The Gut Microbiome and Essential Oils


Sarah LoBisco, ND

Introduction: How the Microbiome Changed Medicine

The 19th century led to a turning point in medicine with the discovery of microorganisms and their link to infectious diseases. Since then, there has been a focus on their eradication to alleviate sickness. The initial interventions that predominated included inoculations, antiseptics, and chemotherapeutics. In the 20th century we were provided with what seemed to be an additional saving grace from these detrimental pathogens, antibiotics.1-3 

In 2007, the understanding of our microbial communities expanded appreciably by the international effort of the five-year long Human Microbiome Project (HMP). Through it, scientists began to uncover and characterize the microbes that existed in and on the human body and their roles in health and disease. We’ve since learned that our co-habitation with these microorganisms was not necessarily harmful. In fact, insight into specific commensals, our symbiotic microbes, shined a bright light on the misapplication of our current heroic measures to fight infections. In our obsession to destroy pathogenic “invaders,” we humbly realized that we were inadvertently killing our own defenders.2-4

Scientists have since been intrigued to glimpse into this yet to be fully discovered organ system of trillions of tiny microbes (microbiota) and how their collective population and genetic information (microbiome) impacts our own physiology. We now believe that we hold 100-fold more microbial than human genetic information.5-6 It is also acknowledged that the gastrointestinal tract alone is home to 1013 cells of thousands of different species of microbiota.7-8 These gastrointestinal bacteria are vital to our everyday functioning and are responsible for neurotransmitter production, immune response, synthesizing systemic signaling molecules, and communicating with our central nervous system.8-9

This symbiotic relationship with our microbiota began early in life as our genetics and perinatal environment influenced their composition. Just as they shape our health through the metabolites they produce and their other biological functions, we in turn can influence their responses through epigenetic factors. These include our lifestyle, diet, exercise patterns, toxin and pesticide exposures, antibiotic use, sleep quality, and how we handle stress.8-15

Research continues to expand on how the microbiome influences our physical and emotional states in vital ways. At the time of this article, it seems that it influences the health of virtually every organ system. 8-14  

Stewards to Our Microbiome (with Natural Medicine)

As our discoveries and medications evolved, it became evident that these microbes were more advanced than we gave them credit for. Just as we thought we had wiped out infectious agents, we helplessly witnessed these superbugs become more astute at resisting antibiotics and transforming into more sleuth mutants. Humbly, we realized our human knowledge of their functioning was pale in comparison to their resiliency.16

As dutiful physicians, we aim to do no harm. With this relatively new knowledge of the microbiome, we were taught to become stewards to antibiotics. We now respect that with great power (to influence the microbiome) comes great responsibility.16

For this reason, many integrative physicians have come to believe that their antimicrobial herbal and supplemental nutrients could also result in a form of dysbiosis like antibiotics. This viewpoint, though rational, may be an error and another underestimation of the power of nature.

In this article, I will present a review on how a specific form of botanical medicine promotes health as it impacts physiology in fighting infectious diseases. First, I will offer a broad discussion of herbal therapy and the microbiome. Next, my focus will shift specifically to essential oils. I will review how they can combat antibiotic resistance and provide a summary of the current studies on how essential oils impact our microbiome. Ultimately, this information demonstrates essential oils do have the ability to be selective in inhibiting pathogens while not harming, and even promoting, gastrointestinal microbial resiliency.

Herbs and the Microbiome

Botanical medicine’s efficacy is often believed to be based on how its active constituents impact our cellular processes, yet it may be more complicated than that. Just as we are learning how the microbiome impacts disease and health risks, we are also realizing it influences how we utilize our food, nutrients, and allopathic and integrative treatments.17-18 Recently, an article explored this complex interaction between the gut microbiota and herbal medicines with a focus on two distinct mechanisms.

First, is the ability of the gut microbiota to break down components of botanicals into absorbable metabolites through their secretion of various enzymes. This leads to secondary, active molecules that are absorbed into the bloodstream. These interfere with cellular signaling patterns (i.e., NFKB, LPS), which favorably influences disease processes.18

Secondly, herbal medicines have been shown to alter the composition of the gut microbiota. These effects also lead to positive pharmacological effects. For example, many herbs contain polysaccharides in which specific microbes, such as Bifidobacterium and Bacteroides, process through various enzymes. In turn, these polysaccharides can further support the growth of beneficial microbial populations.18

These discoveries seem to challenge the allopathic viewpoint that botanical medicine, though having antimicrobial properties, would cause harm to our commensals like drugs. Rather, it provides support for the synergy of herbal medicine to reinstate harmony and enhance resiliency to our whole system. This restoration of health is distinct from using external interventions to simply kill or fight a disease.

