Wait, I need to feed them?

1. Wait, I need to feed them? How to help your microfauna positively affect your health

2. There are HOW MANY in me? • For every one human cell there are 10 single-celled microbes. • Average number of cells in a human is 10 trillion, so number of microbes? • Collectively referred to as “microbiotia” • Fungi • Protozoa • Bacteria

3. 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 oxygen? • We sequence their genes. But this is a huge undertaking! While humans have 30,000 genes, our bacteria have millions.

4. 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.)

5. 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 gain.

6. Wait, there’s more! • Stress decreases bacteriodetes, thereby increasing weight gain. • Firmicutes love amino acids and multiply with diets high in protein. • 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 disease. Even with all of this information and more, we still don’t know which levels of each of these indicates a healthy microbiome.

7. 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. • TMAO levels in the blood can be used to predict heart attacks, strokes and do so independent of other risk factors.

8. 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.

9. 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.

10. 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 children? • 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.

11. 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 edge.

12. 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.

13. The Big Question for People Who Aren’t Healthy “Will switching out my gut bacteria fix these problems?”

14. YES! (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.

15. 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.

16. 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 research. • 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.

17. 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.

18. 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.

19. 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 infantis. • 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 inflammation. So milk is both probiotic (contains some of mom’s bacteria) and prebiotic (contains food for bacteria).

20. 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.

21. 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

22. No, it can’t be beer or wine! • No, ferment something like yogurt, or sauerkraut or kim-chi. • 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

23. 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, nuts • Insoluble fibers – found in whole grains, especially bran, and avocados. • The by-product of fermentation is the short-chain fatty acids that nourish the gut barrier and help prevent inflammation.

24. How Do I Feed the Good Guys? • Bacteroides (the ones that promote slimness) LOVE fructans! • 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 inulin.

25. 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.

26. 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.

27. 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.