Essential Oils and the Gut Microbiome

by Camille Charlier

No Guts, No Glory: The Impact of Essential Oils on the Gut Microbiome

The gut microbiome — everybody’s talking about it, everybody’s gulping down yogurt, everybody’s popping probiotics like their lives depend on it. And in a way… they do.

Trillions of microorganisms make their homes in our bodies, and they basically run the place. Microbes have got their mitts in nearly every aspect of human physiology: regulation of immune function, nutrient absorption and metabolism, neurotransmitter production, emotions, and decision-making.1 They even influence core personality traits like conscientiousness.2

In a word, our health depends on the health of our microbiome. Reduced biodiversity and compositional changes in gut and skin microbiota have been linked to chronic inflammatory diseases, including diabetes, obesity, depression, atopic sensitization (asthma, pollen, food allergies), autoimmune disease (multiple sclerosis and type 1 diabetes), and inflammatory bowel disease (Crohn’s disease and ulcerative colitis). Mess with the microbes, and you mess with us.

There’s strong evidence that the risk for many of these diseases is programmed early in life. It’s a critical developmental window, during birth and just after, when the microbiome is being established. A healthy and diverse microbiome teaches the human immune system how to function properly, crowds out pathogens, helps us absorb nutrients, and supports us in detoxifying noxious chemicals from the outside world. On the other hand, an imbalanced microbiome passed down by the parent, or even a robust one scrubbed off with detergents following delivery or eradicated by antibiotics can set us up for a lifetime of inflammation.

Whether we like it or not, microbes are in cahoots with our immune systems. Here’s why:

Before urbanization and the rise of the concrete jungle, humans spent most of their time outdoors. Our ancestors frequently fraternized with old friends – commensal organisms, soil-derived bacteria, and human-adapted gut bacteria living as spores in the environment — along with some shadier characters: pathogens associated with the “old infections” of human hunter-gatherer populations.

Over the course of evolutionary history, commensals developed a relationship with the human immune system; they learned to live in the body without being obliterated by host defenses. Microbes kept themselves alive by communicating with, and altering, the function of the immune system. They talk to our immune systems, our brains, our whole bodies by mimicking human antigens and manufacturing metabolites that regulate host signaling pathways.3

The rise of inflammatory diseases in modern life is increasingly attributed to the fact that we don’t spend much time with our old friends anymore. Without normal exposure to these microbes, our immune systems don’t know how to develop in a healthy way. They overreact to everything and we end up with chronic inflammation, and all the rampant non-communicable diseases of modern life.

This theory of chronic wide-spread inflammation is known as the “old friends,” or “hygiene” hypothesis. To put it simply, we wash too much, overdo it with the antibiotics, and don’t spend enough time in nature. This theory is linked to the “biodiversity hypothesis,” the idea that diverse natural systems are robust natural systems. It’s a compelling notion: researchers have recently unearthed findings that microbial biodiversity is key for human health. Diversity at the macro or micro level, whether in a tropical rainforest or the human gut, is associated with the health and well-being of that ecosystem. Conversely, loss of biodiversity in the human microbiome is accompanied by skin disease, metabolic syndrome, and inflammation.4

Our relationship with microorganisms is more than skin deep. You’ve probably heard the statistic that there are 10 times as many bacterial cells in our bodies as there are human cells. It’s a recently debunked myth; there’s more like a 60-40% microbe-to-human cell ratio.5 But that’s not accounting for all the non-bacterial microbes in our microbiome: trillions of viruses, fungi, and mites, inside and out.

We’re more microbe than human.

This is where things really get interesting. It’s not just about relative cell count, it’s about genetic contribution. The human genome contains about 20,000 genes. Our microbiome has millions.6,7 Microbial genes aren’t just functional, they’re actually essential for humans. They modulate the immune system, support nutrient absorption, protect against pathogens, maintain barriers to the outside environment, and detoxify foreign substances (xenobiotics).

The human gut is the most densely populated organ in the human body, which means the microbes here pack a big punch in terms of holistic health. Scientists report that the metabolic capacity of the gut microbiota rivals that of the liver. We might think of the microbiome as its own metabolic organ that performs essential functions for human health.8

This may explain why gut microbes have been found to influence fundamental host processes like metabolism, adiposity, maturation, modulation of the immune system, brain function, and even decision-making.

