How the Gut Microbiome affects the Brain and Mind
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One summer afternoon when Doctor Martin Blaser
was still a medical student, he went to see
an eleven-year-old boy who had suddenly become
ill and was hospitalized. He was perfectly
fine until two days earlier when he suddenly
developed a fever and an upset stomach. The
next day the fever worsened, and on the third
day, the boy developed small purplish dots
on his body. The emergency room doctors quickly
realized the boy had Rocky Mountain spotted
fever, something caused by a bite from a tick
infected with a type of bacteria called rickettsia.
This bacterium multiplies within cells lining
blood vessels, invoking an aggressive immune
response. Since this involves the brain’s
blood vessels, it caused a form of encephalitis,
a swelling of the brain provoking a massive
When Blaser accompanied doctors to see the
boy, the room was darkened as the light hurt
his eyes, his body was covered with purple
spots, and he was thrashing around in his
bed covered in sweat. He was yelling incoherently
as loud as he could while hallucinating.
As Dr. Blaser explains in his book “Missing
Microbes,” the boy was started on an antibiotic
called tetracycline and after just five days,
he was discharged from the hospital.
Especially considering the Gut Microbiome
is the big topic in health and science recently,
you may know that not all microbes are bad.
While there are pathogenic microbes like these
just mentioned, at all times there are 500
to 1000 different species of bacteria in the
human body. And the importance of their function
is becoming more apparent as we learn new
things about them.
However, it’s hard to picture how tiny microbes
in our gut contribute to our day to day cognition
and brain function. In the case of rocky mountain
spotted fever it may not be surprising that
the introduction of a deadly pathogen could
induce drastic changes in a person’s mental
state. However, the relationship between the
microbes normally residing in the gut and
how our brain operates becomes apparent when
we take them out.
Scientists observing microbe-free mice living
in sterile bubbles quickly noticed that these
mice have a personality that is distinct from
mice with gut microbes. Microbe-free mice
were found to be more prone to taking risks
and they freely explore their environment.
Risk taking might be good if you’re a young
entrepreneur, but the kind of risk these mice
engage in is wandering further out in an open
field. For a mouse, this is an excellent strategy
for quickly getting killed by a predator.
Not only are the mice unusually reckless,
scientists also noticed that these microbe-free
mice have memory-related defects.
The book “The Good Gut” by Erica and Justin
Sonnenburg describes how a group of researchers
put normal and microbe free mice through some
memory tests. First, the mice were given five
minutes to explore two new objects, a small
smooth ring and a large checkered ring. Then
the objects were removed for twenty minutes.
After that, the large checkered ring and a
new object, a star-shaped cookie cutter, were
put in the cages. Predictably, the mice with
the normal microbiota checked out the cookie
cutter and paid less attention to the checkered
ring because they already knew what it was.
The microbiota free mice, explored the new
cookie cutter, but spent just as much time
checking out the old object – the checkered
ring. It seemed that these mice had completely
forgotten an object they had just seen twenty
The forgetfulness in these mice may be explained
by the fact that the microbe free mice have
lower levels of BDNF. BDNF, brain-derived
neurotrophic factor is a powerful protein
important for learning and memory. It stimulates
the production of new brain cells and strengthens
existing ones. Low levels of BDNF are linked
to depression and anxiety.
Since making microbe-free humans would be
quite unethical, such experiments haven’t
been repeated in humans, but… you may have
heard of the woman who, after receiving a
fecal microbiota transplant, became obese.
The fecal microbiota transplant or FMT is
just as it sounds, it’s taking the poop
from one healthy person and putting it into
another person, in order to share the healthy
microbiota of the donor. FMT is not a common
practice, but it’s the most effective treatment
for a Clostridium difficile infection, which
causes diarrhea and abdominal pain for weeks.
In this case, the woman’s donor was her
16 year old overweight but otherwise healthy
daughter. The transplant went smoothly and
successfully cured the woman’s issues. But,
over a period 16 months, the woman gained
34 pounds. And this happened despite persistent
diet and exercise efforts. She even went on
a medically supervised liquid protein diet
and still could not get the weight off.
On the flipside of this, it’s been found
that putting the microbiota of lean mice into
other mice protects them from gaining weight.
So it looks like a microbiota transplant can
transplant body types, but what about personality?
In 2011, a research group at McMaster University
did an experiment with two different types
of lab mice. One type had a personality that
was the mouse equivalent of anxious and the
other type was sociable and extroverted. To
set a metric for how nervous the mice were,
they put them on an elevated platform and
recorded how long it took for them to step
The mice with the anxious personality spent
an average of four and a half minutes slowly
and carefully making their way off the platform.
The “extroverted” mice jumped down in
seconds. Then, the scientists switched the
microbiota of the two types of mice and did
the platform test again. The mice with the
extroverted personality, after receiving the
microbes of the anxious mice, now took over
a minute to get off the platform. On the other
hand, after getting the microbes from the
extroverted mice, the “anxious” mice got
off of the platform a whole minute quicker.
What this group showed was that in these mice,
behavior and levels of anxiety were dependent
on which microbes were living in their gut.
