Hi there! If you’re new to my site or to microbiome science, this is a great place to get started. If you’re a long-time reader, hopefully this will be a good review and refresher of some microbiome basics!

Note: this article is fairly similar to a podcast episode I recently recorded with Eileen Laird of Phoenix Helix. If you prefer to listen, be sure to check out the interview!

What is the microbiome?

The microbiota is the community of microorganisms that live in and on the human body. This includes trillions of bacteria, along with archaea, fungi, viruses, and eukaryotes that have co-evolved with humans over thousands of years. Of these, the bacteria are the most abundant and well characterized.

The microbiome is all of the collective genes. Often the terms “microbiota” and “microbiome” are used interchangeably, but the technical distinction is that “microbiota” is referring to the microbes, and “microbiome” is referring to their genes.

When most people talk about the microbiome, they are usually referring to the gut microbiome, but we actually also have a distinct microbiome of our skin, nose, mouth, etc.

For the sake of this article, I’m going to focus on the gut microbiome.

Fast facts: gut microbes by the numbers

You may have heard the famous 10 microbial cells to 1 human cell figure to describe how our microbial inhabitants dwarf our human selves.

Recent estimates suggest it’s not quite that the ratio isn’t quite that skewed, but altogether you do have a whopping 38 trillion bacterial cells in your gut – that’s 38,000,000,000,000, or about 1.3 bacterial cells for every human cell!

The genetic potential of these microbes is also enormous. Collectively, the microbes in your gut have around 3.3 million genes, or about 100 times the number of human genes that we have.

Each person has an estimated 300-1000 unique species of microbes that inhabit the gut. However, about half of these microbes are yet to be characterized and understood!

Read more: Discovering my gut microbiome

A brief history of microbiome research

Hippocrates once said “All disease begins in the gut.” Despite documented recognition of the gut as central to disease throughout traditional and early medicine, the microbiome wasn’t generally recognized by modern scientists until the late 1990s.

In 2001, Dr. Jeff Gordon (often considered the father of modern microbiome research) and his laboratory published the first paper on host-microbe relationships in the gut.

Since then, the growth of microbiome research has been nearly exponential. A number of large-scale NIH projects contributed to the field significantly. For example, the Human Microbiome Project, which began in 2008 as an extension of the Human Genome Project, was integral to our understanding of the microbiome across body sites, and to characterize its role in human health and disease.

Today, laboratories across the country and around the world that are either directly studying the microbiome or are seeing that the microbiome has implications for their research. In 2018 alone, there were more than 2,400 clinical trials testing microbial therapeutics.

Read more about my research related to the gut microbiome.

How does the microbiome affect my health?

The microbes in our gut weigh up to several pounds and are essential for our digestion, metabolic function, resistance to infection, and much more.

They can even synthesize vitamins like B12 and folate, regulate our gene expression, generate signaling molecules like short-chain fatty acids that can influence our appetite, or even produce neurotransmitters that can affect our mood and behavior.

The gut microbiota is also in constant communication with the immune system. With 70 percent of our immune cells residing in our gut, it’s no wonder that a disrupted microbiome has been connected to allergies, autoimmunity, and virtually every other chronic inflammatory disease in which it has been studied.

This was how I first became interested in the gut microbiome, because of my personal journey healing from chronic eczema and multiple food sensitivities.

The disappearing gut microbiota

Some researchers have hypothesized that the loss of ancestral diversity in the gut microbiome is what is driving the current epidemic of chronic disease. A theory triumphed by Dr. Martin Blaser suggests that the loss of particular ancestral microbes may impair the normal metabolic, cognitive, and immunological development of the host.

These changes are cumulative across generations, meaning if one generation loses microbes, they aren’t passed on to the next generation. Indeed, some studies suggest that we’ve already lost about 50 percent of the diversity in our microbiome.

It’s more important than ever that we protect our microbes to ensure the health of ourselves and future generations.

For more on this, check out Dr. Martin Blaser’s book “Missing Microbes”

What factors influence the microbiome?

The microbiome varies greatly between individuals. On average, human only share about one third of their gut microbiota with the next person. The other two thirds will depend on genetics and environmental factors.

