What Does A Healthy Gut Microbiome Look Like
Diversity is considered the number one hallmark of a healthy gut microbiome.
When the microbiota of people living in Western cultures were analyzed in comparison with those of people living in rural settings who had hunter-gatherer lifestyles and with those of wild primates like chimpanzees, Western-culture gut microbiota were found to be significantly lacking in both richness and biodiversity. This is directly attributable to diets high in industrially processed foods , which dont supply enough nutrition for our microbiota to thrive. Interestingly, there is even less diversity of gut bacteria in obese people than in lean people: more food does not equal more nutrition, and the worse our diet, the more our gut microbiota suffer.
In the adult human gut, two phyla dominate: Bacteroidetes and Firmicutes. These are present in every human gut, and much smaller proportions of the phyla Actinobacteria, Proteobacteria, Verrucomicrobia, and Fusobacteria can also be present. While there are literally thousands of species of bacteria belonging to each of these phyla , its useful to look at some of the broad strokes when it comes to this birds-eye look at the gut microbiom.
Worsening Of Acne Rosacea And Eczema
If the skin microbiome becomes damaged, it is likely because of an ecological imbalance between the beneficial and harmful bacteria populations. This happens when harmful bacteria overpower the beneficial effects of symbionts and commensals.
For example, an overgrowth of inflammatory acne bacteria will lead to breakouts and flare-ups of acne. In eczema, flare-ups can be worsened by a high density of the dangerous Staphylococcus aureus. Lastly, a high density of Demodex mites has been seen to be responsible for rosacea flare-ups.
As the skin microbiome is depleted of beneficial bacteria, it will struggle to fight back infections and reduce inflammation, which leads to the worsening of most chronic skin conditions.
Improve Your Gut Microbiome Today For The 4rs
There are a number of factors that contribute to the health of your gut microbiome, including your environment, the amount of exercise and sleep you get, and of course, stress. But the number one factor that determines what microbes live in your gut is your diet.
In Functional Medicine, there is a very successful protocol called the 4Rs, which stands for Remove, Replace, Reinoculate, and Repair. There are many resources for learning more about the 4 Rs. I like Raphael Kellman, M.D.s book, The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss.
The beautiful thing about the 4Rs protocol is that it doesnt have to be followed in order. Once you remove the processed foods and toxins from your diet, you can start doing all of the remaining 3 steps together. Unless you suffer from a serious digestive disorder or other condition, you can follow the 4Rs on your own. Or, find a practitioner who can tailor the protocol to your specific needs.
Here are my suggestions for following the 4Rs and improving your gut microbiome starting today:
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Disease Risk Reduction Claims
A disease risk reduction claim is any statement linking the consumption of a food or constituent of food with a reduction in risk of developing a diet-related disease or condition. Regulatory agencies in the United States, Canada, and Europe authorize disease risk reduction claims that are supported by significant scientific agreement . In Canada, premarket review and approval of claims about diseases or health conditions not listed in Schedule A to the Food and Drugs Act are voluntary .
To date, disease risk reduction claims have been authorized for fiber-containing foods and reduced risk of some types of cancer as well as foods that contain fiber from certain foods and reduced risk of coronary heart disease . In 2009, Canada approved nonspecies-specific claims for probiotics in foods with a restricted list of species , but none relate to the gut microbiome. In the United States, guidance was issued on the types of studies from which the FDA can draw conclusions for evaluating health claims , but neither the FDA or Canada has approved any microbiome-specific claims for foods containing prebiotics. The EU-issued draft guidance specifically related to gut and immune function and the characterization of claims referencing a beneficial physiological effect and disease reduction .
What Are The Symptoms Of Dysbiosis
When the gut microbiome is out of balance, symptoms of dysbiosis can arise. These symptoms may be felt principally in the digestive tract as digestive disturbances, but there may also be knock-on effects in other parts of the body, such as the immune system and organs of elimination, for example.
Probiotics produce beneficial metabolites, such as vitamin K and short chain fatty acids, which can be used by the body, whereas pathogens produce toxins. When we have greater quantities of undesirable microbes in the gut, the organs of elimination must work harder to breakdown and then eliminate their toxins. Signs of poor detoxification can often be seen on the skin, with the appearance of skin conditions such as eczema, acne, psoriasis.
Emotional health may also suffer due to the impact of dysbiosis. Psychobiotics is an area of science looking specifically at the impact of the gut microbiome on our mood and mental health. Many studies show a clear link between gut health and emotional health, and the microbiome is now known to play a significant role in our ability to synthesize certain hormones and neurotransmitters. Read more about the gut-brain axis and probiotics.
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How Do You Cultivate A Healthy Plant Microbiome
by University of California – Berkeley
Scientists are homing in on what a healthy human microbiome looks like, mapping the normal bacteria that live in and on the healthy human body. But what about a healthy plant microbiome?