Studies have shown that gut microbiota are indeed causal in the development of obesity. An obese phenotype was found to be transferable from obese mice to germ-free non-obese mice via fecal transplant. Similar results were found for other conditions including inflammatory bowel disease, the liability to develop both non-alcoholic fatty liver disease and alcoholic liver disease, and depression. Obese people with low gut bacterial diversity tended to have higher overall adiposity, insulin resistance, and dyslipidemia, and more inflammation in general, than people with a more diverse microbiota.

One way of thinking about the composition of gut microbiota is in terms of “enterotypes;” patterns of microbial communities in the gut.

Humans have three well-known enterotypes, differentiated from each other by the dominance of a particular “driver” genus:

  • Bacteroides,
  • Prevotella,
  • and Ruminococcus.

These enterotypes are associated with long-term dietary habits. Prevotella is linked to a high-fiber diet, enriched with fruits and vegetables, for example, while Bacteroides is associated with higher consumption of animal fat and proteins. Diet profoundly affects microbial function, and host-microbe relations.

Even short-term changes in diet can alter microbial composition in the gut. Research reveals significant increases in bacterial gene richness following increased consumption of fruits, vegetables, and dietary fiber. Bacterial gene richness is associated with reduced risk of inflammatory diseases, as well as reduced risk of insulin resistance and dyslipidemia, which are both biomarkers of chronic disease.

Intestinal barrier integrity is also strongly influenced by the gut microbiome. If compromised, the intestine can become “leaky,” which leads to systemic inflammation and metabolic dysregulation. Remarkably, impairment of the gut wall can alter immune function in all the mucosa of the body. This is known as the ‘‘common mucosal response.” Basically, antigen presentation at a single mucosal site, a process involved in mucosal immunity and influenced by the microbiome, is thought to stimulate lymphoid cell migration to other mucosal sites in the body. This means that the gut microbiome has the power to influence not just intestinal immune responses, but also inflammation at remote, seemingly unrelated sites like the respiratory tract.9

In addition to influencing metabolism, adiposity, and mucosal inflammation, microbes affect mood via the “microbiota-brain-gut axis.”

Microbe-brain cross-talk is mediated by neural routes, the vagus nerve in particular, as well as by long-distance signaling molecules like cytokines, neuropeptides, and hormones. The microbiome is also able to impact “macro” functions like mood and behavior via metabolic activity on dietary components like amino acids and polyphenols.

Intestinal microbes are predominantly responsible for the conversion of tryptophan to serotonin, for example, as well as the bioactivation of polyphenols. Microbial metabolism thus influences the availability of neurotransmitters. Serotonin and bioactivated polyphenols are both capable of directly and indirectly affecting mood.10

We’re seeing all kinds of diseases caused by an impaired microbiome, from depression to diabetes. So what’s happening in modern life that’s eliciting this dysbiosis?

The Impact of Antibiotics on the Microbiome

Let’s start with antibiotics. Their (over)use, especially early life, can exert long-standing effects on the microbiome, including loss of gut microbiota diversity and low-level inflammation. Antibiotic use is associated with an increased risk of obesity, types 1 and 2 diabetes, inflammatory bowel disease, celiac disease, allergies, and asthma.11

Antibiotics aren’t the only factor to blame, though.


The Impact of Stress on the Microbiome

Psychosocial stress is also a major contributor to intestinal dysbiosis. And it can be passed down from parent to child.

Recent human studies demonstrated that infants delivered by gestational parents with high cumulative stress, as measured by reports of high stress and high cortisol concentrations during pregnancy, had higher abundances of opportunistic pathogens relative to commensal organisms. This pattern was linked with infant health complaints. Gestational parents who experienced depression and anxiety symptoms prior to delivery tended to give birth to infants with allergic disease.

How does stress change the microbiome?

There are several pathways by which stress can cause dysbiosis and immune dysfunction:

  1. Functional alterations in gut physiology that influences microbial populations
  2. Dietary choices that affect microbiome composition
  3. Direct stress hormone activity on microbial populations

Let’s break these three pathways down.

First of all, psychological stress alters gastric secretions and intestinal motility. Stomach acid and intestinal motility are two mechanisms by which the gut keeps microbiota in check. Healthy stomach acid prevents colonization of the gut by problematic microbes, while robust intestinal motility sweeps microbes through the digestive tract, out of the small intestine and into the colon where they belong. Impairment of gastric secretions and motility can lead to intestinal dysbiosis and enteric infections.