Early in life, mode of birth and infant feeding practices are very influential in shaping the development and maturation of the gut microbiome. The majority of a baby’s first microbes come from the mother as it passes through the birth canal, and the complex carbohydrates in breastmilk continue to shape the gut microbiome in the ensuing months. Birth by C-section or formula feeding has been shown to alter the normal development of the infant microbiome.

Throughout life, a number of lifestyle factors can also influence the composition and function of the gut microbiome. Diet has a particularly potent effect on shaping gut communities, with dietary shifts exerting significant changes in the composition and function of the microbiota in less than 48 hours. As part of my graduate work, I also helped elucidate the beneficial effects of exercise on the microbiome.

Of course, there are also a number of factors that can negatively impact the gut microbiome. Antibiotics are particularly detrimental to our gut microbial communities, especially in early life but throughout adulthood as well. Other factors, such as non-antibiotic medications, environmental toxins, a processed Standard American Diet, sedentary lifestyle, stress, and disrupted circadian rhythms can all negatively impact the gut microbiota.

Read more: Diet and the gut microbiome, Part 1: seminal studies. How exercise impacts your gut, Part 1: the microbiome.

Is there one healthy microbiome?

Nope! There do seem to be some shared characteristics of a healthy microbiome, though. For example, microbial diversity and community stability seem to be more frequently associated with health (though in rare cases these can also be associated with diseased states).

A healthy microbiome also seems to be dominated by obligate anaerobes, microbes that thrive in the absence of oxygen, and has few facultative anaerobes, microbes that can grow and reproduce in the presence of oxygen.

We’re still in the early stages of understanding what constitutes healthy. Because there is so much variability between the microbiome of one person to the next, there will likely never be one, universally “healthy” microbiome.

At the moment, a healthy microbiome is probably the microbiome you have when you’re healthy!

What is gut dysbiosis?

Similarly, “gut dysbiosis” is a general term for an “altered state of the gut microbiome, usually associated with disease.”  While there are virtually infinite states of gut dysbiosis, recent research has identified some microbial signatures of dysbiosis that seem to be common across disease states.

One of the most common signatures is a low abundance of butyrate-producers and a high abundance of inflammatory microbes in the group Proteobacteria.

Understanding these patterns that underly dysbiosis may be key to determining how we might be able to manipulate the microbiome to improve health and reverse chronic disease.

Read more: The oxygen-gut dysbiosis connection and What the latest research reveals about SIBO

A complex ecosystem of interactions

It’s also important to keep in mind that the gut is an ecosystem. Just like a rainforest, the gut microbiome is a complex network of interactions, with some microbes preying on other microbes and multiple layers of intricate cross-feeding relationships.

This is why we can’t just look at one or two species to determine the health of the gut ecosystem; we need to understand how our microbes interact with each other and the environment!

This is also why it’s hard to delineate between “beneficial” and “pathogenic” microbes. While some microbes are a bit easier to categorize (e.g. Bifidobacterium species are usually beneficial and Salmonella species are usually pathogenic), most microbes fall in a grey area and their impact on our health is heavily dependent on context.

Read more: The gut ecosystem: why understanding microbial communities can help prevent & treat disease

How does the microbiome influence the immune system?

Our gut microbes play crucial roles in the development and regulation of the immune system. An estimated 70 percent of the immune cells in our bodies reside in the gut. These immune cells are constantly “sampling” microbes and dietary proteins in the gut. In a healthy gut, this sampling process promotes tolerance to harmless commensal microbes and dietary proteins that remain in the gut, while launching a strong immune response against any potential pathogens or invaders.

However, when the gut barrier is compromised or this tolerance process goes awry, inflammation can wreak havoc and lead to chronic allergies or autoimmune disease. Early life is a particularly critical time for establishing tolerance to commensal microbes and harmless dietary and environmental compounds.

Stay tuned for the release of my upcoming course on the gut mucosal immune system!

Which probiotics are best?

Probiotics are live microorganisms which, when administered in adequate amounts, confer health benefits to you, the host. Importantly, probiotics do not actually “re-seed” your gut with healthy microbes. Most of the time, they just pass right on through, but they can confer health benefits during transit through the GI tract.