One other thing: remember BDNF, the protein
that we should like to have more of for better
brain function? Well, the microbiota switch
that made the “anxious” mice more “confident”
also increased their levels of BDNF. The change
in microbiota not only made observable changes
in behavior, but in brain chemistry as well.
In fact, there’s all kinds of chemistry
going on in the gut that can affect the brain.
There’s even research identifying which
specific microbes produce which neurotransmitters.
For example it’s estimated that 90% of our
serotonin is produced in the gut, and it’s
been found that some of this serotonin is
produced by these four microbes.
These two microbes produce gamma-Aminobutyric
acid or “GABA” – our chief inhibitory
neurotransmitter which has relaxing and anti-anxiety
And these two (Bacillus and Serratia) produce
our motivation neurotransmitter, dopamine.
So we basically have this huge mass of little
drug factories sitting in our gut pumping
out different substances that affect our brain.
In fact the gut and its microbes appears to
affect the brain so much that preclinical
research in rodents suggested that certain
probiotics have antidepressant and anti-anxiety
effects. Probiotics are basically substances
you can take orally to stimulate the growth
of microbes. One study even found that a Bifidobacterium
infantis probiotic had anti-depressive effects
on par with that of the anti-depressant drug
I used to think that the only benefit of fiber
was that it helped you poop. However, considering
dietary fiber isn’t food for us but for
our microbes, a diet rich in fiber from a
variety of sources should also be good for
our mental health.
This information about the gut microbiome
makes you start to wonder how many mental
afflictions could be traced back to disruptions
in gut health from, for example, diets rich
in fiberless processed foods and refined carbohydrates,
or from the unmitigated use of antibiotics.
Antibiotics can be a life saver when absolutely
necessary as we saw at the start of the video,
but the most commonly prescribed antibiotic
– a wide-spectrum antibiotic doesn’t just
kill the offending bacteria, but all kinds
of other bacteria get caught in the crossfire.
This is like poisoning your cat along with
a bunch of cockroaches you’re trying to
In the United States alone, tens of millions
of people are prescribed antibiotics for minor
afflictions. 60 to 80 percent of children
taken to the doctor complaining of bad sore
throats or ear pain will walk out with an
antibiotic. It’s estimated that people will
take 30 courses of antibiotics by the age
of 40. But, the highest prescription rate
was for children under the age of two with
1,365 courses per 1000 babies.
So, could all these antibiotics affect the
young gut microbiome and the brain development
of these children?
A 2012 paper by Dr. Derrick MacFabe describes
what happens when rats are injected with something
called Propionic Acid or PPA. The PPA injection
provoked peculiar changes in the rats’ brains
like neuroinflammation, increased oxidative
stress, and glutathione depletion.The rats
also displayed abnormal movements, repetitive
interests, cognitive deficits, and impaired
social interactions. Basically, the results
of this injection were very similar to autism
spectrum disorders. And, PPA is a fermentation
product of bacteria, namely Desulfovibrio,
Bacteroidetes and Clostridia. It was found
that patients with autism have many more species
of the clostridium bacteria and have high
levels of PPA in their feces.
It’s estimated that in one third of patients,
autism doesn’t show up until around 18 to
24 months. Several reports from parents say
that their children were developing normally
until they received antibiotics for upper
respiratory or ear infections. According to
Dr. Sydney Finegold, antibiotics wipe out
or suppress several organisms in the gut,
but Clostridia is one of the ones that persists.
A CBC program titled “The Autism Enigma”
features Ellen Bolte who explains how her
son Andrew’s behavior changed drastically
after 6 courses of antibiotics over a 2 to
3 ½ month period for an ear infection. After
this, he was diagnosed with severe autism.
Digging into the research, Ellen came across
information about the Clostridia bacteria,
so she started searching for a doctor who
would be willing to try an antibiotic called
“vancomycin” on Andrew. Vancomycin is
specifically designed to target the Clostridia
bacteria. After she finally found a doctor
who agreed to test her theory, they tried
the antibiotic and it had impressive effects.
“The results were astounding. Within a matter
of just a few weeks, he became calm. He was
aware of his environment… he’s putting puzzles
together…” The antibiotic brought out improvements
in Andrew that were transient but drastic.
This case lead to a pilot study with Dr. Finegold
and a Dr. R Sandler who found that out of
10 autistic children treated with vancomycin,
8 of them had again transient but significant
Now, jumping to conclusions about the cause
autism has not been… helpful in the past…
but this idea that autism could be the result
of a disturbed gut is gathering more and more
data. A disturbed gut ecosystem would also
explain the very common gastrointestinal issues
autistic children suffer. Some estimates say
that as high as 70% of children with autism
spectrum disorders also have gastrointestinal
Autism is just one of the disorders that can
be linked to a disruption in gut health, and
research on the gut microbiome is growing
quickly. About 3600 related articles on this
topic were published between 2010 and 2015.
At this point, saying the gut microbiome is
important to health is an understatement.
Dr. Martin Blaser says that “losing your
entire microbiome outright would be nearly
as bad as losing your kidneys or liver.”
Unlike the kidneys or liver however, you can
change the makeup of your microbiome with
what you put into your mouth.
I guess Hippocrates knew what he was talking
about when he said “All disease begins in
the gut,” and “Let food be thy medicine.”
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