- What is Microbiome?
- Understanding a Healthy Gut Microbiome
- Good Bacteria vs. Bad Bacteria In Your Gut
- About Microbiome Testing or Sequencing (And When to Get It)
- 5 Steps to Repair Your Microbiome and Gut
- The 9 Best Foods for a Healthy Microbiome
- The Top 13 Supplements for Restoring Gut Health
The human microbiome is a relatively new, rapidly growing field in medicine and biology
All the novel research findings are exciting, but the task of separating credible research from conjecture is often challenging.
Additionally, overzealous claims from commercial interests also muddy the waters.
Fortunately, many of the new findings are worth exploring, especially for people who are enthusiastic about their health, or who have gastrointestinal or immune health issues.
In this article, we’ll explore the significance of a healthy microbiome, ways to determine your gut health, simple steps to repair your microbiome (or maintain a healthy microbiome), and the best foods and supplements for a healthy gut.
What is the Microbiome?
The word microbiome comes from prefix micro- meaning “very small” and the English word biome, meaning “ecological community.”
Originally, the word may have referred to the genetic makeup of microbes inhabiting a particular ecosystem or niche, while the word microbiota referred to the microorganisms themselves 
Today, though, scientists use the term microbiome to refer to “the microorganisms (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions” 
Humans and other animals are hosts to trillions of bacteria and other microorganisms, with most of them residing in the gut or gastrointestinal tract 
After the gut, the areas of the human body with the highest number of bacteria are the mouth, skin, genitals, airways, and urinary tract 
Your microbiome can contain a mix of helpful and harmful bacteria, but most of them are symbiotic, meaning their relationship with you is mutually beneficial 
The frontier of gut microbiome studies is one of the fastest-growing areas of human health research 
Keep reading to learn what the latest science says about how your gut bacteria influence your health and wellness.
How the Gut Microbiome Affects Your Overall Health
According to current research, your gut microbiome influences your health, wellness, and disease risk in the following important ways 
- Immune health and infectious disease risk: A healthy microbiome is essential for a functioning immune system, and disturbances in gut bacteria can increase the risk of infection 
- Autoimmune conditions: Recent research links problems with the gut microbiome to the development of autoimmune conditions including type 1 diabetes and multiple sclerosis  
- Brain health and cognitive function: A network of neuroendocrine, neural, and neuroimmune signalling pathways exists by which the brain and gut communicate.  Although the mechanisms aren’t yet well-understood, research strongly suggests the microbiome regulates human cognition and behavior  
- Psychological wellbeing and depression risk: The microbiome can modulate (change) the production of neurotransmitters including dopamine and serotonin  . Evidence for microbiome involvement in neuropsychiatric disorders, especially depression, is growing 
- Metabolism, obesity, and type 2 diabetes: The effects of diet quality on the composition of the microbiome appear to account, at least partially, for the growing rates of obesity and type 2 diabetes 
- Inflammation, gout, and rheumatoid arthritis: Gut microbiome changes appear to precede chronic inflammatory diseases including rheumatoid arthritis and gout, and their prevention may be possible by addressing imbalances in gut bacteria 
- Cardiovascular health and hypertension: Gut microbiome composition is associated with markers of atherosclerosis and arterial stiffness, and early evidence suggests that microbiome changes could be the cause of sodium-sensitive hypertension 
- Cancer risk: According to some research, the composition of individuals’ microbiomes may account for upwards of 20% of cancers worldwide 
- Infant health and early development: Microbiome composition influences infants’ and children’s health including allergies, asthma, inflammatory skin conditions, cognitive development, and more 
- Aging, longevity, and lifespan: During aging, intestinal microbes shift in composition and function  . Chronic inflammation due to gut bacteria imbalances appears to be one cause of age-related degenerative diseases and unhealthy aging  . New research reveals that gut microbes can affect the aging process via multiple pathways, and anti-aging microbiome technologies may follow 
Keep in mind that the field of microbiome studies is relatively new, and has only become well-established in the past decade 
The effects your microbiome has on your overall health are only beginning to be understood, and it is certain that scientists will uncover additional details in the coming decades.
Understanding a Healthy Gut Microbiome
A healthy microbiome goes beyond what can simplistically be termed as “good” or “bad” bacteria.
