What is the gut microbiome? A researcher’s guide to the basics
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, this will be a good refresher of some microbiome basics. Along the way, I’ll also clear up a few popular microbiome myths.
What is the microbiome?
The microbiota is the community of living microorganisms that inhabit a particular environment, such as the human gut. This includes trillions of bacteria, along with archaea, fungi, and other microbial eukaryotes that have co-evolved with humans over millions of years. Of these, the bacteria are the most abundant and well characterized.
The microbiome is a broader term. For many years, it was used to describe the collective genes of the microbiota. In 2020, an international panel of microbiome researchers proposed an updated consensus definition: the microbiome includes the microbiota plus their “theatre of activity.” This encompasses the genes they carry, the metabolites and signaling molecules they produce, and their surrounding environment. In other words, the microbiota describes who is there, while the microbiome includes who is there, what they are doing, and the environment that they are shaping and responding to.
In practice, the terms “microbiota” and “microbiome” are often used interchangeably.
When most people talk about the microbiome, they are usually referring to the gut microbiome, but we also have a distinct microbiome of our skin, nose, mouth, and elsewhere. This article will focus on the gut microbiome.
Fast facts: gut microbes by the numbers
You may have heard the famous figure of 10 microbial cells to 1 human cell, often used to describe how our microbial inhabitants dwarf our human selves.
Recent estimates suggest the ratio isn’t quite that skewed, but altogether you do have a whopping 38 trillion bacterial cells in your gut, or about 1.3 bacterial cells for every human cell!
The genetic potential of these microbes is also enormous. Researchers have now catalogued nearly 10 million microbial genes in the human gut across populations, and each individual carries hundreds of thousands of them, many times the roughly 20,000 protein-coding genes in the human genome.
Each person has an estimated 300 to 1000 species of microbes that inhabit the gut. Thanks to large-scale sequencing efforts, scientists have now assembled genomes for thousands of gut species that had never been grown in a lab. However, for many of these microbes, we still know very little about what they actually do!
Read more: Discovering my gut microbiome
A brief history of microbiome research
The idea that the gut is central to health dates back to ancient times (with the quote “All disease begins in the gut” often attributed to Hippocrates). But it wasn’t until the rise of DNA sequencing in the late 1990s and 2000s that scientists could study the gut microbiome in depth.
In the early 2000s, Dr. Jeff Gordon (often considered the father of modern microbiome research) and his laboratory published a series of landmark studies showing how gut microbes shape host physiology, affecting everything from gut development to metabolic health.
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 around the world 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. And in 2022 and 2023, the FDA approved the first microbiome-based therapeutics, both for preventing recurrent C. difficile infection.
Read my research related to the gut microbiome.
How does the microbiome affect my health?
The microbes in our gut 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. The gut is home to the largest population of immune cells in the body, so 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 put forth 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, studies comparing industrialized populations with hunter-gatherer and rural communities consistently find that industrialized gut microbiomes are less diverse, and are missing many microbes that were common throughout human history.
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, and even close family members share only a portion of their gut microbes. Both genetics and environmental factors play a role, but large studies suggest that lifestyle and environmental factors have a much bigger influence than our genes.
Early in life, mode of birth and infant feeding practices are among the strongest influences on how the gut microbiome develops. During vaginal birth, a baby is exposed to a wide range of maternal microbes, especially those from the maternal gut. After birth, the complex carbohydrates in breastmilk (human milk oligosaccharides) continue to shape the gut microbiome in the ensuing months. Birth by C-section, formula feeding, and early antibiotic exposure have all been shown to alter the normal development of the infant microbiome. Many of these differences narrow after the first year, but this early window appears to be especially important for immune development.
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?
There is no one healthy microbiome, but there do seem to be some shared characteristics. 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 (recently renamed Pseudomonadota).
Understanding these patterns that underlie 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. The gut houses the largest population of immune cells in the body. 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, 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.
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 great natural source of potential probiotics (and their metabolites). However, strains will vary from batch to batch, so therapeutic effects are harder to predict.
A notable 2021 study found that healthy adults who gradually increased their fermented food intake to six servings per day over ten weeks saw an increase in gut microbiome diversity and a decrease in markers of systemic inflammation.
Just as with probiotics, we should not expect fermented foods to “re-seed” the gut with healthy strains. Those with mast cell activation syndrome or histamine intolerance should also proceed extremely carefully, or avoid fermented foods until they are further along their healing journey.