Secondly, stress can cause people to reach for their favorite comfort foods. Unless you’re snagging a bag of arugula under duress, your dietary choices may be contributing to dysbiosis. Junk foods — highly palatable, energy-dense, nutrient-poor, additive-rich, highly processed foods low in fiber, phytochemicals, and essential fatty acids — are strongly implicated in intestinal dysbiosis.

Thirdly, stress hormones can directly affect the growth of microbial populations as well as their virulence. Studies show that the fight-or-flight chemical norepinephrine increases the growth of commensal and pathogenic E. coli. Furthermore, the hormonal cascade caused by sympathetic nervous system activation affects microbial adherence to mucosal surfaces. This is significant because the capacity of microorganisms to adhere to human tissues is an essential step in pathogenesis and infection.12

On top of antibiotic use and psychosocial stress, environmental degradation contributes to dysbiosis. We depend on our ecosystems to provide the microbes we need to be healthy (the prefix “eco” stems from the Greek roots oἶκoς; oikos; a house or dwelling place). Unfortunately, our modern dwelling spaces aren’t working out so well for our old friends, or for us. Dysbiosis is associated with environmental pollutants such as airborne particulate matter, lead, mercury, polycyclic aromatic hydrocarbons, and phthalates, and grey space saturation.13,14

Intestinal dysbiosis is also known to accompany urban lifestyle elements like excess alcohol consumption and tobacco exposure, sedentary behavior, the availability of highly processed and “fast” foods, insufficient sleep, and disturbances in circadian rhythms.15

Finally, habits of “hygiene” play a key role in our modern anti-microbial mess. Detergents, hygienic products, soaps, moisturizers, and cosmetics all alter microbial composition. The timing and frequency with which new babies are bathed in the critical developmental window following delivery significantly affects the microbiome. Research suggests that excessive washing with detergents in the perinatal period impairs the barrier function of the skin and alters skin colonization, which increases the risk of eczema.16

We know that the products we use on our bodies and the foods and medicines we consume can affect the microbiome, and often not for the best. But what effects do essential oils have? Do they harm our old friends? Essential oils are notoriously anti-microbial… Does that make them anti-microbiome?

Research indicates that may not be the case.

Some essential oils have been found to exert a selective effect on the microbiome, inhibiting the growth of potential pathogens while promoting populations of beneficial commensals.

A 2018 study published in Biochemical and Biophysical Research Communications found that orally-administered microencapsulated sweet orange (Citrus ×sinensis) essential oil altered the gut bacteria of obese rats in accordance with this pattern. Sweet orange essential oil was found to increase the prevalence of commensal microbes like Bifidobacteria while reducing levels of gut endotoxin, a substance produced by gram negative bacteria.

The pathogenesis of obesity is likely due to shifts in the microbial profile that favor endotoxin-producing opportunistic pathogens. Endotoxins can trigger systemic inflammation, which sets the stage for insulin resistance, lipidemia, diabetes, and obesity. Sweet orange essential oil protected the gut barrier by increasing the prevalence of friendly bacteria, which reduced endotoxin and inflammation, and resulted in weight loss in obese rats. Microencapsulation was found to increase solubility and bioavailability of the essential oil.17

Another 2018 study published in Frontiers in Microbiology found that essential oil constituents carvacrol and thymol, found in high concentrations in oregano, thyme, and wild bergamot, modified the intestinal microbial composition and metabolic profiles in weaned piglets in similar ways. Microbial changes were characterized by an increase in the relative abundances of beneficial bacterial species, and a decrease in potential pathogens. Specifically, Lactobacillus increased, while Enterobacteriaceae dwindled. The latter is a family of gram-negative bacteria often associated with food poisoning… think unsavory characters like E. coli, Salmonella, and Shigella.

Treatment with carvacrol and thymol, in addition to promoting commensals while inhibiting potential pathogens, shifted the microbial balance in the gut to one that promoted energy absorption. Specifically, metabolomics analysis indicated that essential oil constituents promoted protein biosynthesis, carbohydrate metabolism, amino acid metabolism, and lipid metabolism. Furthermore, the type of bacterial populations known to produce short-chain fatty acids were increased. Short-chain fatty acids are known to improve gut barrier function, protect the host against colonic diseases, and exhibit anti-inflammatory effects.