As you’re about to discover, some bacteria can be both depending on their circumstances, which is one reason why researchers have established other ways to gauge the health and integrity of an individual’s microbiome.
The latest research suggests bacterial cells in your body outnumber human cells by a ratio of 1.3 to 1, and other microbes like viruses could be ten times more abundant still 
The bacteria and other microbes of the gut are extremely diverse. Based on an estimated 1,000 bacterial species in your gut, containing an average of 2,000 genes per species, the 2,000,000 genes in your gut bacteria alone would outnumber your human genes by a factor of 100 
Instead of focusing solely on the presence of particular, individual species of interest, researchers also assess microbiome health in terms of diversity and abundance.
In other words, the number of different species and the total number of members of beneficial species in your gut are also relevant to your health and wellness.
A loss of diversity and abundance relates to many modern diseases including Crohn’s disease, ulcerative colitis, type 1 and type 2 diabetes, multiple sclerosis, celiac disease, allergies, obesity, and cancer 
Poor diet quality, Western or “standard American diet,” preservatives in processed foods, the use of antibiotics, and disrupted circadian rhythms are documented factors that can cause the loss of diversity and abundance in your microbiome  
The importance of the microbiome for general health is undeniable, but the role of specific species and strains is often much less clear. In the next section, you’ll learn what the best research says about different types of microbes.
Good Bacteria vs. Bad Bacteria In Your Gut
Researchers refer to an imbalance of gut bacteria or other organisms--resulting from the loss of beneficial species or the gain of harmful species--as dysbiosis, literally meaning “bad or difficult life or way of living” in contrast to symbiosis (a mutually beneficial relationship) 
And as we discussed in the previous section, the shifting composition of the microbiome in modern humans appears to be associated with the onset of chronic, inflammatory diseases 
But with around a thousand estimated different species of bacteria in your gut, cataloging the pros and cons and specific effects of each species is a monumental task.
The majority of published analyses so far rely on statistical modeling to draw correlations from case-control studies, which compare the microbiome of people with a specific disease to those without it 
Some scientists have criticized current perspectives on gut bacteria and health as being circular and observational, rather than borne out in experimental studies  . And up to two-thirds of bacterial species remain uncultured 
To make matters even more complicated, current research shows that the microbiome varies geographically and seasonally among hunter-gatherers, which makes the concept of a “healthy” microbiome even harder to define in modern humans 
Nonetheless, the following phyla, genera, and individual species are the ones with the strongest evidence for being beneficial or harmful for modern people living in industrialized societies.
And as you’ll see, in some cases a particular species of bacteria or archaea may be beneficial in certain situations, yet appear to be harmful in others.
Bacteroidetes is a diverse phylum of bacteria found in every type of habitat on earth.
This phylum is Gram-negative, meaning their cell walls consist of a very thin layer of peptidoglycan (a polymer substance made of sugars and amino acids) and an outer membrane with a polysaccharide component (large molecules consisting of a lipid and a polysaccharide bound together).
They are a major component of animals’ gastrointestinal microbiome, and appear to function as specialists in breaking down proteins and polysaccharide carbohydrates 
Species from Bacteroidetes living in the large intestine ferment complex carbohydrates that are resistant to digestive enzymes and would otherwise reach the colon intact.
The end-products of Bacteroidetes fermentation are short-chain fatty acids (SCFAs) including butyrate, propionate, and acetate.
SCFAs represent an additional 7-10% of daily energy available to humans, and some of them have antiinflammatory effects and help support gut health 
Alongside the Bacteroidetes phylum, the Gram-positive Firmicutes phylum represents the vast majority of the bacterial population in the gut microbiome 
Compared to Gram-negative bacteria, Gram-positive bacteria like Firmicutes have a thicker cell wall structur made of peptidoglycan.
