Powerpoint on Microfauna

How to help your microfauna positively
affect your health
There are HOW MANY in me?
 For every one human cell there are 10 single-celled
 Average number of cells in a human is 10 trillion, so
number of microbes?
 Collectively referred to as “microbiotia”
 Fungi
 Protozoa
o Bacteria
Anaerobic vs. Aerobic
 Most of the bacteria in the gut are anaerobic, or live
without oxygen.
 But until recently, to study the bacteria in the gut, they
were grown in petrie dishes (in oxygen).
 So how do we identify species which won’t grow in
 We sequence their genes. But this is a huge
undertaking! While humans have 30,000 genes, our
bacteria have millions.
Types of Bacteria
 There are about 100 phyla of bacteria. Human
microbiomes are dominated by four:
 Actinobacteria
 Bacteriodetes
 Firmicutes
 Proteobacteria (contains a lot of bad guys – E. coli,
salmonella, etc.)
Firmicutes vs. Bacteriodetes
 Heavier Americans have been discovered to have more
Firmicutes than Bacteriodetes.
 Dieting causes a decrease in Firmicutes and an
increase in Bacteriodetes.
 Bacteriodetes suppress a hormone that facilitates the
storage of fat WHILE also suppressing an enzyme that
stops fat from being burned, thus preventing weight
Wait, there’s more!
 Stress decreases bacteriodetes, thereby increasing weight gain.
 Firmicutes love amino acids and multiply with diets high in
 Bacteroidetes like carbs, helping us extract nutrients from
oranges, apples, potatoes, and wheat germ.
 Prevotella (a bacteriodete) like whole grains, so you’d think
they’d indicate good health, but they are also found in large
quantities in patients with HIV and have been linked to heart
Even with all of this information and more, we still don’t
know which levels of each of these indicates a healthy
Gut Bacteria and Heart Attacks
 Gut bacteria make most of the formic acid in humans.
 The amount of formic acid in the urine is inversely related to
blood pressure.
 Killing off those bacteria reduces atherosclerosis, and thereby,
heart attacks.
 Gut bacteria also turn lecithin (found in eggs, liver, beef,
pork and wheat germ) into an artery-clogging compound,
 TMAO levels in the blood can be used to predict heart
attacks, strokes and do so independent of other risk factors.
Gut Bacteria and Type 2 Diabetes
 Morbidly obese people can have a procedure done
called a Roux-en-Y, which reduces the small intestine,
thereby reducing food absorption. This causes them
to lose weight.
 A side effect is that in 80% of the cases, the person’s
type 2 diabetes disappears as well.
 It is believed the intestinal bypass disrupts the
influence of the microbiome on the sensitivity of body
cells to insulin.
Gut Bacteria and Parkinson’s
 Studies have shown patients whose constipation was
treated with antibiotics saw their Parkinson’s
symptoms disappear.
 It is thought the bacteria causing Parkinson’s travels
from the gut to the brain via the vagus nerve.
 In severe cases, the antibiotics wiped out all of the gut
flora and as a result these patients then received fecal
transplants (will explain later). And then other
diseases affecting these patients were alleviated;
- Multiple Sclerosis, Chronic Fatigue Syndrome,
Rheumatoid Arthritis.
The Complicated Case of Helicobacter Pylori
 Helicobacter Pylori definitely can cause ulcers and stomach
cancer, but rarely and usually in older people. Most people with
H. Pylori have no problems with it.
 In fact, in studying this bacteria, scientists discovered it benefits
the body by regulating levels of stomach acids, prevents asthma
and reduces the chances of overeating by regulating the
hormone ghrelin. (Good news)
 Too bad fewer than 6% of American children carry this bacteria.
(Bad news)
 Could this explain the rise of asthma and obesity in American
 One possible suggested solution – inoculate children with H.
Pylori for its benefits early on in life and then get rid of it with
antibiotics around age 40.
Gut Bacteria and Autism
 The majority of people with autism have a gut rich in
Clostridia bacteria.
These bacteria use phenols to kill competing bacteria in
the gut. Phenols work because they are toxic. They are
toxic to the competing bacteria as well as to human cells.
Humans therefore neutralize these phenols with sulfur.
But sulfur is needed for brain development.
It is not proven that this is what causes autism.
But note – many autistic people have a genetic defect which
interferes with their sulfur metabolism and having an
infection with Clostridia could be pushing them over the
Why Am I So Healthy Then?
 “Invasion Resistance” probably.
 Most people’s microbiome is healthy and work to
keep pathogens from gaining a toehold by occupying
potential niches.
 But at the same time our microbiomes are also
making the environment inhospitable to foreigners.
The Big Question for People
Who Aren’t Healthy
“Will switching out my gut bacteria fix these problems?”
(in some cases)
 The most dramatic results are found in patients with
severe Clostridium difficile infections.
 C.difficile kills about 14,000 Americans a year.
 Most effective treatment? Re-poop-ulating the patient.
 That’s right. Replacing their gut bacteria with that
from a healthy donor. The scientific name for this is
fecal-microbiotia-transplantation or FMT.
Studying Gut Bacteria
 In 2012, NIH and the European Commission have
pledged more than $170 million over the next five years
to identify and characterize the human microbiome.
