by Olivia Moeller
We often talk about the importance of a healthy microbiome, but what does that exactly look like? Our lead nutrition resident, Olivia Moeller, MS, CNS takes a deep dive into the literature to help us define just that. Going beyond definitions, Olivia explores dietary strategies to support gut resilience and diversity which are critical for optimal gut health. This article highlights the intricacies of the human microbiome and reminds us just how much personal power we have over our own health! – DrKF
How much control do we have over the state of our microbiome? How can our dietary and lifestyle choices impact the resilience and diversity of our microbiome? Although the research is still unfolding, evidence is beginning to point towards several strategies for improving our gut health and therefore our overall health. But first, let’s cover some foundational concepts, starting with a definition of the microbiome – the ecosystem of trillions of microbial cells which play a role as our biological control center.
Defining the Microbiome and Microbiota
Although microbiome and microbiota are sometimes used interchangeably, their definitions are slightly different. Microbiome is defined by the Human Microbiome Project as “the collection of all the microorganisms living in association with the human body.” The microbiome encompasses the microbiota which refers specifically to the ecological community of microorganisms, such as bacteria and archaea, in a defined environment such as our guts or lungs.
Our microbiomes are in constant flux in early life as composition, growth, and colonization are determined by infant transitions such as type of childbirth delivery, feeding methods, weaning period, and antibiotic use. As we age, our microbiota becomes relatively stable. However, acute factors such as antibiotic usage and longer-term dietary and lifestyle habits can induce changes.
Although healthy adults share a common majority of bacterial species which constitute a “core microbiota” such as Escherichia coli, research has also shown there is a vast diversity in the microbiome across human populations. These differences amongst individuals are due to different enterotypes and external factors such as exercise, environment, dietary habits, BMI level, stress, medication use, etc. Enterotypes are defined by clusters of bacteria and provide a way to stratify microbiota differences across individuals. There are currently three primary enterotypes: Bacteroides (enterotype I), Prevotella (enterotype II), or Ruminococcus (enterotype III).
Due to these differences, defining a baseline for a “healthy gut” is difficult. However, we do know that the microbiome can be perturbed and shifted into an altered state. And when this altered state becomes prolonged, or even permanent, the microbiome is said to be in a state of “dysbiosis”.
The state of ‘Dysbiosis’
Our microbiota is part of our biology, both self and non-self, and therefore it has been shown to impact a range of physiological processes including obesity, energy metabolism, blood pressure, glucose homeostasis, and even behavior. Given this deeply integrated relationship between the microbiota and the host, if the microbiome is in an altered state, it can affect intestinal health as well as extra-intestinal health. There are several reasons why the microbiome may be perturbed, and depending on the health of the ecosystem, it may or may not return to a state of equilibrium. This altered state, or ‘dysbiosis’, has been linked to several non-communicable chronic diseases and disorders such as IBS, IBD, colorectal cancer, metabolic syndrome, and neurological degeneration.
What can cause such alterations in our microbiome? Here are just a few contributing factors:
- Use of antibiotics or other medications
- Extreme dietary changes
- Stress
- Infections
Going back to the definition of a healthy microbiome, researchers have identified several key features which could predict the microbiome’s ability to shift back to a stable state after an acute perturbation. These attributes include increased diversity, gene richness, the proportion of butyrate produced, metabolic flexibility, and functional redundancy. Let’s dive into some of these so-called “features of a healthy gut” and explore how our dietary and lifestyle choices can help promote these attributes in our own microbiome.
Resilience and Diversity – Attributes of a “Healthy Gut”
Resilience
Resilience is the amount of stress or disturbances that the gut microbiota can handle before its trajectory pivots towards an alteration in its equilibrium state. This altered state may be less productive or less desirable and lead to increased susceptibility to exogenous microbes or chronic problems such as diarrhea or inflammation. It’s also important to note that gut microbiota may be in an altered state and still have high resilience, which may contribute to chronic problems as is inherent with IBD and IBS. This shows that resilience is just part of the picture.
We can turn to the natural world to help us understand this better. We know that in macro-ecosystems, species richness is a critical parameter for promoting resilience, as this helps prevent a small number of species to overgrow and outcompete everything else. Therefore, in addition to resilience, we also need microbiota diversity.
Diversity and Richness
There are two types of diversity that are often referred to in the context of the microbiome: alpha diversity and beta diversity. Alpha diversity measures the level of diversity within a sample using a measure of “richness” and “evenness” and beta diversity measures the level of diversity between samples. “Richness” is the total number of bacterial species present, and “evenness” is the level of distribution between those species. If certain species outnumber others, this may lead to an imbalance and provide an opportunity for pathogenic or opportunistic bacteria to grow. Observational research has shown that low alpha diversity is associated with dysbiosis.
So how can we support resilience and diversity through diet and lifestyle?
There’s plenty that we can do to help our microbiomes become more resilient and diverse! Starting with the food we eat, we can positively modulate the gut microbiota through diet by increasing our intake of:
- Microbiota Accessible Carbohydrates (MACs)
- Diverse variety of plants
- Polyphenols and flavonoids
- Vitamin A, C & E
- Probiotic and prebiotic-rich foods
- Omega-3
Even exercise and spending time in nature can have beneficial effects on the microbiome! Wondering what the gut-supporting mechanisms behind some of these strategies are? We did too, so let’s dive into the top three a bit further.
