/2012/10/121022081236.htm.
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The oxygen-gut dysbiosis connection

November 14th, 2019

Virtually every cell in the human body requires oxygen. That is – every human cell. Most of our microbial cells on the other hand, thrive in an environment devoid of oxygen. If oxygen leaks into the gut, it can promote bacterial imbalances and inflammation. Read on to learn more about the oxygen-gut dysbiosis connection, and how we might use this knowledge to improve gut health.

The human body requires oxygen for survival. But we’re only about 43 percent human.1 The other 57 percent are microbes – most of which do not tolerate oxygen very well. Fortunately, these microbes reside in the colon, which in a healthy state is a low-oxygen environment.

If the state of the gut is perturbed, however, oxygen can start to leak into the gut, beginning a vicious cycle of gut dysbiosis, cellular energy starvation, and inflammation. In this article, I’ll break down the oxygen-gut dysbiosis connection and discuss its potential implications in shaping gut treatment.

Fair warning: this one is going to be dense, as this is the culmination of several months of independent research, but it is probably one of the most important articles I’ve ever written. As always, I’ll provide a succinct summary & takeaways section at the end for anyone who just wants the actionable insights.

The healthy colon: a low oxygen environment rich in microbes

The human gut is home to a dense community of microbes. The healthy human colon contains an estimated 38 trillion bacterial cells, which are predominantly obligate anaerobes. These are bacteria that can only grow and reproduce in an environment largely devoid of oxygen. Many of these bacteria are crucial to breaking down complex carbohydrates to produce important gut metabolites like short-chain fatty acids.

The healthy colon may also contain a small number of facultative anaerobes, which are capable of growing and reproducing in an environment with or without oxygen. Facultative anaerobes include many gut pathogens. The low oxygen concentration of a healthy gut and the abundance of obligate anaerobes both suppress the growth of these facultative anaerobes.

Butyrate helps maintain “physiologic hypoxia” in the colon

One of the metabolites produced by obligate anaerobes is butyrate. Butyrate is a short-chain fatty acid (SCFA) produced when these bacteria metabolize dietary fiber in the colon. I’ve written before about the benefits of butyrate for health, including its ability to attenuate neuroinflammation, protect against colon cancer, and help maintain gut barrier function. It wasn’t until recently, however, that I learned about the role of butyrate in maintaining low gut oxygen levels.

In the healthy gut, butyrate supplies about 70 percent of the energy required by colonocytes. These are the cells that line the colon and form the gut barrier. After uptake by colonocytes, butyrate and other SCFAs are broken down in the mitochondria through a process called beta oxidation. This process utilizes large amounts of oxygen. As it turns out, this colonocyte oxygen consumption is very important to maintaining gut homeostasis.

In 2015, a research group led by Dr. Sean Colgan at the University of Colorado demonstrated that gut metabolism of butyrate was required for maintaining “physiologic hypoxia” in the colon.2 Through a series of experiments, they demonstrated that butyrate, and to a lesser extent, the SCFAs propionate and acetate, deplete oxygen levels in colonocytes. This leads to the stabilization of a protein called hypoxia-inducible factor (HIF), which acts as a sort of “oxygen sensor” in the cell. When oxygen levels are low, HIF promotes the expression of genes that help coordinate gut barrier protection. If oxygen levels rise, HIF is no longer stabilized, and these gut-protective genes are no longer expressed.

The researchers wondered whether antibiotics could affect this state of hypoxia. After just three days of broad-spectrum antibiotics, butyrate levels had dropped dramatically, gut oxygen levels had risen, and the state of epithelial hypoxia was lost. The oxygen-sensor HIF was no longer stabilized, and the gut-protective genes were no longer expressed, leading to a loss of gut barrier function.

And it wasn’t just a lack of fiber, the substrate for butyrate production. The gut microbiota of the antibiotic-treated mice had completely lost its ability to produce butyrate or other SCFAs from dietary fermentable fibers! Fortunately, they went on to find that the administration of supplemental butyrate was able to rescue the “physiologic hypoxia” and gut barrier function. But more on that later.

A microbial signature of gut dysbiosis: low abundance of butyrate producers and an expansion of facultative anaerobes

For now, we’re going to switch gears a bit. The term “gut dysbiosis” generally refers to an altered state of the gut microbiota, often associated with disease. In the last decade, advanced sequencing techniques have allowed us to characterize gut dysbiosis in hundreds of different diseases. While there are virtually infinite states of the gut microbiota that could be considered dysbiosis, there do seem to be a few patterns that are most frequently associated with disease.