Essential Oils and Antibiotic Resistance

One concern of using antibiotics is that eventually they will lead to resistance and more superbugs. Essential oils (EO) have various mechanisms that make them antimicrobial. Due to their hydrophobicity and their molecular weight/mass being below 500 Da, they can gain entry into various pathogens cellular membranes and exert their multiple effects.19 This complexity of all the constituents present in EO, and their multifactorial actions, are likely why many that are deemed “antimicrobial” very rarely promote resistance. In fact, some have shown potential to even increase susceptibility to antibiotics and overcome resistant bacteria in experimental studies.20-24

Furthermore, there are also reports emerging in human studies on how essential oils can counter resistant organisms, specifically MRSA (methicillin-resistant Staphylococcus aureus).25-27 One small case series of 12 subjects with MRSA reported a reduction in size of wounds after treatment with tea tree oil, though colonization persisted.25 Arguably, for such a robust infection, the dosage used was relatively small (3.3% solution), and further research verified this low potency may in fact be the reason better results were not reported.26-27

For example, in a later study with 32 subjects, a “10% topical tea tree preparation was effective in reducing the quantity of colonized MRSA in and promoting healing of chronic wounds among elderly.”26

A larger randomized trial also found that this 10% potency for tea tree may be the sweet spot to counter MRSA. In this study, 114 subjects received the standard drug treatment for MRSA whereas 110 participants were provided with a tea tree oil regimen of 10% cream and 5% body wash. The was no significant difference found in MRSA carriage after the treatments (49% in the standard treatment vs. 41% in the tea tree oil regime). However, mupirocin was found to be more effective than tea tree for nasal clearance.27

It will be interesting to watch as more trials emerge using these natural agents against resistant organisms. Now, I will review studies on how essential oils further differ from antibiotics with their ability to be selective to pathogenic overgrowths.

Essential Oils (EO) and Selective Inhibition of Microorganisms

Experimental, animal, and human trials, exist that demonstrate essential oils likely promote or maintain microbiome health while decreasing pathogenic microbes.19,28-34

In an in vitro study evaluating eight different essential oils on 12 species of common human intestinal bacteria, it was found that the oils had a high degree of selectivity. Specifically, Carum carvi (caraway), Lavandula angustifolia (lavender), Trachyspermum copticum (ajowan caraway), and Citrus aurantium var. amara (neroli) essential oils inhibited the growth of potential pathogens while leaving commensals unaffected.28

As physicians, we are aware that experimental studies help to determine mechanisms, but we are more inclined to pay attention to how interventions, specifically EO, act in living creatures. Below are more studies of discriminatory inhibition of pathogens in animals.

1. A 2018 study in obese rats found that orally administered microencapsulated sweet orange (Citrus ×sinensis) essential oil increased the prevalence of commensal microbes, such as Bifidobacteria, while reducing levels of endotoxins from gram-negative bacteria. Suppressing endotoxins resulted in protection of the intestinal lining, amelioration of inflammation, and weight loss.29

2. In a study with rabbits, it was demonstrated that thyme oil increased antioxidant status in the blood plasma and liver and decreased oxidative harm in the small intestine. It also positively influenced intestinal integrity and stimulated beneficial microbiota in the rabbits’ gastrointestinal tract. The authors stated:30

Thyme oil significantly increased the value of total antioxidant status (TAS) in the blood plasma and glutathione peroxidase (GPx) activity in the liver, and it decreased malondialdehyde (MDA) concentration in the duodenal tissue.

Thyme oil resulted in strengthened intestinal integrity, as the essential oil supplementation significantly increased TEER values in the experiment. The faecal microbiota of rabbits was almost completely balanced in both groups, and only a slight decrease was found in the microbial population at day 42 of the trial. In both groups, the bacterial counts were generally lower in the caecum than in the faecal samples.