Similar to Bacteroidetes, some members of the Firmicutes phylum play a role in the fermentation of otherwise indigestible carbohydrates in the gut, resulting in production of short-chain fatty acids like butyrate 
Animal experiments and observation of human subjects suggest that Firmicutes abundance has a relationship to obesity, and that higher abundance increases fatty acid absorption, energy efficiency, and harvesting 
Some microbes from the Firmicutes phylum may modify lipolysis and other physiological activities of hosts, resulting in a reduced rate of fatty acid oxidation (fat-burning) 
Butyrivibro crossotus, a member of Firmicutes, does not appear to correlate with any disorders, and its abundance may help protect against weight gain and obesity 
Lactobacillus spp. are well-known symbiotic species with a decades-long history of use in probiotic treatments. They aid digestion and vitamin absorption and help prevent diarrhea, IBS, and overgrowth of pathogens 
Conversely, Clostridium difficile infection results in diarrhea. Research points to a link between antibiotic overuse in humans and animals and a resulting overabundance of C. difficile 
Proteobacteria is a phylum of gram-negative bacteria that includes pathogens, symbiotic bacteria, and freeliving organisms.
Many species from Proteobacteria play a critical environmental role in nitrogen fixing, which makes nitrogen from the atmosphere available to plants.
The presence of Proteobacteria appears necessary for normal function of a healthy gut microbiome, but some species are associated with inflammatory conditions 
For example, Desulfovibrio piger and Escherichia coli both exist as symbiotic strains, but increased abundance or an imbalance of either is associated with increased risk of IBD and IBS    
Heliobacter pylori, another member of Proteobacteria, is what is known as an amphibians--an organism that can have either a pathogenic or symbiotic relationship with the host depending on context.
However, it’s also associated with decreased incidence of reflux esophagitis and childhood-onset asthma 
Like Proteobacteria, members of Fusobacteria are Gram-negative bacteria that appear to act in pathogenic as well as symbiotic roles.
Unlike Proteobacteria, Fusobactera are exclusively anaerobic.
Although they are commonly found in the human gastrointestinal tract, some species like F. nucleatum are linked with IBD, chronic gut inflammation, and increased cancer activity 
F. nucleatum is also linked with periodontitis and appendicitis 
Cyanobacteria and Melainabacteria
Cyanobacteria are a phylum of Gram-negative bacteria that produces energy via photosynthesis. They are the only photosynthetic prokaryotic organisms that can produce oxygen 
While many members of Cyanobacteria produce toxins, other members play key ecological roles in producing fatty acids, amino acids, antioxidants, vitamins, and minerals 
Organisms from the phylum Melainabacteria, which evolved from Cyanobacteria, are found in the human gut alongside Cyanobacteria species and synthesize K and B vitamins including B2, B3, B7, and B9 
Verrucomicrobia are a phylum of tiny, wart-shaped Gram-negative bacteria commonly found in freshwater and soil.
To date, one member of Verrucomicrobia, Akkermansia muciniphila, has been identified and isolated and identified in the human gut.
Some researchers consider A. muciniphila to be a marker species of a healthy gut due to its anti-inflammatory and immunostimulant properties, as well as its ability to improve gut barrier function and protect against obesity, insulin resistance, and colon cancer 
Archaea are a domain of single-celled prokaryotic (lacking nucleo) organisms that resemble bacteria, but possess distinguishing characteristics like different cell wall structures and methane production.
Three distinct species of Euryarchaeota have been detected in the human body to date: Methanobrevibacter smithii, M. stadtmanae, and M. oralis 
These methane-producing bacteria use hydrogen (H2) to reduce Carbon Dioxide (CO2) and methane for their metabolism.
As part of the normal human diet, proteins and carbohydrates enter the gut. During the metabolism and fermentation of these macronutrients, abundant amounts of H2 gas are created.
However, elevated levels of methanogenic archaea are linked with increased levels of mono-, di-, and trimethylamine, which may increase the risk of cardiovascular disease 
Other potential disease states linked with high levels of methanogenic organisms and methane production include colorectal cancer, obesity, anorexia, IBD, and IBS 
About Microbiome Testing or Sequencing (And When to Get It)
Until a few years ago, having your microbiome tested was only possible if you participated in a study or your doctor requested a stool sample analysis looking for specific pathogenic microbes.
But personal microbiome sequencing and testing using the same technology found in studies and medical labs is now available commercially.
Microbiome testing requires a stool sample, which is then sequenced using microbial DNA and analyzed for its bacterial content, diversity, abundance and metabolites.
The most common sequencing method relies on characterization of the 16S rRNA gene, which is present in all bacteria . 16S refers to Svedberg units, a measure of sedimentation rate (how rapidly the ribosomal subunits sink when passed through a centrifuge, which relates to their size  )
You can think of 16S rRNA genes as a “DNA barcode.” Mutations and other variations in bacterial 16S rRNA genes allow for efficient identification of species, as well as establishing taxonomic diversity.