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 sometimes be helpful in shifting the composition of the gut microbiome, though studies have shown that 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? 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: A comprehensive guide to stool and microbiome testing
How do 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 supplemental butyrate 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!
What is the gut microbiome? A researcher’s guide to the basics
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, this will be a good refresher of some microbiome basics. Along the way, I’ll also clear up a few popular microbiome myths.
What is the microbiome?
The microbiota is the community of living microorganisms that inhabit a particular environment, such as the human gut. This includes trillions of bacteria, along with archaea, fungi, and other microbial eukaryotes that have co-evolved with humans over millions of years. Of these, the bacteria are the most abundant and well characterized.
The microbiome is a broader term. For many years, it was used to describe the collective genes of the microbiota. In 2020, an international panel of microbiome researchers proposed an updated consensus definition: the microbiome includes the microbiota plus their “theatre of activity.” This encompasses the genes they carry, the metabolites and signaling molecules they produce, and their surrounding environment. In other words, the microbiota describes who is there, while the microbiome includes who is there, what they are doing, and the environment that they are shaping and responding to.
In practice, the terms “microbiota” and “microbiome” are often used interchangeably.
When most people talk about the microbiome, they are usually referring to the gut microbiome, but we also have a distinct microbiome of our skin, nose, mouth, and elsewhere. This article will focus on the gut microbiome.
Fast facts: gut microbes by the numbers
You may have heard the famous figure of 10 microbial cells to 1 human cell, often used to describe how our microbial inhabitants dwarf our human selves.
Recent estimates suggest the ratio isn’t quite that skewed, but altogether you do have a whopping 38 trillion bacterial cells in your gut, or about 1.3 bacterial cells for every human cell!
The genetic potential of these microbes is also enormous. Researchers have now catalogued nearly 10 million microbial genes in the human gut across populations, and each individual carries hundreds of thousands of them, many times the roughly 20,000 protein-coding genes in the human genome.
Each person has an estimated 300 to 1000 species of microbes that inhabit the gut. Thanks to large-scale sequencing efforts, scientists have now assembled genomes for thousands of gut species that had never been grown in a lab. However, for many of these microbes, we still know very little about what they actually do!
Read more: Discovering my gut microbiome
A brief history of microbiome research
The idea that the gut is central to health dates back to ancient times (with the quote “All disease begins in the gut” often attributed to Hippocrates). But it wasn’t until the rise of DNA sequencing in the late 1990s and 2000s that scientists could study the gut microbiome in depth.
In the early 2000s, Dr. Jeff Gordon (often considered the father of modern microbiome research) and his laboratory published a series of landmark studies showing how gut microbes shape host physiology, affecting everything from gut development to metabolic health.
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 around the world 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. And in 2022 and 2023, the FDA approved the first microbiome-based therapeutics, both for preventing recurrent C. difficile infection.
Read my research related to the gut microbiome.
How does the microbiome affect my health?
The microbes in our gut 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. The gut is home to the largest population of immune cells in the body, so 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 put forth 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, studies comparing industrialized populations with hunter-gatherer and rural communities consistently find that industrialized gut microbiomes are less diverse, and are missing many microbes that were common throughout human history.
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, and even close family members share only a portion of their gut microbes. Both genetics and environmental factors play a role, but large studies suggest that lifestyle and environmental factors have a much bigger influence than our genes.
Early in life, mode of birth and infant feeding practices are among the strongest influences on how the gut microbiome develops. During vaginal birth, a baby is exposed to a wide range of maternal microbes, especially those from the maternal gut. After birth, the complex carbohydrates in breastmilk (human milk oligosaccharides) continue to shape the gut microbiome in the ensuing months. Birth by C-section, formula feeding, and early antibiotic exposure have all been shown to alter the normal development of the infant microbiome. Many of these differences narrow after the first year, but this early window appears to be especially important for immune development.
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?
There is no one healthy microbiome, but there do seem to be some shared characteristics. 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 (recently renamed Pseudomonadota).
Understanding these patterns that underlie 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. The gut houses the largest population of immune cells in the body. 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, 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.
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 great natural source of potential probiotics (and their metabolites). However, strains will vary from batch to batch, so therapeutic effects are harder to predict.
A notable 2021 study found that healthy adults who gradually increased their fermented food intake to six servings per day over ten weeks saw an increase in gut microbiome diversity and a decrease in markers of systemic inflammation.
Just as with probiotics, we should not expect fermented foods to “re-seed” the gut with healthy strains. Those with mast cell activation syndrome or histamine intolerance should also proceed extremely carefully, or avoid fermented foods until they are further along their healing journey.