In a 2017 review paper, Litvak et al. wrote:

Perhaps the most consistent and robust ecological pattern observed during gut dysbiosis is an expansion of facultative anaerobic bacteria belonging to the phylum Proteobacteria.” 3

Proteobacteria is one of five major bacterial phyla that are commonly found in the human gut. It includes a wide variety of genera, including Escherichia, Shigella, Salmonella, Helicobacter, Vibrio, Yersinia, Pseudomonas, Campylobacter, and Desulfovibrio. Most of these are considered opportunistic pathogens – microbes that are harmless at low abundance, in the context of a balanced ecosystem, but quickly expand and cause issues when the environment becomes particularly suitable for their growth.

One environmental factor that leads to a rapid expansion of Proteobacteria is – you guessed it – oxygen. Most Proteobacteria are facultative anaerobes, meaning they can survive and reproduce in the presence of oxygen. This gives them a significant competitive advantage over beneficial obligate anaerobes in an environment that contains oxygen.

Notably, the expansion of Proteobacteria is almost always accompanied by a reduction in the abundance of butyrate-producing bacteria. This pattern – high Proteobacteria and low butyrate-producers – is a microbial signature of dysbiosis and has been associated with a number of chronic diseases, including:

  • Inflammatory bowel disease4
  • Irritable bowel syndrome5
  • Colorectal cancer6
  • Diverticulitis7
  • Histamine intolerance8
  • Type 2 diabetes9
  • Obesity10

As we’ll learn in the next few sections, this signature also suggests an underlying epithelial dysfunction.

Epithelial cell metabolism drives gut dysbiosis

Epithelial cells are the cells that line the wall of the gut and are the primary interface for host-microbe communication. Recall from earlier that when the gut is healthy and in a state of homeostasis, colonocytes primarily metabolize fatty acids like butyrate through processes that utilize large amounts of oxygen. The resulting hypoxia (lack of oxygen) in the gut mucosa helps to maintain a gut microbiota dominated by obligate anaerobes. These obligate anaerobic bacteria in turn promote health by fermenting fiber into SCFAs like butyrate, which are absorbed by colonic epithelial cells. This positive feedback loop maintains a state of gut health.

However, when a disturbance shifts the metabolism of colonic epithelial cells away from beta oxidation of fatty acids, the system breaks down. Energy-starved colonocytes must look for other sources of energy. They end up pulling glucose from the bloodstream and fermenting it to lactate, a process that does not utilize oxygen.11 The resulting inflammation also leads to increased production of nitrate. Without anywhere else to go, oxygen, lactate, and nitrate “leak” into the gut mucosa.

This environmental change favors pathogens in the Proteobacteria phylum, such as Salmonella, Klebsiella, Citrobacter, and E. coli, which can tolerate oxygen and thrive on lactate and nitrate. At the same time, the oxygenation of the colon inhibits the growth of obligate anaerobes, including the ever-important butyrate-producers. In other words, the metabolism of colonocytes functions as a control switch of the gut microbiota, mediating a shift between homeostatic and dysbiotic communities.” 11

So, what causes epithelial cells to make this switch that ultimately leads to gut dysbiosis? In the next few sections, I’ll discuss a few known inducers of this epithelial switch: antibiotics, infections, and a low fiber diet.

Antibiotics deplete colonic butyrate and drive oxygen leakage into the gut

Last spring, I had the pleasure of meeting Dr. Sebastian Winter, a professor of microbiology and immunology at UT Southwestern and one of the few prominent researchers trying to understand this control switch and its impact on host health.

In an animal model, Dr. Winter’s lab demonstrated in 2016 that a single dose of the antibiotic streptomycin resulted in a four-fold reduction in gut butyrate concentrations.12 This was primarily attributed to depletion of populations of Clostridia, a class of bacteria that consists of many known butyrate-producers, including Eubacterium, Roseburia, Butyrivibrio, Clostridium, Coprococcus, and Ruminococcus species.

Using a special staining technique, they went on to demonstrate that the antibiotic treatment had increased colonocyte oxygenation and resulted in a loss of hypoxia in the gut mucosa. This loss of hypoxia allowed for the oxygen-driven expansion of Salmonella and other facultative anaerobes.