Microbiota Accessible Carbohydrates
Much of the carbon and energy needed to fuel the microbiota is provided by carbohydrates of plant or animal origin. More specifically, these carbs for gut fermentation can be derived from 1) dietary or host-derived animal glycans, 2) synthesized by other food-borne molecules such as the yeast cell wall, and 3) dietary fiber, which is the most common fuel.
Recently, this last group of carbohydrates that are metabolically available to gut microbes has been termed “Microbiota Accessible Carbohydrates” (MACs). These MACs can alter the composition of the microbiota and dictate its functionality and metabolic output, by producing several metabolites, such as short-chain fatty acids (SCFAs). These SCFAs are biologically active molecules that interact with the physiological pathways of the host (ie. immunoregulation, metabolism).
- SCFAs, namely acetate, butyrate, and propionate, play a key role in health and disease and are found at lower concentrations in populations consuming a Western diet when compared to those consuming the traditional diet of their ancestors.
- Cotillard et al., 2013 demonstrated an increase in microbiota gene richness amongst 49 obese individuals when energy intake was decreased, and dietary fiber consumption was increased over the course of 6 weeks.
- Human intervention studies have revealed that dietary fiber and whole-grain intake increase the diversity of the gut microbiota (Martinez et al., 2013; Tap et al., 2015)
- Many studies have shown that fibers impact the composition and function of the microbiota, especially the production of short-chain fatty acids (Holscher, 2017).
Diverse intake of plants
Consuming a diverse amount of plant foods, rich in fiber, color, and phytonutrients helps support microbiome diversity, and the science proves it:
- High-level consumption of plant foods is associated with beneficial metabolomic profiles. Significant associations were detected between consumption of vegetable-based diets and increased levels of short-chain fatty acid producers, Prevotella and Firmicutes.
- McDonald et. al 2018 found that eating 30 types of plants per week is associated with increased diversity in microbial communities as well as SCFA-producing species such Faecalibacterium prausnitzii.
- McDonald et. al 2018 also discovered that diverse plant consumption was associated with a reduction in certain antibiotic resistance genes. Individuals who consume 30+ types of plants had a significantly reduced abundance of antibiotic resistance genes compared to those who consume 10 or fewer.
- Vegetables grown under organic practices exhibit larger microbial biodiversity than conventionally grown vegetables. (Fliessbach et al., 2007; Schmid et al., 2011).
Polyphenols
Polyphenols such as flavonoids, phenolic acids, and lignans from fruits, vegetables, tea, coffee, and wine have been a point of interest due to their anti-oxidative, anti-inflammatory, and anti-carcinogenic effects. In vitro studies have suggested that polyphenols have prebiotic-like activities and can modulate the microbiota by inhibiting pathogenic organisms such as H. pylori and promoting the growth of beneficial bacteria such as Lactobacillus.
- Multiple polyphenol groups have the ability to modulate the gut microbiota by promoting the abundance of Bifidobacterium, Lactobacillus, Akkermansia, and Fecalibacterium according to In vitro and preclinical studies. The mechanism here was primarily attributed to the production of SCFAs and other bacterial metabolites.
- Axling et al. (2012) found that green tea powder along with Lactobacillus plantarum could significantly increase bacterial diversity and increase the abundance of Lactobacillus and Akkermansia in the colon of mice.
- A small number of clinical trials have reported changes in the composition of the microbiome following consumption of polyphenol-rich foods such as cocoa, red wine, green tea, and vegetables & fruits. Consumption of cocoa-derived polyphenols (494mg/day) for 4 weeks significantly increased the fecal abundance of Bifidobacterium and Lactobacillus compared to a low polyphenol diet (23mg/day).
Final thoughts:
Altered gut microbial patterns or dysbiosis have been linked to several chronic diseases. However, we now know that both dietary and lifestyle interventions can help positively modulate the microbiome, indicating an area of opportunity to support a microbiome that is both resilient and diverse. By promoting resilience and diversity, we can reduce the impact that external stressors have on the microbiome and increase the microbiome’s ability to shift back to a state of equilibrium. Eating a whole foods diet, rich in fiber, phytonutrients, and omega-3s, along with exercise, stress management, and natural environment exposures can help support this resilience and diversity.
The information given here is generalized to a broad audience. Remember to check with your own functional medicine practitioner for a more individualized care plan. If you’re interested in becoming a patient with the Sandy Hook Clinic, be sure to check out our new patient contact form HERE.
This article was contributed by Olivia Moeller. Olivia is a clinical nutritionist and Lead Resident in our nutrition residency program for CNS candidates. You can find Olivia at livnutritiously.com or on Instagram at @livnutritiously.
More gut health resources on DrKaraFitzgerald.com:
A Few Surprises About Ketogenic Diets and Their Effects on the Microbiota and Th17
Fecal Microbiota Transplant Passes Phase 1 Clinical Trial for Alcohol Use Disorder
New Diagnostic Test Suggests Chronic Lyme Disease Associated with Altered Gut Microbiome