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This is an older article that may not reflect Dr. Mercola’s current view on this topic. Use our search engine to find Dr. Mercola’s latest position on any health topic.
By Dr. Mercola
Your gut microbiota plays a crucial role in your health, and the 100 trillion or so microbes living in your gut feed on the foods you eat. In this way, your diet influences your health not just by the micronutrients it contains, but also by how it affects the bacterial colonies residing in your intestinal tract.
In the featured video, Rhonda Patrick PhD, a biomedical scientist, interviews intestinal microbiota researchers Justin and Erica Sonnenburg about the interactions between diet and gut bacteria—specifically those living in your colon—and the effects on your health.
Justin Sonnenburg is an associate professor of microbiology and immunology at Stanford, and Erica Sonnenburg is a senior research scientist in the Sonnenburg Lab,1 which is part of the department of microbiology and immunology at Stanford.
The Importance of Fiber for Gut Health
Much of the discussion pivots around the role of dietary fiber, which promotes health by fueling beneficial bacteria to produce compounds that help regulate your immune function.
For starters, these compounds help increase T regulatory cells, specialized immune cells that help prevent autoimmune responses and more. Via a process called hematopoiesis, they're also involved in the formation of other types of blood cells in your body.
Few Americans get the standard recommendation of 30 to 32 grams of fiber per day, and when fiber is lacking, it starves these beneficial bacteria, thereby setting your health into a downward spiral. As noted by Patrick:
"This has an effect not only on the immune system and autoimmune diseases but also results in the breakdown of the gut barrier, which leads to widespread inflammation and inflammatory diseases."
Toward the end of the video, Erica Sonnenburg also delves into the effects of C-sections, explaining how avoiding vaginal birth negatively impacts the baby's health by depriving him or her of exposure to bacteria present in the mother's vaginal canal.
She also explains how infant formula may affect your child's health, as it does not contain human milk oligosaccharides—special carbohydrates found only in breast milk that specifically nourishes your baby's gut flora.
High-Fiber Diet Reduces All-Cause Mortality
Mounting research suggests that a high soluble fiber diet can help reduce your risk of premature death from any cause, likely because it helps to reduce your risk of a number of chronic diseases.
This includes type 2 diabetes, heart disease, stroke, and cancer. Studies have also linked a high-fiber diet to beneficial reductions in cholesterol and blood pressure, improved insulin sensitivity, and reduced inflammation—all of which can influence your mortality risk.
Most recently, a meta-analysis2,3 evaluating the impact of a high soluble fiber diet on mortality with pooled data from nearly 1 million Europeans and Americans found a 10 percent drop in mortality risk with each 10-gram per day increase in fiber.
Organic psyllium is one of the best ways to radically increase your intake of soluble fiber. I believe most people could benefit from more fiber. I shoot for 50 grams of fiber per 1,000 calories consumed and personally take about 6 tablespoons of organic psyllium a day, which supplies 75 grams of soluble fiber, about half of my daily fiber intake.
Other recent studies have produced similar results:
- A 2014 study4,5 found that every 10-gram increase of soluble fiber intake was associated with a 15 percent lower risk of mortality.
Those who ate the most fiber had a 25 percent reduced risk of dying from any cause within the next nine years, compared to those whose fiber intake was lacking.
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Research6 published in 2013 found that for every 7 grams more soluble fiber you consume on a daily basis, your stroke risk is decreased by 7 percent. This equates to increasing your consumption of fruits and vegetables by about 2 additional portions per day.
The Links Between Antibiotics, Your Microbiome, and Obesity
Your gut microbiome also exerts a powerful influence on your weight. Gut microbes known as Firmicutes have been detected in higher numbers in obese individuals, who also may have 90 percent less of a bacteria called bacteroidetes than lean people.7 In a Medscape interview8 published in April, 2015, Dr Martin Blaser, who heads up the Human Microbiome Center at New York University, discussed the links between your gut microbiome, obesity, and chronic disease.
As noted by Dr. Blaser:
"The basic idea is that the microbiome is ancient. The organisms that we carry are not random; they have been selected over eons of evolution. They are important for our physiology, and there is a lot of evidence for that. My big point is that they are changing. As a result of the change, there are health consequences ...
I believe that there is a general paradigm that we are losing important organisms early in life, and that is fueling some of the diseases that are epidemic today."