In conclusion, dietary supplementation with 0.5 g/kg DM thyme oil may improve intestinal integrity, and it may have an antioxidant effect. A tendency was also found for thyme oil to stimulate the abundance of some microbes beneficial in the rabbit gut. [30]

3. One experiment in mice assessed how lavender essential oil would impact enteric microbiota in induced acute ulcerative colitis caused by Citrobacter rodentium. It was found that lavender essential oil enhanced the microbiota within the phylum Firmicutes, which assisted in protecting against the damaging effects of C. rodentium. Lavender essential oil also decreased the opportunistic pathogens, γ-Proteobacteria and inhibited C. rodentium growth and adherence. The latter effect was primarily due to the constituents 1,8-cineole and borneol.31

Overall, oral lavender oil was found to decrease severity of disease, morbidity, and mortality in rodents. This coincided with decreased proinflammatory cytokines and a lower inflammatory response of neutrophils and macrophages.31

4. A study in chickens also demonstrated that essential oils and herbs had negligible effects on gut microflora while benefiting digestion and alleviating pathogenic microbes.32

5. In a 2020 literature review, the author summarized various other animal studies with essential oils that included chickens, rats, piglets, mice, and shrimp.19 Again, EO supplementation was connected to inhibition of growth of bacterial species that were pathogenic while benefiting the gut microbiota. It was stated:

On the basis of these studies, it can be concluded that EO and their compounds target different sites in microorganisms. Due to the large number of diverse groups of chemical compounds and multiple consequences of one effect, the action of EO may not be attributed to a particular mechanism. Selective inhibition of EO may help balance gut microbiota. Thus, gut microbiota can adapt according to supplementation with EO. The sensitivity of some G+ve pathogens and the relative resistance of the Bifidobacteria and Lactobacilli to EO under anaerobic conditions may be advantageous for EO. [19]

6. In a 2020 study, a combination of an herb extract and EO was given to pigs to assess its impact on their microbiome. The pigs ingested an oregano extract combination with peppermint and thyme essential oils. It was demonstrated that the combination of plant extracts had a positive effect on the gastrointestinal tract of these animals. Specifically, there was an increase in the number of probiotic bacteria.33

The authors were further able to verify in their experiment that the population of the microbiome of pigs were not altered or different than the controls following the intervention in the cecum and rectum. Yet, there was some slight variation in the small intestine:33

On average, the number of probiotic bacteria in all three intestines as a part of the total amount of bacterial load was 22.5% and 27.2% in the control and experimental groups…

The main changes were associated with an increase of Escherichia (almost three times) and Lactobacillus (five times) and a decrease of Prevotella (59 times) in the experimental group, compared with control pigs. [33]

7. In yet another review article on the use of essential oils and nanoparticles on the gut microbiome, the authors also echoed the modulatory vs. inhibitory impact of essential oils on the gut microbiome in vivo:34

EOs are widely studied for their gastrointestinal interference, being potent modulators for gut inflammation, metabolic reactions and microbiota diversity. [34]

“Obesity”, the Microbiome, and Essential Oils

“Obesity” is deemed a disease and a public health concern by the Centers for Disease Control and Prevention (CDC).35 The debate on if obesity is truly a disease or if it’s a causative factor in others, an association, a result of undiagnosed, underlying dysfunction, and/or related to toxins or processed chemicals is a topic for another article. Regardless, there have been correlative studies demonstrating that an alteration in the microbiome impacts body size. Furthermore, we know that antibiotics, which can cause dysbiosis, have been linked to a greater likelihood of weight gain. In fact, they are often used in agriculture for increasing growth of animals.19,36

For example, studies have reported that the proportion of Bacteroidetes and Firmicutes were associated with the development of obesity. Yet, this too has been recently challenged due to its simplistic viewpoint. Likely, the influence of the gut microbiome on weight is more nuanced and intricate than the ratios of two of the predominant human microbial phyla (the others being Actinobacteria, Proteobacteria, Fusobacterua, and Verrucomicrobia). 19,36-38

Other factors that impact microbial interaction and their composition include lifestyle, dietary composition, and environmental exposures. These influence microbiota makeup and their resulting microbial metabolites that impact inflammation, satiety signals, and energy harvesting.19,36-38

What does this have to do with the microbiome and essential oils (EO)?

Literature exists on the effectiveness of EO in weight loss through their effect on the gut microbiota. As noted, essential oils have been shown in many studies to act as antimicrobials, which may impact weight, but their mode of action is more complex than a drug. 19,39  

For example, there is also in vivo evidence of certain components in EO leading to sympathetic nerve stimulation of white fat, decreased food intake, and inhibition of lipid metabolism. Furthermore, anti-lipase activity has been associated with polyphenols, saponins and terpinenes found in essential oils. Two review articles have also suggested that citrus oils and their constituents not only had anti-inflammatory, antioxidant, and fat-burning properties, but also acted as prebiotics in vivo, “feeding” the good guys.19,39

There was also a human study on EO and metabolic syndrome (MS) patients. MS can lead to acute and chronic infections due to metabolic deregulation and inflammation which alters microbiota populations. In a study with 106 metabolic syndrome patients, the impact of organum vulgare (oregano) essential oil (EOO) was evaluated as an antibacterial in comparison to allopathic treatment. The subjects were divided into four subgroups which included staphylococcal, Escherichia coli, streptococcal, and no infection (control). The concentrations of the essential oil of oregano exhibited higher zones of inhibition than the antibiotics of erythromycin, levofloxacin, tetracycline, and azithromycin of the selected bacteria.