Another less common but more accurate technique, whole genome sequencing, has been shown to detect and amplify more genera of bacteria, archaea, viruses, and eukaryota compared to 16S sequencing 
Once either type of test analysis is complete, buyers receive a customized report, usually with recommendations included.
Companies like Viome, BIOHM, Psomagen, and others claim their personalized diet plans and other advice can help users lose weight, improve gut health, and more--all based on the unique contents of each individual’s microbiome.
Unfortunately, there is no peer-reviewed evidence in support of individualized diet or supplement recommendations based on microbiome at this time.
And as you probably noticed in the preceding section, the line between “good” and “bad” species of bacteria is blurry at best. Oftentimes, an individual species can have desirable or undesirable associations depending on other factors.
That’s not to say the idea has no merit, but rather that the insights of microbiome sequencing are in their very early stages, and it would be premature to draw conclusions about current personalized recommendations, especially without high-quality evidence.
It also doesn’t mean that microbiome testing is a waste of money. Individuals who enjoy trying out new technologies may find it worthwhile, and it could potentially provide valuable information for people with severe gut issues who have exhausted other treatment options.
But commercial microbiome testing or sequencing is not a requirement to improve your gut health or ensure you maintain a healthy microbiome.
You should speak to your doctor if you have severe health problems that you think may be linked to gut health.
He or she can help rule out other, unrelated causes, and may order specific tests based on your medical history (such as use of antibiotics or other drugs).
As we’ll cover in a moment, even if you’re dealing with gastrointestinal problems, you can take steps today to repair your microbiome without paying for a commercial test.
5 Steps to Repair Your Microbiome and Gut
The basic, foundational steps for improving or maintaining your gut health are the same regardless of whether your gut health is excellent, fair, or poor.
That said, your current health status can help determine the best approach.
For instance, if you’re free of diseases and symptoms, you might prefer to make gradual changes to realize the best results possible as conveniently as possible over time.
Or if you’ve got Crohn’s disease, IBD, antibiotic-associated diarrhea, or another condition, you might be desperate, and could dive into a gut health protocol geared towards the fastest possible relief.
It’s also possible that you’ve been dealing with a gut condition for a long time, in which case your best bet could be to troubleshoot each possible factor one at a time.
In any case, here are the steps you’ll need to take for better gut health.
1. Eliminate These Causes of Poor Gut Health
For most people, eliminating causes of poor gut health is the best place to start.
Taking probiotics and other supplements for gut health is less likely to be effective if you’re still consuming harmful foods and being exposed to other influences that detract from gut health.
According to research, these are the most common and significant causes of poor gut health to avoid:
- Packaged, processed foods with a poor nutritional profile and long shelf-life, including soft drinks and sweet and savory snacks 
- Acellular nutrients, which are nutrients that are freed by processing or added to food and not found in their natural form (inside of cells as part of whole food) and can contribute to growth ofharmful gut bacteria 
- Other unnatural food additives, including preservatives, emulsifiers, and artificial sweeteners 
- Antibiotics and other drugs shown to alter microbiome composition, which according to one recent survey include proton pump inhibitors, laxatives, and metformin  . (Another analysis of 1,000 prescription drugs found that 24% of drugs, including psychotropic medication, can affect microbiome composition  ).
Once you’re avoiding causes of poor gut health to the greatest extent possible, the next step is to focus on a diet and lifestyle that support a healthy microbiome.
2. Eat a Healthy, Microbiome-Friendly Diet
As is the case with microbiome studies as a whole, research into the influence of specific foods and diets on microbiome health is relatively new 
Along with eliminating food additives and other artificial ingredients, the foundation of a microbiome-friendly diet seems to be eating as many fresh, whole foods as possible 
Carbohydrates, fiber and prebiotics, high-quality protein, and healthy fats are all essential for a healthy microbiome 
Micronutrients, phytonutrients from plants, and antioxidants also play a role in shaping the microbiome and regulating health through related mechanisms 
The best sources of the above nutrients are minimally-processed whole foods. For the most part, dietary supplements that provide acellular nutrients in non-naturally-occurring forms have the potential to disrupt the microbiome balance by feeding pathogenic bacteria 
Probiotic and fermented foods, especially homemade and traditional varieties, are also helpful in supporting gut health  . You’ll learn more about those in the next section, “The 9 Best Foods for a Healthy Microbiome.”