In his book, "Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues," Dr. Blaser attributes rising obesity and disease rates to factors that have altered the microbial composition of our microbiome. This includes:
- Increased rates of C-sections
- Excessive use of antibiotics in medicine
- Inappropriate use of antibiotics in food production. As noted by Dr. Blaser: "Farmers found that they could increase the growth of their livestock by giving them low doses of antibiotics ... the earlier in life they gave the antibiotics, the more profound the effect—and that is what we are doing to our kids"
- Dietary changes, switching to diets low in fat and high in carbohydrates
- Switching from breast milk to infant formula. This dietary change, he believes, is the most adverse of all
Moreover, he believes the effects are "cumulative over time and cumulative across generations," noting that: "We've done studies in mice in which we can show that giving mice antibiotics early in life makes them fat. Putting mice on a high-fat diet makes them fat, and putting them on both together makes them very fat, suggesting the idea of additive risk."
How Gut Bacteria Helps Regulate Your Appetite
Recent research has shed even more light on the links between gut bacteria and weight problems. Here, the researchers decided to investigate the possibility that bacterial proteins might act directly on appetite-controlling pathways. The hypothesis was that since bacterial survival depends on maintaining a stable environment, the bacteria must have some way of communicating their nutritional needs to the host.
Indeed, this is what they discovered. In essence, it appears gut bacteria play a role in appetite regulation by multiplying in response to nutrients, and stimulating the release of satiety hormones. The research also suggests bacteria produce proteins that can linger in your blood for a longer period of time, thereby modulating satiety pathways in your brain.
As reported by Medical News Today:9
"The researchers studied the growth dynamics of E. coli K12 ... when exposed to regular nutrient supply ... After 20 minutes of consuming nutrients and expanding numbers, it was found that E. coli bacteria from the gut produce different kinds of proteins than they do before feeding. The 20-minute mark coincides with the time taken for a person to begin feeling full or tired after a meal ...
[T]he researchers began to profile the bacterial proteins before and after feeding ... 'Full' bacterial proteins were found to stimulate the release of ... a hormone associated with feeling full while "hungry" bacterial hormones did not ...
The investigators next tested for the presence of one of the 'full' bacterial proteins, called ClpB. Levels of CLpB in mice and rats 20 minutes after eating ... did correlate with ClpB DNA production in the gut, suggesting a mechanism linking gut bacterial composition with the host control of appetite.
The researchers also found that ClpB increased production of appetite-reducing neurons. Evidently, bacterial proteins produced by satiated E. coli influence the release of gut-brain signals, as well as activating appetite-regulated neurons in the brain."
Another recent study10 found that probiotics helped protect against weight gain. The probiotic product in question was a commercial product simply referred to as VSL#3, containing multiple bacterial strains, including Lactobacillus acidophilus and Bifidobacterium longum. After four weeks, men who consumed this probiotic mix gained less weight and fat compared to those who received a placebo.
A Course of Antibiotics Can Alter Your Gut Microbiome for Up to a Year
It's really important to understand the impact antibiotics have on your overall health, as they're indiscriminate killers, wiping out not just the disease-causing bacteria but the beneficial bacteria too. Recent research demonstrates that when you take a course of antibiotics, your gut microbiome may be adversely affected for up to a year afterwards, depending on the antibiotic you're taking.
Such dramatic shifts in your microbiome can also allow pathogens such as the deadly Clostridium difficile to gain a strong foothold, as evidenced in a recent animal study.11 This is a significant reason for limiting antibiotics to severe infections only, as a healthy gut microbiome is part of your immune function, serving as a primary defense against all disease.
The randomized, placebo-controlled clinical trial,12,13,14,15 which took place in Sweden and Great Britain, evaluated the effects of four commonly-prescribed antibiotics: clindamycin, ciprofloxacin, minocycline, and amoxicillin.
The bacteria in the participants' oral and gut microbiomes were analyzed before the experiment, right after finishing the one-week long course of antibiotics, and again one, two, four, and 12 months afterward. While the oral microbiome normalized fairly quickly, the gut microbiome typically did not.
As reported by The Atlantic:16
"People who took clindamycin and ciprofloxacin saw a decrease in types of bacteria that produce butyrate, a fatty acid that lowers oxidative stress and inflammation in the intestines.
The reduced microbiome diversity for clindamycin-takers lasted up to four months; for some who took ciprofloxacin, it was still going on at the 12-month check-up. Amoxicillin, on the plus side, seemed to have no significant effect on either the oral or gut microbiome, and minocycline-takers were back to normal at the one-month check-up."