Of course, Dr. Winter’s lab chose streptomycin specifically because it is particularly effective at depleting Clostridia, so that they could examine the effects of butyrate depletion on colonic metabolism. Streptomycin is not typically used orally in humans; however, many other broad-spectrum antibiotics are known to impact butyrate-producing bacteria, so it’s likely that a 1-2 week course of other antibiotics would also drive oxygen leakage into the gut via this same mechanism.

Pathogenic bacteria can hack colonocyte metabolism to promote gut dysbiosis

Certain pathogens may also exploit this colonocyte switch to gain a competitive advantage in the gut. If you’ve ever come down with an acute case of food poisoning and had trouble with your gut health afterwards, this could explain why.

In the same paper highlighted in the previous section, Byndloss et al. further demonstrated that certain strains of Salmonella (specifically Salmonella enterica serotype Typhimurium, hereafter abbreviated S. Tm) can manipulate the host epithelium to promote gut dysbiosis.12

S. Tm is a particularly virulent bacterium that invades the host mucosa, causing severe inflammation. This inflammation led to a depletion of butyrate-producing Clostridia, which further enhanced the ability of S. Tm to proliferate in the gut. In other words, this suggests that certain pathogens may “hack” gut metabolism to increase their own fitness, to the detriment of healthy bacteria.

Notably, the depletion of butyrate-producers appeared to be more gradual than with antibiotic treatment, occurring over about 1-3 weeks, but was also much slower to recover. At four weeks post-infection, the abundance of Clostridia was still two and a half orders of magnitude below baseline levels.

The inflammation induced by S. Tm also resulted in the release of reactive oxygen and nitrogen species into the gut, which reacted with simple sugars to form substrates that selectively fed S. Tm and other microbes within the Enterobacteriaceae family (Proteobacteria phylum).

This is not just true of S. Tm. In 2007, Lupp et al. demonstrated in a mouse model that Citrobacter rodentium and Campylobacter jejuni infection are also capable of causing host intestinal inflammation and driving overgrowth of Enterobacteriaceae.13

Overall, this suggests that gut infections may contribute to oxygenation of the colon and promote a prolonged state of gut dysbiosis. Thus, clearing existing infections may be a key step to restoring the normal metabolism of the gut epithelium and a healthy gut microbiota.

A low fiber diet may drive oxygen leakage and Proteobacteria expansion

So far, we’ve seen two examples where butyrate depletion led to gut oxygenation and dysbiosis. Given that the #1 source of butyrate is from dietary fiber, it’s likely that a low fiber diet could, in theory, promote the expansion of Proteobacteria via the same mechanism. If dietary fiber intake is low, butyrate and other SCFAs will not be produced at sufficient levels to provide for the energy needs of colonocytes. Colonocytes will turn to anaerobic glucose metabolism. Anaerobic metabolism will consume less oxygen and result in increased oxygen leakage into the gut.

While all of the steps in this mechanism have yet to be as elegantly demonstrated with a low fiber diet as they have for antibiotics and gut infections, several studies have indeed linked low fiber intake with higher levels of Proteobacteria:

  • A large-scale comparative study among children from urban areas in Europe and children from a rural African village in Burkina Faso found that European children had higher levels of Enterobacteriaceae.14 The researchers speculated that this was due to the low fiber content in the Western diet.
  • A 2009 study found that individuals on a gluten-free diet had lower relative abundance of Bifidobacterium and Lactobacillus, and higher amounts of Enterobacteriaceae. The gluten-free diet had significantly reduced the participants’ intake of polysaccharides.

What about a low carb, ketogenic diet? As I’ve discussed before, the ketone bodies acetoacetate and beta-hydroxybutyrate can supplement butyrate as a fuel source for gut epithelial cells. Thus, it’s unlikely that a low-fiber, ketogenic diet would activate this mechanism to drive gut dysbiosis. In fact, ketones might be beneficial in helping to restore epithelial hypoxia. We’ll come back to that later.

Other agents that contribute to gut inflammation may also drive gut dysbiosis

Intriguingly, all of these drivers of gut dysbiosis – antibiotics, gut infections, and a low fiber, processed diet – are associated with intestinal inflammation.