So far, no particular eating pattern has been proven to be more effective than other healthy diet types for gut health or microbiome support.
Vegetarian, vegan, ketogenic, gluten-free diet, low-FODMAP, and the Mediterranean diet all show distinct, unique effects on microbiome composition 
If you’re troubleshooting a chronic gut health issue, you should definitely experiment with different ways of eating to see which one provides the most relief from symptoms.
Otherwise, you can choose any healthy diet that fits your preferences, as long as it primarily consists of fresh, unprocessed or minimally-processed whole foods.
Last but not least, food quality also matters. Organic produce appears to have greater microbial diversity compared to non-organic, and similarly, wild-caught, pastured, or grass-fed animal products are less likely to contain pesticides and other toxins and may be more nutrient-dense  
3. Live a Lifestyle That Supports a Healthy Microbiome
Beyond your dietary choices, your living environment and lifestyle have significant effects on the composition and balance of your microbiome.
Here are the factors that current research suggests can make a positive difference:
- Effective stress management may help prevent microbiome disruption 
- Minimizing exposure to man-made chemicals and toxins at home and at work supports a healthy microbiome. Chemicals to avoid include heavy metals, pesticides and other pollutants, and antimicrobial cleaning agents 
- Skincare and cosmetics are another area to consider chemical exposure, with the average person being exposed to about 126 unique chemicals with unknown microbiome effects from personal care products each day according to a 2004 study from the Environmental Working Group (EWG) 
- Breathing fresh, unpolluted air may result in a healthier microbiome 
- Increasing direct exposure to natural environments like soil or forests, and spending more overall time in nature, can increase microbiome health and diversity 
- Maximizing exposure to daytime natural light, minimizing exposure to artificial lights (especially at night), and minimizing exposure to electromagnetic fields (EMFs) from home electricity and cell phones could support a healthy microbiome   
- Getting plenty of sleep and maintaining a healthy, consistent twenty-four-hour schedule (circadian rhythm) may benefit microbiome composition and function   
As you can see, lifestyle factors can be a major factor in achieving or maintaining a healthy gut and a balanced, properly-functioning microbiome.
4. Use Targeted Supplements to Rebalance Your Microbiome and Repair Your Gut
Not everyone needs to use supplements for microbiome repair and gut health. For people who don’t have existing gut issues or symptoms, they probably aren’t worth the cost.
If you do decide to use them, make sure you understand the purpose and function of each one, and don’t assume that the statements from the manufacturer are correct. In most countries, dietary supplement makers can make health-related claims with little or no evidence
The basic categories of gut health supplements you may want to consider are digestive aids and enzymes, supplements that support a healthy epithelium or gut barrier, prebiotics to feed “good” bacteria, probiotics to augment your microbiome and reduce inflammation, and supplements that safely aid the elimination of gastrointestinal parasites and opportunistic bacteria.
We’ll cover more supplement details in an upcoming section.
5. Consider Fecal Microbiota Transplantation, Bacteriotherapy, and Other Measures
If nothing else works, you can consider cutting-edge therapies for your microbiome.
One such therapy that is backed by clinical evidence is fecal microbiota transplantation, which uses fecal matter with intact microbes from a healthy donor to repopulate and restore a healthy microbiome to the recipient  . The method of delivery is either through an upper gastrointestinal delivery route (such as a feeding tube) or rectally.
Other forms of bacteriotherapy and fecal transplantation involve treating an active infection with antibiotics prior to restoring the microbiome balance with donor microbes.
However, you should approach fecal transplantation with caution, and avoid attempting it without professional supervision.