Is there even such a thing as a healthy plant microbiome in today’s agricultural fields, with acres of identical plants assaulted by pesticides and herbicides and hyped up on fertilizer?
A new study by University of California, Berkeley, microbial ecologists used experimental evolution to help identify the core microbiome of commercial tomatoes. They selected for those microbial taxa that best survived on the plants and then showed that these “domesticated” microbial communities are able to effectively fend off random microbes that land on the plants. In other words, these selected communities look like a stable, healthy plant microbiome, akin to what a robust tomato plant might pass to its offspring.
The results are good news for growers who hope that manipulating the plant microbiome, perhaps with probiotics, will make for healthier fields that need less fertilizer and less or no pesticides to produce good yields.
Koskella, lead author Norma Morella, who is now a postdoctoral fellow at the Fred Hutchinson Cancer Research Center in Seattle, and their colleagues reported their findings online this week in the journal Proceedings of the National Academy of Sciences .
How do seedlings get microbiomes from their mothers?
The new study is encouraging.
Our Evolving Understanding Of The Healthy Microbiome
Early studies sought to identify the normal set of microbes that colonize healthy people, primarily in the gut, by culture and characterization of physiological properties. Such studies best highlight organisms that grow well in the lab environment, such as Escherichia coli. This bias led to the perception that E. coli is an abundant and prevalent member of the human gut microbiome . The introduction of strictly anaerobic techniques in the 1970s allowed the recovery of more than 300 bacterial species from the gut alone furthermore, the counting of viable cells within standardized serial dilutions in selective media permitted quantification of these species. A summary of four large studies from this era looking at stool samples from 141 Americans on different diets found that bacteria of the genus Bacteroides and anaerobic cocci were both prevalent and abundant, whereas the genus Clostridium was ubiquitous in lower abundance, though no single species was observed in all subjects. Other prevalent but lower-abundance bacteria included members of the genera Bifidobacterium, Eubacterium, Lactobacillus, and Streptococcus, as well as facultative anaerobes such as Escherichia.
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Pay Attention To Stress Levels
Stress is inevitable, but too much can disrupt your entire system, and your gut is especially vulnerable. Too much stress can lead to immune reactions that contributes to gut imbalance.
And this effect is seen with any type of stressphysical, emotional, and environmental. While its impossible to get rid of stress completely, its important to get all types of stress levels under control. You have to find what works best for you, but some common stress reduction techniques include:
- Reducing your workload
‘live And Active Cultures’
On a yogurt, for example, while some consumers believe live and active cultures means probiotics, at a basic level, it just means that the product contains a certain amount of Lactobacillus bulgaricus and Streptococcus thermophilus at the time of manufacture .
However, one clear side benefit of these cultures is that they break down lactose and therefore improve the digestion of dairy products for people with lactose intolerance, which could technically be considered a probiotic effect, observes Dr Freitas.
Its a very particular benefit, so its not about the immune system, for example. Id say yogurt has bacteria that helps with lactose intolerance.
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Signs You Have A Gut Balance Issue + How To Support It
When your gut is healthy, the rest of your body often hums along happily. That’s because your gut influences everything from your digestion to your brain and your immune system.
However, if your gut isn’t at its healthiest, your body tends to have a way of sending signals. That may look like obvious digestive support needs or some less obvious signs .
Luckily, there are a number of ways to check in with your body to see if you have gut health needs, plus expert-backed strategies to cope.
How Microbiota Benefit The Body
Microbiota stimulate the immune system, break down potentially toxic food compounds, and synthesize certain vitamins and amino acids, including the B vitamins and vitamin K. For example, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals.
Sugars like table sugar and lactose are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine. There, the microbiota help to break down these compounds with their digestive enzymes. The fermentation of indigestible fibers causes the production of short chain fatty acids that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders. Clinical studies have shown that SCFA may be useful in the treatment of ulcerative colitis, Crohns disease, and antibiotic-associated diarrhea.
The microbiota of a healthy person will also provide protection from pathogenic organisms that enter the body such as through drinking or eating contaminated water or food.
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How To Support A Healthy Gut Microbiome
Diet is the single biggest influence on microbiota composition. In fact, diet is directly responsible for more than 60% of the variation in bacterial species in the gut.
We know that inadequate fiber intake, high intake of omega-6 polyunsaturated fats , high intake of saturated fat and low levels of vitamin D all cause a shift in the gut microbiota from probiotic to commensal, opportunitistic and pathogenic strains. In particular, inadequate fiber tends to shift the population of gut bacteria from majority Gram-positive strains to more Gram-negative strains . High omega-6 fat intake depletes growth of both Firmicutes and Bacteroidetes phyla. And, high saturated fat intake skews microbiota unfavorably towards more Bilophila, Turicibacter, and Bacteroides. Vitamin D deficiency leads to shift toward pathogenic bacteria , whereas supplementation restores levels of probiotic bacteria .