In 2007, Lupp et al. demonstrated in animal models that gut inflammation itself is enough to disrupt the gut microbiota and promote overgrowth of Enterobacteriaceae. Both exposure to dextran sodium sulfate, a chemical that disrupts gut barrier integrity, or severe genetic predisposition, via knocking out IL-10, were  able to drive gut dysbiosis.13

Other, more mild inflammatory agents could also promote the expansion of these inflammatory bacteria. Chassaing et al. (2015) demonstrated that feeding mice carboxymethylcellulose and polysorbate-80, two emulsifiers commonly used in processed foods, for 12 weeks reduced microbial diversity and resulted in increased mucosa-associated Proteobacteria.15 Similarly, Palmnas et al. found that feeding rats the non-caloric sweetener Aspartame for 8 weeks resulted in increased Enterobacteriaceae.16

Stress can also promote inflammation and gut dysbiosis. Langgartner et al. reported an expansion of Proteobacteria in a mouse model for chronic psychosocial stress.17

Unrecognized food intolerances may also contribute to gut inflammation, altered colonocyte metabolism, and gut dysbiosis, though more research is needed to confirm this.

Alright, so we’ve reviewed a number of things that can cause gut hypoxia and drive gut dysbiosis. For the remainder of this article, I want to focus on things we can do to potentially interrupt this cycle and restore gut homeostasis. First up: butyrate!

Butyrate helps maintain gut hypoxia and protects against pathogen expansion after antibiotics

Ever since publishing my article on why probiotics might not be the best choice after antibiotics, I have received a lot of questions about what we can do to protect our gut health when we do have to take antibiotics.

At the time, I didn’t have a great answer. Now, having dug deeper into the research, I think there is enough evidence to suggest that butyrate supplementation might be particularly helpful! Over the next few sections, I’ll lay out the research that supports this hypothesis, and close with my recommendations for putting this into action.

In Dr. Winter’s studies mentioned above, streptomycin treatment depleted butyrate-producers and caused oxygenation of the mucosa – that is, unless the mice were treated with oral tributyrin, a form of butyrate that is targeted for release in the gut: “Remarkably, tributyrin supplementation restored epithelial hypoxia in streptomycin-treated mice and significantly increased the concentration of cecal butyrate.” 12

In the experimental infection model, tributyrin supplementation also reduced the fitness advantage of pathogenic bacteria! After streptomycin treatment alone, S. Tm had a significant competitive advantage in the gut, expanding to fill a greater percentage of the overall ecosystem. However, when tributyrin was provided orally three hours post-infection, the competitive advantage was lost.

Butyrate restores hypoxia and protects against C. difficile-induced colitis

In 2019, Fachi et al. demonstrated in a mouse model that administering butyrate alongside antibiotics could attenuate C. difficile-induced colitis.18 Clostridioides difficile (previously classified as Clostridium difficile and commonly abbreviated C. diff) is a gram-positive, spore-forming bacterium that is a common cause of intestinal infection after antibiotic use.

Supplemental butyrate was started one day before antibiotics and continued throughout the antibiotic course and 5-day infection challenge. Interestingly, butyrate had no effects on C. difficile colonization or toxin production, but through stabilizing HIF-1 and increasing gut barrier integrity, butyrate reduced intestinal inflammation and the movement of bacteria across the gut barrier.

The researchers went on to test two additional strategies for providing butyrate. High dose tributyrin administered in the three days surrounding infection was equally as protective as butyrate, as was feeding a high-fiber diet (containing a whopping 25 percent inulin) after antibiotics but prior to infection.

So clearly, butyrate protects against pathogen expansion after antibiotics. But can butyrate prevent the full spectrum of dysbiosis associated with antibiotics, by supporting colonocyte metabolism? This remains to be determined in controlled studies, but as we’ll see in the next section, the pieces certainly seem to fit together nicely.

PPAR-gamma as the control switch for colonocyte metabolism

So far, I’ve been talking rather abstractly about a “switch” in colonocyte metabolism that leads to gut dysbiosis. But it turns out that researchers have identified a particular gene, PPAR-gamma, that appears to mediate this switch. PPARs (which is short for peroxisome proliferator-activated receptors) are a group of proteins that bind to DNA to directly influence gene expression. PPAR-gamma is expressed in a number of cells but is most highly expressed in the adipose (fat) tissue and colon.

In a healthy gut, butyrate not only provides energy for colon cells, but also enhances PPAR-gamma activation. This acts a positive feedback loop: PPAR-gamma activates genes that increase metabolism of butyrate and other fatty acids. This reduces the oxygen concentration in the epithelium and gut mucosa, which inhibits the growth of pathogenic Proteobacteria and promotes the growth of beneficial, butyrate-producing bacteria.