Indeed, probiotics have been studied and shown to be beneficial in hundreds of randomized controlled trials. However, it’s important to choose probiotics wisely, and ideally select strains that have validated safety and efficacy in clinical trials. The average probiotic formula you’ll find at the grocery store is not likely to provide any significant therapeutic benefit.

Read more: Are probiotics useless? A microbiome researcher’s perspective and The complete guide to soil-based probiotics

What about fermented foods?

Fermented foods include things like kombucha, sauerkraut, kimchi, pickled vegetables, yogurt, and kefir. These foods are a natural source of potential probiotics (and their metabolites) and may aid in digestion. While such wild ferments are a fine choice in healthy individuals, they can’t necessarily be relied upon for therapeutic effects because the strains will vary so widely from batch to batch.

Just as with probiotics, we should not expect fermented foods to “re-seed” the gut with healthy strains. In cases of gut inflammation, it’s also possible that the wrong strains, whether from probiotics or fermented foods, could actually exacerbate gut permeability, also known as “leaky gut”.

Read more: Probiotics: helpful or harmful for leaky gut?

What are prebiotics?

Prebiotics are foods or substances that are selectively utilized by gut microbes, stimulating their growth and conferring a health benefit to the host. The most common prebiotics are dietary fibers, such as inulin, resistant starch, and oligosaccharides, though other plant compounds, such as polyphenols and flavonoids can also promote the growth of beneficial microbes.

Prebiotics can certainly be helpful in shifting the composition of the gut microbiome, though not always in the way you think! Your baseline microbiome composition will in large part determine how you respond to a prebiotic fiber intervention.

In general, I recommend getting prebiotic fibers from whole foods, rather than supplementing with isolated prebiotic powders. It’s also usually best to focus on bringing down gut inflammation before introducing too many prebiotics.

Is fiber necessary for a healthy microbiome, though? Maybe, but maybe not! The dominant paradigm that fiber is essential for a healthy microbiome is primarily based on the idea that metabolites from prebiotic fiber (ie. butyrate) provide energy for the cells that line our gut. But as it turns out, metabolites from protein fermentation or ketones from fat metabolism may also supply abundant energy to our gut cells. This suggests that the gut is metabolically flexible and can likely adapt to a wide range of diets.

Read more: Is a high-fat or ketogenic diet bad for the gut?

Is stool testing useful?

Stool testing can be very useful to look for severe bacterial imbalances, pathogenic overgrowths, fungal infections, and parasitic infections. Some tests also offer a look at markers of digestion and absorption of carbohydrates, fat, and proteins, along with inflammatory and immune markers.

However, it’s important to get a test that is utilizing reliable methodologies. Many popular stool testing companies are using culture-based methodologies or have issues with reproducibility (the ability to get the same result multiple times from the same sample).

Read more: The benefits of comprehensive stool testing

How to I support a healthy gut and microbiome?

Every individual is a bit different and there is much we still have to learn about gut health. However, the following is a good general guide for supporting a healthy gut and microbiome:

Step 1: Get the major health behaviors in place: eat a nutrient-dense diet, move every day, get enough sleep, manage stress, and maintain social connections. This will do far more than any probiotic or prebiotic supplement. Over time, small habits can make a huge difference.

Step 2: If you have all of these healthy behaviors in place and are still experiencing symptoms, consider adding in intermittent fasting and an evidence-based probiotic, ideally one that has been clinically tested for your particular condition.

Step 3: If you still have symptoms after implementing steps 1 and 2, there may be an underlying infection or other pathology that needs to be treated. Comprehensive stool testing under the guidance of an integrative or functionally trained practitioner may be helpful.

Step 4: If you’ve seen multiple practitioners and done the standard gut treatments but are still stuck in a cycle of never-ending dysbiosis, it might be worth trying some of the out-of-the-box ideas I presented in my recent article on the oxygen-gut dysbiosis connection.

Learn more about working with me to optimize your gut health, or subscribe to my newsletter to get all of the latest insights in gut research!

What excites you most about microbiome research? What else do you want to know? Leave your thoughts and questions in the comments below and I’ll try to cover them in a future blog article!