The authors also assessed intestinal side effects and phase angle. They concluded:40

The results suggest that EOO may exhibit an antibacterial effect, similar to the antibiotic treatment, without promoting MS-specific dysbiosis, and it also improves the phase angle in patients, which is used as an index of health and cellular function. [40]

The Human Microbiome and Essential Oils

There are few other studies on the impact of EO on the human microbiome.

In 2015, the essential oil compounds of thymol, geraniol, eugenol, nerolidol, and methyl eugenol were studied for the effect they had on beneficial and pathogenic strains of bacteria in human fecal fermentations of six omnivorous, healthy individuals. Based on their findings, the authors theorized that thymol and geraniol, at a concentration of 100 ppm, were capable of suppressing pathogens in the small intestine without interfering with commensal colonic bacteria. It is important to note that the results were based not on essential oils, but isolated compounds.41

In a comprehensive metabolomics study of 31 females, the metabolic changes in urine after exposure to aroma inhalation for 10 continuous days was evaluated. Significant alterations of metabolic profiles in subjects responsive to essential oil were found. Notably, “the metabolites from tricarboxylic acid (TCA) cycle and gut microbial metabolism were significantly altered.” 42

Interestingly, these changes were related to symptom improvement, indicating that shifts in metabolic and microbiome selectivity were individualized. Unfortunately, there were significant limitations to the study. Instead of purely, standardized distilled EO, essential oil “incense” was used. Furthermore, the participants were told to eat blander foods for ten days and placed in a closed room, which could have impacted the results in amino acid and carbohydrate profiles. Still, the study did provide evidence of positive shifts in metabolics and microbial metabolism based on aroma, aromatic compounds, and their interaction with the limbic system.42

Essential Oils: The “Magic” of Their Multiple Actions for the Benefit of Our Microbiome and Overall Health

Unlike a drug which targets a specific organism, EO have multiple actions and additional properties. For example, EO act as natural antioxidants. Their phenolic compounds exhibit high redox properties and a chemical structure that allows for the ability to neutralize free radicals, chelate transitional metals, and quench singlet and triplet oxygen. This results in the delocalization or decomposition of peroxides both in humans and animals.33

In my previous articles in Townsend Letter, I reviewed more mechanisms of action of essential oils that would further support microbiome balance besides quenching oxidative stress. This includes the use of essential oils for digestive support and clearing dysbiosis, relieving stress, acting on the nervous system, and mediating various pathways involved in inflammation.43-44

Conclusion

In this article, I’ve reported on how botanical medicine can promote health and balance our physiology while fighting infections. Unlike antibiotics, which can kill the microorganisms and damage the microbiome, essential oils seem to combat antibiotic resistance and benefit our microbiota.

Although we can always benefit from more research, the current evidence, as well as their long history of use, demonstrates that essential oils do have the ability to be selective in inhibiting pathogens while not harming, and even promoting, gastrointestinal microbial resiliency and overall wellness.


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Published July 15, 2023


About the Author

Sarah LoBisco, ND, IFMCP is a graduate of the University of Bridgeport’s College of Naturopathic Medicine (UBCNM). She is licensed in Vermont as a naturopathic doctor and has earned her certification in functional medicine through the Institute of Functional Medicine (IFM).  Dr. LoBisco also holds a Bachelor of Psychology from State University of New York at Geneseo and an Applied Kinesiology certification. 

She is a speaker on integrative health, has several publications, and does independent contracting for companies regarding supplements, nutraceuticals, essential oils, and medical foods. Dr. LoBisco currently incorporates her training as a naturopathic doctor and functional medicine practitioner through writing, teaching, private practice, and through her independent contracting work. She maintains her private wellness consultation practice through virtual consultations. Dr. LoBisco also enjoys continuing to educate and empower her readers through her blogs and social media. Her recent blog can be found at dr-lobisco.com.