In a dysbiotic gut, however, there is not enough butyrate or other substrates to activate PPAR-gamma. Lower PPAR-gamma expression results in increased expression of Nos2, the gene encoding inducible nitric oxide synthase (iNOS) and increased nitrate release into the gut. This, along with the lactate and oxygen from anaerobic glycolysis, fuels the growth of pathogenic bacteria.

PPAR-gamma activation is also crucial for the maintenance of gut innate immunity. A study published in the journal PNAS in 2010 demonstrated through a series of experiments that PPAR-gamma helps to maintain constant expression of the antimicrobial peptide β-defensin, which regulates microbial colonization of the colon.19 Mice that were deficient in PPAR-gamma showed defective immune defenses against Candida albicans, Bacteroides fragilis, Enterococcus faecalis, and E. coli. PPAR-gamma is also required for the production of secretory IgA.20

Could stimulating the PPAR-gamma pathway prevent or reverse gut dysbiosis?

Several studies have demonstrated that PPAR-gamma activation could potentially prevent or reverse gut dysbiosis and tissue injury associated with immune activation. For instance, PPAR-gamma expression is significantly reduced in inflammatory bowel disease (IBD).21 Rosiglitazone, a drug that binds to PPAR-gamma and increases its activity, has been shown to prevent dysbiosis and reduce symptoms of colitis in animal models, when given acutely.22 While this drug is still sometimes used in the U.S. as an antidiabetic drug, it has several unwanted side effects, and is not ideal for long-term use. Nonetheless, it demonstrates the ability of this pathway to exert significant changes on the gut microbiota.

Researchers kept looking for other options to stimulate this pathway. Another drug, mesalamine, can also activate PPAR-gamma, but to a moderate extent. It has more localized action in the gut and therefore has fewer systemic side effects. This drug is now used as the first-line treatment of IBD. Notably, the anti-inflammatory effects of this drug are mediated through its ability to upregulate PPAR-gamma.23 Moreover, controlled studies have demonstrated that mesalamine treatment reduces Proteobacteria abundance and increases the abundance of Faecalibacterium and Bifidobacterium species!24

A group of researchers in Beijing have also identified Danshensu Bingpian Zhi (DBZ) as a PPAR-gamma agonist with potential for preventing or reversing gut dysbiosis. DBZ is a synthetic version of two compounds that are naturally found in the traditional Chinese medicinal formula Fufang Danshen. DBZ was found to activate PPAR-gamma to a lesser extent than rosiglitazone and other classic thiazolidinedione drugs, yet was still able to confer significant protection against the gut dysbiosis, intestinal barrier dysfunction, insulin resistance, and body weight gain in a mouse model of diet-induced obesity.25

Butyrate supplementation has also been shown to shift the gut ecosystem in humans. A prospective, randomized, placebo-controlled study of 49 patients with IBD found that 1800 milligrams per day of butyrate not only reduced inflammation and improved quality of life, but also increased the number of butyrate-producing bacteria! After two months of supplementation, individuals with Crohn’s disease had increased abundance of Butyricoccus and Subdoligranulum, while those with ulcerative colitis had a major increase in Lachnospiraceae.26 While the researchers did not directly measure PPAR-gamma, the involvement of this pathway is likely given such a dramatic change in the abundance of butyrate producers and inflammatory markers.

Altogether, this is an incredibly intriguing area of study that will no doubt get more attention in the years to come. As Litvak et al. wrote in their recent review published in the journal Science:

“Metabolic reprogramming of colonocytes to restore epithelial hypoxia represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.” 11

In other words, if we can target the metabolism of colonocytes, we can restore the low oxygen environment in the gut and potentially reverse dysbiosis. I am actively pursuing research collaborations to determine whether butyrate and other PPAR-gamma agonists can prevent the full spectrum of antibiotic-induced dysbiosis.

Strategies to target PPAR-gamma and support gut hypoxia

Below is a summary of interventions that can potentially increase PPAR-gamma activity in the gut to support gut hypoxia. I believe that a combination of the following may be helpful for difficult cases of gut dysbiosis that do not respond to other treatments, particularly those characterized by high Proteobacteria and a low abundance of butyrate-producers.

Disclaimer: I write about a lot of these detailed mechanisms and pathways to help people who have tried almost everything and are still struggling with their gut health. If you don’t already have the major health behaviors in place — eating a healthy/ancestral-type diet, getting regular exercise, adequate sleep, sunlight, and healthy social interaction – this is where your focus should be. 