Antibiotics Also Raise Your Risk of Antibiotic-Resistant Disease
But that's not all. The study also demonstrated that when you take an antibiotic, you may also raise your risk of antibiotic-resistant disease. Antibiotic resistance genes were found in both British and Swedish participants at the outset of the study, although the British had on average a 1.13-times-higher load of antibiotic resistance genes than the Swedes.
The authors speculate that this may be a result of the fact that Sweden has significantly decreased use of antibiotics over the past 20 years, due to the Swedish Strategic Program for the Rational Use of Antimicrobial Agents and Surveillance of Resistance (STRAMA), launched in 1994. After exposure to antibiotics, the antibiotic resistance gene load increased across the board.
According to the authors:
"Among the antibiotics tested, exposure to amoxicillin resulted in the least discernible effects on the microbiome composition, while these samples
had the highest number with antibiotic resistance-associated genes and the most classes that were increased in the predicted metagenomes and in the full metagenomes, respectively, a week after the exposure ...
Clearly, even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome."
Antibiotics in Infancy Increases Risk for Obesity, Asthma, and Allergies
Similar research done on infants show that antibiotic treatment alters your baby's gut microbiome for 2 months or longer, and shifts the balance to allow the potentially disease-causing Proteobacteria to become dominant. The study also found that treated infants had an increased risk for developing obesity, asthma, and allergies. As reported by the American Society for Microbiology:17
"In the study, 9 infants were treated with intravenous ampicillin/gentamicin within 48 hours of birth, and over the 2 month study period, their gastrointestinal flora were compared to that in 9 control infants. At 4 weeks, bacteria from the beneficial genera, the Bifidobacteria and the Lactobacilli, were significantly reduced, and although the numbers bounced back by the study's end, the species diversity did not ...
"This research suggests that the merits of administering broad spectrum antibiotics—those that kill many bacterial species—in infants should be reassessed, to examine the potential to use more targeted, narrow-spectrum antibiotics, for the shortest period possible," says [co-author Catherine] Stanton.
Healthy Sources of Fiber
It's easy to be fooled when it comes to fiber. Most processed grain products claim to supply you with fiber, but breads and cereals are far from ideal. Not only do cereal grains promote insulin and leptin resistance, which is at the heart of obesity and chronic disease, most are also contaminated with glyphosate.
For example, about 15 years ago, farmers began dousing non-organic wheat with glyphosate just before harvest—a process known as desiccation—which increases yield and kills rye grass.
As a result, most of the non-organic wheat supply is now heavily contaminated with glyphosate, which has been linked to celiac disease and other gut dysfunction. Needless to say, this is the exact converse of what you're trying to achieve by adding fiber to your diet. Instead, focus on eating more vegetables, nuts, and seeds.
The following whole foods, for example, contain high levels of soluble and insoluble fiber. Psyllium in particular has been shown to improve glycemic control in people at risk for Type 2 diabetes.18
| Organic psyllium seed husk, flax hemp, and chia seeds |
Berries |
Vegetables such as broccoli and Brussels sprouts |
| Root vegetables and tubers, including onions, sweet potatoes, and jicama |
Raw almonds |
Peas |
| Green beans |
Cauliflower |
Beans |
Healthy Fiber Provides Fodder for Beneficial Gut Microbes
As you can see, many of the health benefits associated with fiber involve its impact on the microorganisms in your gut. Not only does soluble fiber serve as a prebiotic but it is also converted to short-chain fatty acids that are then converted to healthy ketones that feed your tissues.
Alterations of the human microbiome through inappropriate and unnatural diet changes (especially reverting away from breastfeeding infants, and avoiding fresh vegetables and other fiber-rich whole foods) appear to be part and parcel of rising disease rates. In essence, we've strayed too far from our natural diet, which promotes a healthy gut flora.
A major culprit is food processing, which removes many of the vital nutrients. Add to that the use of agricultural chemicals such as glyphosate, and decimated soil nutrients secondary to industrial agriculture , and it should be clear that what we're eating today is very far indeed from what our ancestors ate even two or three generations ago. As a result, our microbiome is changing, and it's changing for the worse.
Soluble fibers, such as psyllium, are ideal nourishment for beneficial bacteria that assist with digestion and absorption of your food, and play a significant role in your immune function. Opting for an organic version of psyllium will prevent exposure to pesticides, herbicides and chemical fertilizers that are present in nearly all commercial psyllium products.
I also recommend choosing one that does not contain additives or sweeteners, as these tend to have a detrimental effect on your microbiome. Sugar, for example, feed potentially pathogenic microorganisms, which is the converse of what you're trying to achieve.