Its not just a question of which kinds of bacteria our diet nourishes but also a question of bacterial metabolism . Just as a high-sugar diet causes oxidative stress in our bodies , a high-sugar diet causes oxidative stress in our gut bacteria. Those bacteria adapt by altering their metabolism, which greatly affects our health.
The good news here is that the population of microbes in the gut adapts quite rapidly to changes in diet, in a matter of a few days to a few weeks.
Fermented Foods Are Gut
Fermented foods are another great source of probiotics. The crowd favourite is yogurt, however, if youre going to be eating a lot of yogurt, make sure that it is sugar-free! There are several other options that are a great source of good bacteria. Kombucha is becoming a very popular source of probiotics. You can also eat things like pickles, kimchee, and kefir to ensure that youre getting enough live cultures to keep your gut healthy and happy.
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Eat Your Probiotics And Prebiotics
Probiotic-rich foods like raw fermented sauerkraut, kimchi, yogurt, kefir and kombucha are all great sources of dietary probiotics. Eating them regularly can help strengthen the health of your gut microbiome.
Additionally, you want to be eating prebiotic-foods as well, which act as food for the probiotics in your microbiome. Specifically that includes fiber-rich foods like garlic, onions, legumes, oats, bananas and leafy greens. Your gut bacteria breaks down the fiber for their own energy helping to support colonization of healthy bacteria in the gut.
How Long It Takes For Food To Move Through Your Gut
Another important indicator of gut health is how long it takes for a meal to be digested and for the food, you eat to travel through your gut – this is called gut transit time.
A healthy gut transit time isnât too short or too long. Our research suggests that transit time varies widely between people, with a typical time of around 28 hours.
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What Type Of Information Is Needed To Define A Healthy Gut Microbiome
Despite the importance of the gut microbiota and diet-microbiome interactions for human health, North American and European regulatory agencies have not approved microbiome-specific health claims. This is likely due to the inherent challenges and complexities that surround the definition of a healthy microbiome and a lack of validated biomarkers or surrogate end points to define and measure microbiome-host interactions. For regulatory agencies to evaluate and enforce claims related to the microbiome and its impact on host health, critical information is necessary that requires a comprehensive, multidisciplinary research agenda. In addition to existing data, prospective and cohort studies are needed to elucidate relationships between the gut microbiome and biomarkers or surrogate end points in the host that are accepted indicators of normal biological processes, pathogenic processes, or responses to an exposure or intervention, including therapeutic interventions , regardless of structure or biological sample . Just as biomarkers have been identified and validated as surrogate end points for cardiovascular disease and diabetes , similar efforts are needed for the gut microbiome and host responses to the gut microbiome.
Consensus should also be achieved regarding mandatory baseline and follow-up data collection , and processing of samples should be standardized to understand microbiome-host relationships and allow microbiome studies to be compared and/or combined.
Technical Challenges In Studying Gut Microbiome And Host Interactions
Measuring the human microbiome requires proper sample acquisition, handling, storage, and analysis. Procedures and analytical methods need to be reproducible and consistently applied across studies and populations to obtain accurate diet and dietary intake assessments and to minimize technical variation in metagenomic data . For the most part, samples are obtained from defecated stools . Before genetic sequencing, each physical, chemical, and biological step involved in the molecular analysis of a microbial sample can be a source of bias, which could lead to a distorted perspective of the real microbiome . When extracting microbial nucleotides , microbial proteins, or microbial metabolites, each step can induce species-specific bias . DNA extraction is a common source of variation among laboratories , partially because Gram-positive bacteria cell walls are more difficult to lyse.
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What The Research Says
No studies have proven explicitly that the microbiome diet works to improve a persons microbiome or that it can treat health conditions.
However, the idea that diet can benefit the microbiome and that this, in turn, can benefit human health, does have evidence to support it.
As the microbiome plays a role in immunity and inflammation, a healthy microbiome may reduce the risk of diseases,
- other gastrointestinal conditions
However, scientists are still trying to understand how specific foods and bacterial species affect the microbiome.
A 2019 study found that similar foods could affect peoples gut flora in very different ways, depending on the individual. This suggests that how a diet influences the microbiome is also individualized.
As genetics have an impact on how changes to the microbiome affect human health, people may need a more personalized approach to nutrition than the microbiome diet. This is especially true if a person has any underlying health conditions.
Overall, scientists need to carry out more research on the ways that specific food choices and probiotic strains impact the microbiome.
Evidence suggests that a healthy and diverse microbiome is beneficial to human health. The microbiome diet could support this by encouraging people to eat plant-based foods.
Plant-based diets can also benefit people who are overweight to reach a healthier weight .