In at least one case documented in the New England Journal of Medicine, a mistake resulted in the death o the recipient due to pathogenic E. coli bacteria 
Other fatalities have occurred from problems like complications during sedation or possibly-unrelated infections 
The 9 Best Foods for a Healthy Microbiome
In many ways, the best foods for a healthy microbiome resemble those found in a primal or Paleo-style diet
Here’s what to eat to support a healthy microbiome:
- Probiotic fermented foods, especially homemade fermented foods or traditional probiotic foods like kefir, yoghurt, kombucha, and water kefir. Some evidence suggests that eating fermented foods is a more effective route of administration for beneficial bacteria than probiotic supplements 
- Berries and other fruits high in prebiotic soluble fiber and polyphenol antioxidants and relatively low in fructose 
- Colorful yellow, orange, and red fruits and vegetables, which are high in the antioxidant vitamins called carotenoids that support a balanced microbiome 
- Leafy greens and other vegetables that are nutrient-dense and high in prebiotic soluble fiber 
- Extra virgin olive oil, which is an excellent source of the monounsaturated fatty acid oleic acid and is high in anti-inflammatory phenolic antioxidant compounds 
- Fatty fish and shellfish high in anti-inflammatory omega-3 polyunsaturated fatty acids, which may be able to restore the Firmicutes/Bacteroidetes ratio and increase production of short-chain fatty acids 
- Food sources of conjugated linoleic acid (CLA, a polyunsaturated fatty acid), which include grass-fed ruminant animal products such as beef, lamb, butter, and other full-fat dairy products 
- Beef, calf, chicken, duck, or goose liver and other organ meats for their incredibly high content of fat-soluble vitamins in the natural, cellular form 
- Complete vegan or vegetarian proteins such as pea protein or whey protein, as well as highquality grass-fed or pastured animal proteins 
As we already discussed, you should avoid highly-processed foods altogether
And even some natural foods, such as wheat or other grains, contain irritants and antinutrients that may impai gut barrier function or affect digestion 
The Top 13 Supplements for Restoring Gut Health
As mentioned in the previous section entitled “5 Steps to Repair Your Microbiome and Gut,” most people don’t require supplements for a healthy microbiome.
If you think you may benefit from supplementation, these are the best supplements to consider for restorin your gut health:
- An ultra-high-quality freeze-dried cold storage probiotic like VSL #3 for short-term usage
- Prebiotics like MegaPreBiotic, Biome Bliss, or Ultimate Fibre taken together with probiotics
- Grass-fed hydrolyzed collagen and vitamin C to restore tight junctions in the gut  
- Curcumin or turmeric powder to decrease inflammation  
- High-quality L-glutamine to aid in immune function and cellular repair 
- Sodium butyrate or calcium magnesium butyrate to reduce inflammation and support an abundant population of healthy bacteria 
- Ginger powder or ginger extract for easier digestion and relief of symptoms like nausea and possible increase of bile release  
- Digestive enzymes (protease, lipase, amylase, and others) to assist with food digestion if necessary
- An immunoglobulin-based supplement designed to neutralize environmental toxins and rebuild protective intestinal barriers  
- Salts of D-glucaric acid to decrease viability of pathogenic bacteria and assist the excretion of toxic compounds  
- Colostrum or lactoferrin if required to combat opportunistic bacteria and as an anti-biofilm agent 
- Peppermint oil or oil of oregano if needed as a broad spectrum antimicrobial, taken separately from probiotics 
- Low doses of activated charcoal to bind endotoxins if you experience a severe Herxheimer or “detox” reaction  . Consult the label recommendations, limit your doses, and take away from meals.
Remember that supplements are secondary to the core practices of eliminating causes of poor gut health, eating a diet that supports a healthy microbiome, and living a lifestyle that’s conducive to a healthy population of microbiota.
Conclusion: The Importance of a Thriving Microbiome
Microbiome research is exciting, but still very new. As you pay attention to what the latest research reveals, keep in mind that most findings are inconclusive and experimental evidence is currently lacking.
And still, even the best research paints a picture that can be confusing, with all phyla and even some species playing “good” and “bad” roles for gut health in different contexts.
Fortunately, the science behind establishing or maintaining a healthy microbiome is relatively clear
Microbiome testing may be interesting or useful in some cases, but it’s by no means a requirement to achieve a healthy gut.
Instead, begin by removing causes of poor gut health from your life, then prioritize a healthy, whole-foodsbased diet with plenty of nutrient dense and probiotic foods.
A healthy lifestyle is another important yet easily overlooked requirement for a balanced microbiome.
Finally, if you have severe, pervasive symptoms of a disrupted microbiome that do not respond to basic measures, you may wish to resort to supplements or advanced procedures like a medically-supervised fecal microbiota transplant