 The two major goals are:
 to identify where the bacteria are located in/on the
human body
 compile a reference set of genetic sequences that
correspond to each bacterial species which will go into a
shared international database.
The American Gut Project
 The American Gut project builds on the Human
Microbiome Project (what the NIH is funding) by
allowing ANYONE to participate in bacterial gut
 Simply sign up, donate $99 bucks, use the supplied kit
and find out which microbes have made your skin,
your mouth and your gut their home.
 Your results are emailed to you along with the results
from the average American for comparison.
Babies and Gut Bacteria
 Babies come with sterile intestines.
 During vaginal birth, the baby takes in most of the
mother’s microbiome.
(C-section babies pick up SOME of their mother’s
microbiome while being breastfed, but it mostly from skin,
which may account for the higher rates of allergy, asthma
and autoimmune problems in C-section babies. Their
immune systems may fail to develop properly.)
 Within weeks, the baby has its own microbiome, but this
microbiome changes with the baby as solid food is
introduced and as weaning occurs.
 About age 3 the child’s microbiome resembles that of the
adults it lives with.
Evidence for Co-evolution
 Breast milk contains loads of carbs called glycans.
 Humans do not have the gene containing the
instructions to make the enzyme that breaks down
glycans into simple sugars.
 Bacteria in our gut regularly make glycoside hydrolase,
which CAN digest glycans, thus releasing energy from
breast milk to the child.
What else is in Breast Milk that
provides even more evidence?
 Mother’s milk contains lots of oligosaccharides, which
infants cannot digest, nor use.
 So why are they present in the milk?
 It turns out they are a favorite nutrient for Bifidobacterium
 When there are a lot of B. infantis present, there is no room
for less savory microbes.
 But more importantly, B. infantis nurture the lining of the
intestines, protecting the infant from infection and
So milk is both probiotic (contains some of mom’s
bacteria) and prebiotic (contains food for bacteria).
Gut Bacteria and Termites
• African children who eat a high fiber diet (and the
occasional termite) have bacteria in their guts that break
down fibers, releasing nutrients the children can absorb.
• These bacteria are commonly found in the stomach of
termites, but not in most humans.
• Interestingly enough, these bacteria were found to make
short chain fatty acids that give people energy and protect
them from inflammatory gut diseases such as Crohn’s and
Inflammatory Bowel Disorder.
• AND these African children had fewer diarrhea-causing
bacteria in their gut, which is weird because they routinely
drink water polluted with such bacteria.
So How Do I Get Healthy Bacteria?
 Do things that expose you to a variety of bacteria.
 Garden
 Compost
 Raise worms
 Have a dog
 Disinfect less around your house
 Be outside, in the dirt, getting dirty
 Make raw-milk cheese
 Ferment something and consume it
No, it can’t be beer or wine!
 No, ferment something like yogurt, or sauerkraut or kim-
 Fermented vegetables contain some great bacteria such as
bifiobacteria and Lactobacillus plantarum.
 And then eat these foods without pasteurizing them first.
 Eat fewer processed foods (very sterile and full of additives
that we have no idea how they affect our microbiomes).
 Al dente pasta is better than soft pasta
 Steel-cut oats are better than rolled
 Raw or lightly cooked vegetables are better than overcooked
Increase Your Internal Fermentation
 A key to health is fermentation in the large intestine. This
means eating a variety of plants with their variety of fibers,
such as:
 Resistant Starches – these are found in bananas, oats, beans
 Soluble fibers – found in onions and other root vegetables,
 Insoluble fibers – found in whole grains, especially bran, and
 The by-product of fermentation is the short-chain fatty
acids that nourish the gut barrier and help prevent
How Do I Feed the Good Guys?
 Bacteroides (the ones that promote slimness) LOVE
 What contains fructans?
 Asparagus, artichokes, garlic, onions
 Eat antibiotic-free meat.
 Most of our gut bacteria love polysaccharides (complex
carbs including fiber), but each bacteria has its own
preferences, so eat a large variety.
 The food industry likes to add inulin (from chicory root)
as fiber, but only a limited number of bacteria even like
What about eating Probiotics?
 Well, remember that they contain only bacteria that can be
grown in aerobic conditions…. Which don’t include most of
our healthy microbiome.
 However, studies have shown they may be effective in a
variety of ways:
 Reducing allergic responses
 Shortening the length and severity of colds in children
 Relieving diarrhea and irritable bowel symptoms
 And improving the function of the intestinal epithelium
 Keep in mind - this market is unregulated . One study
tested 14 commercial probiotics and found only one
contained the exact species stated on the label.
Restoration Ecology
 With all the widespread antibiotic use in the world,
processed foods, modern birth methods, where can
one find a healthy diverse human microbiome?
 In humans who haven’t been exposed to the Western
world yet. Research is currently going on to collect
samples from tribesmen in the remote Amazon.
We are assuming they have a healthy microbiome, but the
reality is we really don’t know enough to recognize what
a “healthy” microbiome looks like.
What does the future hold?
 Synbiotics
 Suites of targeted, next generation probiotic microbes
administered along with the appropriate prebiotic
nutrients to nourish them, replacing the generic
repoopulation (or fecal transplants) of today.
Scientists in the field agree - Synbiotics will be the next
Big Pharma field.

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