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
In the featured video, Dr. Rhonda Patrick PhD, a biomedical
scientist, interviews Drs. Justin and Erica Sonnenburg about the
interactions between diet and
gut bacteria—specifically those living in your colon—and the
effects on your health.
Dr. Justin Sonnenburg is an associate professor of microbiology
and immunology at Stanford, and Dr. Erica Sonnenburg is a senior
research scientist in the Sonnenburg Lab,1
which is part of the department of microbiology and immunology
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
Few Americans get the recommended 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 Dr. 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
Toward the end of the video, Dr. 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
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
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.
Most recently, a meta-analysis2,
3 evaluating the impact of a high soluble fiber diet
on mortality with pooled data from nearly one 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 personally take about 3
ounces a day, which supplies 75 grams of soluble fiber, about
half of my 150-gram 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.
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
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
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
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.
"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
A Course of Antibiotics Can Alter Your Gut Microbiome for Up to
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
The randomized, placebo-controlled clinical trial,12,
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.
"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
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
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
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 sampleshad 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,
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
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 a two or three generations ago. As a
result, our microbiome is changing, and it's changing for
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
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.