Furthermore, the following information should NOT be taken as medical advice. Always be sure to consult with your physician or gastroenterologist about whether a particular treatment is appropriate for you.

  • Mesalamine (5-ASA): this drug is commonly used as first-line treatment of IBD. It’s anti-inflammatory effects have been shown to be mediated through its ability to upregulate PPARgamma.23
  • Danshensu Bingpian Zhi (DBZ): this compound is derived from tanshinol and borneol, found in the traditional Chinese medicinal formula Fufang Danshen. It upregulates PPAR-gamma, and has demonstrated potential for attenuating dysbiosis.25 Note: Herbals should be sourced and dosed carefully, ideally under the direction of a physician experienced in herbal medicine.
  • Butyrate: a short-chain fatty acid and potent stimulator of PPAR-gamma. Even low concentrations of butyrate have been shown to increase PPAR-gamma protein expression by 7-fold. I typically recommend ProButyrate, though ButyCaps Tributyrin may also be a viable option (no affiliations).
  • Ketones: beta-hydroxybutyrate and acetoacetate almost certainly activate PPAR-gamma in intestinal epithelial cells, just as butyrate does. A ketogenic diet has been shown to upregulate PPAR-gamma across a number of tissues and also provides substrate for beta oxidation and epithelial energy production. I am hoping to support more research in this area.
  • Fasting/caloric restriction: One study found that intestinal PPAR-gamma was required for sympathetic nervous system activation during caloric restriction.27 However, the degree to which fasting or caloric restriction induces this pathway in the gut is still unclear.
  • Exercise: one research group found that the protective effects of voluntary exercise on the gut in both a colitis model and a diet-induced obesity model were mediated by the ability of exercise to increase endogenous glucocorticoids in the gut and upregulate PPAR-gamma!28,29 Future studies in our lab will be studying the potential implications of exercise on this pathway.
  • Stress management: stress reduces PPAR-gamma expression in the gut.20
  • Cannabinoids: cannabidiol (CBD) reduced iNOS activity in rectal biopsies of patients with ulcerative colitis, an effect that was mediated through activation of PPAR-gamma.30
  • Sulforaphane: a 2008 found that this phytochemical from cruciferous vegetables enhances components of innate immunity via activation of PPAR-gamma.31
  • Curcumin: one study found that curcumin inhibited chemically-induced colitis in mice by activation of PPAR-gamma.32 The oral dosage required to achieve these effects is unknown.
  • Other herbals: chamomile, angelica, silymarin, licorice root, and lemon balm are all partial activators of PPAR-gamma. These herbs can be taken individually but are all found within the product Iberogast, which has been shown to be clinically effective for IBS and functional GI disorders.33
  • Fatty acids: Conjugated linoleic acid (CLA)34 and omega-3 fatty acids (DHA)35 both enhance expression of PPAR-gamma.
  • Probiotics: In vitro studies on colonocytes have demonstrated the ability of Saccharomyces boulardii to increase PPAR-gamma expression.
  • Prebiotics: in vitro studies on colonocytes have shown that the anti-inflammatory effects of the oligosaccharides alpha3-siallylactose and FOS are mediated through their ability to induce PPAR-gamma.36
  • Vitamin A: retinoic acid, a form of vitamin A, is required for the activation and function of PPAR-gamma.

The importance of mitochondrial health

Mitochondria are essential to butyrate metabolism and oxygen utilization, and are therefore crucial to maintaining the low-oxygen environment of the gut. PPAR-gamma activation itself helps support the formation of new mitochondria through a process called mitochondrial biogenesis. However, supplemental nutrients like L-Carnitine, CoQ10, alpha lipoic acid, and others may also be useful to optimize mitochondrial health and oxygen consumption.

Harnessing synergy for breaking the cycle

While each of these components may be helpful on their own, there is also potential for synergism between these components. For instance, mesalamine combined with curcumin or butyrate has been shown to be more effective for the treatment of IBD than mesalamine alone.37,38

The synergistic potential of more than two components together has not yet been studied, but we might imagine that an integrative approach, using a combination of mesalamine, curcumin, DHA, and CBD to activate PPAR-gamma, butyrate and ketones to provide energy for epithelial cells, and L-carnitine to ensure these substrates actually get into the mitochondria to be utilized.