This study built on previous research in swine and poultry that reported essential oil constituents promoted resistance to infection, and improved antioxidant status, intestinal morphology, and barrier function. In these studies, carvacrol and thymol were found to reduce the amount of potential pathogens E. coli and Clostridium perfringens, while increasing the number of commensal Lactobacilli in the intestines of poultry.18

A 2018 study published in the International Journal of Food Sciences and Nutrition reports that an essential oil blend of eucalyptus, oregano, thyme, and sweet orange added to the feed of rainbow trout did not measurably influence the gut microbiome, but did result in decreased oxidative stress. Oxidative stress is a major player in causing chronic inflammation. Looks like there’s a number of mechanisms by which essential oils may be anti-inflammatory that don’t necessarily involve compositional changes in the gut microbiome.19

A 2012 study published in the American Journal of Physiology found that lavender essential oil achieved similar results in mice with acute ulcerative colitis caused by Citrobacter rodentium. Populations of commensals were promoted, while pathogen load was controlled. Importantly, enteric microbiota composition is known to affect the susceptibility of mice to C. rodentium-induced colitis. In this study, treatment with lavender essential oil enriched the microbiota with members of the phylum Firmicutes, microbes known to protect against the damaging effects of C. rodentium. Lavender essential oil also decreased the prevalence of γ-Proteobacteria, some of which are opportunistic pathogens. Lavender oil directly inhibited C. rodentium growth and adherence, primarily due to the constituents 1,8-cineole and borneol.

Researchers found that orally administered lavender essential oil ultimately resulted in less severe disease in colitic mice. These improvements were characterized by decreased morbidity and mortality, reduced intestinal tissue damage, and decreased infiltration of neutrophils and macrophages. Levels of proinflammatory cytokines were reduced (TNF-α, IFN-γ, IL-22, macrophage inflammatory protein-2α), as was the expression of inflammation-associated inducible nitric oxide synthase. Treatment with lavender essential oil was also linked to increased levels of regulatory T cell populations compared with untreated colitic mice. In sum, lavender essential oil promoted the prevalence of commensals, inhibited pathogens, and ameliorated C. rodentium-induced ulcerative colitis in mice.20

Similar findings have been reported in in vitro studies of the human gut microbiome. A 2015 study published in Microbiology investigated the effect of essential oil constituents on commensal and pathogenic strains of bacteria in human fecal fermentations. Based on their findings, the authors theorize that thymol and geraniol, at a concentration of 100 ppm, are capable of suppressing pathogens in the small intestine without interfering with commensal colonic bacteria.21

This builds on an earlier study published in the Alternative Medicine Review. Researchers tested eight different essential oils on 12 species of common human intestinal bacteria in vitro. They found that Carum carvi (caraway), Lavandula angustifolia (lavender), Trachyspermum copticum (ajowan caraway), and Citrus aurantium var. amara (neroli) essential oils demonstrated a high degree of selectivity, inhibiting the growth of potential pathogens while leaving commensals unaffected. These herbs have a long history of usage for gastrointestinal disorders.22

Based on the available research, essential oils seem like a promising approach for dysbiotic conditions.
Before we get too excited, though, there are some caveats we need to consider.

Many of these studies were conducted with essential oil constituents as opposed to whole oils, in livestock instead of humans, or in vitro — in a petri dish. The degree to which we can generalize these findings to human in vivo settings is limited. For example, it’s unclear what effect digestion and absorption will have on the microbe-regulating activity of essential oils. Ultimately, we’ll need clinical trials to determine tolerability and safe dosing practices.

That being said, there is plenty of research in humans that demonstrates the efficacy of orally administered essential oils in safely treating dysbiosis-associated conditions.

For our current purposes these studies suffer from the limitation that they did not consider the effect of essential oils on commensals. But they’re worth taking a look at regardless.

One particularly well-researched topic is the use of peppermint oil to treat irritable bowel syndrome (IBS) and its primary trigger, small intestinal bacterial overgrowth (SIBO). SIBO is associated with many functional somatic disorders in addition to IBS, including fibromyalgia and chronic fatigue syndrome. SIBO — the inappropriate expansion of colonic bacteria into the small intestine — is often caused by intestinal stasis (impaired intestinal motility) and/ or hypochlorhydria (clinically low stomach acid). This can be caused by factors like stress, medication, and diet.

Successful eradication of SIBO has been correlated with a reduction in gastrointestinal complaints, and, in the case of those with SIBO and chronic fatigue syndrome, is linked to significant improvements in memory, concentration, pain, and depression.