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 sometimes be helpful in shifting the composition of the gut microbiome, though studies have shown that 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? 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: A comprehensive guide to stool and microbiome testing
How do 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 supplemental butyrate 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!
Hi Lucy,
Wondering what impact you think the anhydrous ammonia in Lean Finely Textured beef (LFTB aka Pink Slime) has on gut health? Please see: https://nobull.mikecallicrate.com/2023/07/04/price-and-deception-threaten-new-food-system-development/
Thanks,
Mike Callicrate
Colorado Springs, CO
I have read your stool test guide and I am considering booking some time with you to go over whichever test I decide. My question is I see you recommend the GI Effects test. It appears that this was written back in Oct 2021. Now GI Effects have three different stool tests and I wanted to see if it is worth the cost to purchase Preferred or even the Premier? Or which you recommend? (https://connect.gdx.net/products/gut-health) Any help would be much appreciated
[…] gut dysbiosis. Gut dysbiosis generally means “altered state of the gut microbiome, usually associated with disease.” (Mailing, 2021) That altered state means less of the microorganisms with positive effects and […]
Hey Lucy, thanks for your great work. I was wondering which tests currently available in the USA &/ EU would you recommend for sequencing the microbiome?
It appears that a lot of different suppliers have popped up which makes it all the more confusing. Thrive, Viome, Sun Genomics, Cosmos ID, Thorne – Onegevity, Mymycrozoo etc. …
Which ones do you recommend (obviously no limited to the above)?
Best
Jacob
Hi Jacob! In my opinion, Thorne (previously Onegevity) is currently the best option for microbiome sequencing. They are using metagenomics and offer you the ability to download your raw data, which will essentially allow us to see every single microbe in your gut known to science! I also like the Genova GI Effects Comprehensive Profile for a more clinical picture of the gut, but it only tests for a handful of the most common microbes and uses qPCR, which is slightly less accurate than metagenomics. I have no affiliation with either of these companies – I simply think they are the best options available at the moment. I have an old article on all of the stool testing options that I plan to update very soon!
Hello, You have been recommended to me and I’ve just emailed you. I would like to book an appointment . I have a 7yr old who has been seriously ill and doctors can’t seem to help. Thank you. M
Hi Lucy,
Great reading your information on gut health. I have diffuse diverticulosis and have had 8 diverticulitis infections in the past 10 years resulting in lots of antibiotics. (The most recent – 1 year ago was an exception… Per Mayo Clinic research… I went on a clear liquid diet for 3 days and the infection resolved without antibiotics.) I was first diagnosed at age 47. Have been referred to a surgeon twice and both times deemed inoperable due to widespread diverticulosis with documented infections throughout my colon.
I am generally very healthy, active, thin, don’t eat much, no dairy, red meat or bacon, have a high fiber diet – both soluble and insoluble, lots of water, intermittently fast – 16/24 hours, have a fairly healthy/low sugar diet, take pre and pro biotics. For decades I have had extreme boating when eating. Sugar testing 2 years ago resulted in possible sensitivity to fructose and lactose. Negative SIBO test results. I’ve researched “food combining” and have noticed less bloating implementing food combining guidelines.
I was told by the surgeon to figure out what my infection triggers are (they are bacon and food poisoning) and stay away from them. My gynecologist was the first doctor (not the gastroenterologist or surgeon) who gave me hope by saying that I needed to manage the condition with lots of fiber and water.
Do you feel that a private consultation with you would be of any benefit to me?
Thanks so much for your time, Chris
I would love to hear your perspective on how someone should treat a dysfunctional gut microbiome. Also how microbes can cause fat malabsorption and damage to microvilli. Thank you
Hello Lucy, I think you have a typo on your http://www.lucymailing.com landing page: “…reverse chronic disease, optimize health, and liver better.” I suspect good gut health will make my liver better too.
On another topic, I recently purchased a yogurt maker… and I ended up making some of Dr. William Davis’ l. reuteri yogurt (https://www.luvele.com/blogs/recipe-blog/new-improved-l-reuteri-yogurt-method) and was wondering if you had an opinion on his hypothesis.
What effect does our microbiota have on brain fog?
I would be interested in hearing about how IBD affects the gut microbiome and any research on the most beneficial diet plans to follow, ie FODMAP, Mediterranean, etc.
Thanks for the suggestion, Joyce! I’ll try to incorporate that into future content!