I am currently trialing such approaches in my one-on-one work with clients and will post the results once I have a chance to test this out more. Please note that these individuals are working very closely with their gastroenterologists to implement this. I am not a licensed physician and do NOT recommend using the more potent PPAR-gamma agonists without the close oversight of a medical doctor.

What about dysbiosis of the small intestine?

So far, all of the research I’ve discussed has been focused on colon metabolism and colonic dysbiosis. But we now know that small intestinal dysbiosis, rather than bacterial overgrowth, is responsible for a great deal of gut symptoms, especially the abdominal discomfort and bloating that underlies irritable bowel syndrome (IBS).

As of this writing, this metabolic switch has only been shown in the colon, or large intestine. While PPAR-gamma expression is much lower in the small intestine than the colon, it’s entirely plausible that the same switch occurs in the small intestine.

Indeed, one 2016 animal study published in PNAS found that a processed high-sugar, high-fat diet downregulated PPAR-gamma in the small intestine almost two-fold, which led to altered antimicrobial gene expression and small intestinal dysbiosis.39  This was reversed when the mice were treated for one week with rosiglitazone, a PPAR-gamma agonist.

Glutamine, an amino acid that serves as the primary fuel for small intestinal epithelial cells, has also been shown to induce PPAR-gamma40,41, much like butyrate does in the large intestine.

What about mesalamine for IBS? Several research groups have explored the off-label use of this IBD drug for treating IBS. Most studies have found fairly low efficacy for IBS symptoms; however, a recent study using a higher dosage (1500 mg once per day) for 12 weeks demonstrated significant benefit in IBS-D patients.42

As in the colon, I believe that integrative, synergistic treatments may have potential for restoring small intestinal homeostasis. It’s possible that mesalamine or DBZ combined with glutamine and ketones would be more efficacious than mesalamine alone for IBS, though this remains to be tested in controlled studies.

Regrettably, treatment of “SIBO” has largely focused on antibiotics, which often reduce symptoms in the short-term, but may further stress the gut epithelium, leading to relapse or even the worsening of symptoms in the long-term. Rather than quelling bacterial overgrowth, we need to shift our focus towards creating a gut environment that favors growth of healthy microbes.

Summary & takeaways: how this knowledge may inform treatment

That was a lot of information and nitty-gritty pathways, but hopefully you can see the enormous potential of this knowledge for shaping how we approach gut dysbiosis and disease! Below are the key takeaways from this body of research and potential ways to put this knowledge into practice:

1) An abundance of Proteobacteria and lack of butyrate-producers is a common signature of gut dysbiosis and typically indicates epithelial metabolic dysfunction and gut inflammation. There are several commercially available microbiome tests that will allow you to check your abundance of Proteobacteria and butyrate-producers.

2) Antibiotics, gut infections, low fiber intake, or stress can all deplete gut butyrate, lead to oxygen leakage into the gut, and promote gut dysbiosis. Avoiding antibiotics whenever possible, treating existing gut infections, eating plenty of fiber, and managing stress are key to supporting healthy gut metabolism and in turn, a healthy gut microbiota.

3) This new understanding of how oxygen drives gut dysbiosis directs future research and offers important insight as to how we might be able to reestablish a healthy ecosystem. In other words, if we can overcome the epithelial energy starvation and restore gut hypoxia, we may be able to restore a healthy gut ecosystem and reverse dysbiosis.

4) If you have to take antibiotics, take butyrate! Antibiotics wipe out butyrate producers, putting significant stress on the cells that line the large intestine. If we can support epithelial metabolism with supplemental butyrate until our butyrate-producers can recover, theoretically, we may be able to prevent an environment that favors opportunistic pathogens. (Likewise, supplementing with glutamine may prevent antibiotic-induced dysbiosis in the small intestine.)

5) If basic diet and lifestyle interventions are not enough, targeting PPAR-gamma and colonic energy starvation may be the key to breaking the cycle and reversing gut dysbiosis. This may be particularly useful for those with IBD and those with very stubborn “SIBO” or IBS symptoms.

6) There are numerous interventions with the potential to synergistically “reprogram” colonocytes, ranging from drug therapies to nutrients and lifestyle factors. I discussed many of the known interventions in this article but am hopeful that future research will further explore these therapies, both in isolation and in combination, to elucidate the best therapies to treat gut dysbiosis.

That’s all for now! Let me know what you think in the comments below, subscribe to my newsletter to be notified of any updates, and please share your experience if you use any of this information to improve your own health!

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