One case study of a 29 year old woman diagnosed with IBS and SIBO found that a 20-day course of enteric-coated peppermint oil (Mentha x piperita) at a dose of 0.2 mL three times daily significantly reduced bacterial load and improved IBS symptoms. The subject reported marked improvements in bowel function, decreased bloating, pain, and eructation, and increased frequency of normal bowel movements. Symptom improvements, per patient report, persisted 10 days after treatment, with no aggravation of symptoms after the essential oil treatment concluded.23

The BMJ, originally known as the British Medical Journal, published a 2008 systematic review and meta-analysis of 392 patients that corroborate these findings. Peppermint oil was found to be more effective than placebo in treating irritable bowel syndrome, with no significant adverse effects.24

A 2019 meta-analysis of 12 studies with 835 patients published in BioMed Central Complementary and Alternative Medicine likewise reports that peppermint oil is “a safe and effective therapy for pain and global symptoms in adults with IBS.” According to the authors, peppermint oil is likely ameliorative in IBS due to its antispasmodic (motility-promoting) effects, as well as antimicrobial, anti-inflammatory, antioxidant, immunomodulating, and anesthetic activities.25

We still have a long way to go to scientifically confirm the impact of essential oils on the human microbiome. Ultimately, we’ll hold out for randomized, double-blind, placebo-controlled human trials using the “gold standard” of microflora assessment techniques — 16S ribosomal RNA sequencing — to determine with confidence the effect of ingested essential oils on gut microflora.

Even so, scientific research isn’t the only means of gathering information. Internationally-renowned aromatherapy educator Robert Tisserand offers a balanced perspective. He writes in his blog:

It would be useful to know more about particular oils, doses, routes of administration and their effect on the body’s microbiome. But in the meantime, it is rash to assume that essential oils negatively affect the balance of bowel flora, because there is no clinical evidence that this happens. On the other hand, decades of clinical experience by doctors in France suggests that essential oils frequently heal both acute and chronic infections without the damaging, and often long-lasting effect on bowel flora that comes from the use of antibiotics.26

Jade Shutes, director of education at the School for Aromatic Studies, has directly encountered the French practices and culture of using essential oils internally to treat infections. While studying aromatic and herbal medicine in France, Jade observed that internal essential oil use is a common practice: essential-oil containing tablets and gel capsules are readily available over the counter at pharmacies across the country. Based on modern scientific research, and rich traditions of usage, Jade advocates for the internal use of essential oils that target pathogens while preserving a healthy microbiome.



Importantly, we don’t see the same negative bowel outcomes with antimicrobial essential oils that we see with antibiotics. This difference may be due to the capacity of essential oils to selectively inhibit potential pathogens, while allowing commensals to flourish.

Antibiotics are the nuclear approach, the “everything killers” of the biological realm. They are, literally, anti-life. Our antimicrobial attitude and our mistreatment of the living world has led to devastating dysbiosis, a crisis of inflammatory disease, and lost quality of life.

Perhaps essential oils can be part of the solution: a nuanced treatment approach that sends pathogens packing… and welcomes our old friends — and our vitality — back.


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7 Li, D., Wu, H., Dou, H., Guo, L., & Huang, W. (2018). Microcapsule of sweet orange essential oil changes gut microbiota in diet-induced obese rats. Biochemical and Biophysical Research Communications, 505(4), 991–995.
8 Ipci, K., Altıntoprak, N., Muluk, N. B., Senturk, M., & Cingi, C. (2017). The possible mechanisms of the human microbiome in allergic diseases. European Archives of Oto-Rhino-Laryngology: Official Journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS): Affiliated with the German Society for Oto-Rhino-Laryngology – Head and Neck Surgery, 274(2), 617–626.
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12 Stamper, C. E., Hoisington, A. J., Gomez, O. M., Halweg-Edwards, A. L., Smith, D. G., Bates, K. L., … Lowry, C. A. (2016). The microbiome of the built environment and human behavior: implications for emotional health and well-being in postmodern western societies. International Review of Neurobiology, 131, 289–323.
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17 Li, Y., Fu, X., Ma, X., Geng, S., Jiang, X., Huang, Q., … Han, X. (2018). Intestinal microbiome-metabolome responses to essential oils in piglets. Frontiers in Microbiology, 9.
18 Ceppa, F., Faccenda, F., De Filippo, C., Albanese, D., Pindo, M., Martelli, R., … Parisi, G. (2018). Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout (Oncorhynchus mykiss). International Journal of Food Sciences and Nutrition, 69(3), 318–333.
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