Microbiome 101
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Presentation by Dr. William DePaolo at the North City Tech Meetup, Lake Forest Park, WA Sept. 16, 2019.
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Microbiome 101
- 1. Microbiome 101 An introduction to the human gut microbiome William DePaolo, PhD Associate Professor | Medicine Director | CMiST University of Washington
- 2. Definitions Microbiota Every bug, all of their genes, and everything they produce • Fungus = mycobiome • Virus = virome • The actual “bugs” that reside within and on us • Referred mostly to bacteria Microbiome
- 3. Our microbial self 1014 or 100 trillion Bacteria within our gastrointestinal tract 1:1 Ratio with our own human cells 100-300:1 Number of bacterial genes to our own human genes
- 5. Stomach 102 Lactobacillus Candida Streptococcus Heliobacter pylori Peptostreptococcus Duodenum 102 Streptococcus Lactobacillus Jejunm 102 Streptococcus Lactobacillus Proximal ileum 102 Streptococcus Lactobacillus Distal ileum 108 Clostridium Streptococcus Bacteroides Actinomycinae Corneybacteria Colon 1012 Bacteroides Clostridium Bifidobacterium Enterobacteriacae
- 6. Your intestines have good & bad bacteria Good Bad
- 7. What does all of this bacteria do? Boosts immunity • 90% of our immune system is located within the gut • Produces factors that replace mucus and prevent infections • Maintains an acidic pH Improves mental health Synthesizes neurotranmitters Supports healthy weight Produce chemicals that promote satiety Increases energy levels Absorption of nutrients Promotes cardiovascular health Improves cholesterol levels Regulates hormones Estrogen, B12, folic acid and vitamin D
- 8. Your microbiome is given to you at birth • Our microbiome is imprinted during birth • Route of birth • Bottle vs breast fed • As infant develops, they will receive probiotics (“good bacteria”) from the food that they ingest Lactobacillus
- 9. Diversity of the microbiome is acquired throughout youth
- 10. We shape its composition Stress Over use of antibiotics Over-nutrition Living with pets Hygiene = shifts in the composition, location or the function of your Microbiome
- 11. What is dysbiosis? Composition 16S rRNA sequencing Function (purpose) Metagenomics Meta-transcriptomics Metabolomics Location Must sample different sites “Healthy” microbiome
- 12. The microbiome is stable & resilient Must sample different sites
- 13. Evolution of food practices Paleolithic era • Wild plants • Animals • Nuts & seeds Agricultural (Neolithic) revolution • Grains, legumes, dairy • Domesticated plants • Fermented foods Industrial revolution • Processed foods • Refined grains & fatty domesticated meats • Alcohol & vegetable oils • Fast foods
- 14. A western diet has impacted our health 1985 1995 2005 2015
- 15. A western diet reduces bacterial diversity
- 16. A 3-day cleanse changes the microbiome but, it is transient Knight Lab UCSD and American Gut
- 18. What is a probiotic? Live microorganisms which, when administered in adequate amounts, confer a health benefit on the host -World Health Organization, 2002
- 19. Definitions Probiotic Non-digestible products that promote the growth of “healthy” gut bacteria Live microorganisms administered in adequate amounts, confer a health benefit Prebiotic Synbiotic Products containing both pre- and probiotics
- 20. A brief history of probiotics
- 21. The bible states “ Abraham owed his longevity to the consumption of sour milk.” In 76 BC the Roman historian Plinius recommended the administration of fermented milk products for treating gastroenteritis 1907 Metchnikoff proposed that the acid producing bacteria in fermented milk if consumed regularly, lead to a longer, healthier life early 1930’s, in Japan, Minoru Shirota developed a fermented milk product calledYakult 1965 NewYork, Lilly & Stillwell coined the term probiotic 1857 Lactobacillus discovered at the Pasteur Institute
- 22. Where do probiotics come from? Probiotics are naturally occurring in some foods
- 23. Where do probiotics come from? • Probiotics are actually members of a group of bacteria that reside within our intestines • This group of bacteria is called the microbiota
- 24. Should you be taking a probiotic? The number of diseases that have been linked to bacterial imbalance including depression, arthritis, IBS and cancer.
- 25. Irritable bowel syndrome Antibiotic-associated diarrhea Weak immune system Eczema Ulcerative colitis Anxiety & depression Cholesterol Diseases proven to benefit from probiotics Infectious diarrhea
- 26. How probiotics work: preventing infection
- 27. How probiotics work: strengthening our barrier Enhance barrier function Reduce pHPrevent intestinal barrier dysfunction Immunomodulation Inhibit bacterial adhesion Secrete anti- microbial peptides
- 28. How probiotics work: strengthening our barrier Pre-carcinogens Enzymes in our bodies Carcinogens Lactobacillus
- 29. Are probiotics safe? Don't start taking probiotics without talking to your doctor especially if you have an immune deficiency or are being treated for cancer. FDA does not monitor probiotics so a lot of variation and mis- marketing Erzebet S Art Collections
- 30. What to look for… Genus, species and strain of the microorganisms Lactobacillus reuteri ATCC55730 Genus StrainSpecies
- 31. What to look for… • Number of organisms contained in a single dose Remember more is not always better • How often you should take it and when be taken shortly after eating) * * Pick one that has at least 7 strains and 5 billion CFUs (colony forming units) * *
- 32. What to look for… How should this specific probiotic be stored • refrigeration • dark cool space *always keep away from moisture and heat
- 33. What to look for… “Viable through end of shelf life” vs “Viable at time of manufacture” Encapsulated pills or other delayed-rupture technology ensure the bacteria survive the acidity of stomach & reach your colon.
- 34. What to look for… Certification by an independent third party The Food and Drug Administration (FDA) does not regulate most probiotics & therefore the amount of bacteria stated on the label might not be what’s actually in there.
- 35. Not all probiotics are created equal • Yeast probiotic • Effective at treating Crohn’s Disease • Anti-toxin • Anti-microbial Saccharomyces boulardii • Supports healthy skin • Fights UTIs • Reduces stress hormones and GABA neurotransmitter which reduces anxiety Lactobacillus rhmanosus • Supports liver function • Reduces inflammation • Removes toxins Bifidobacterium longum • Relieves gas, bloating • Improves lactose intolerance • Lowers cholesterol • Reduces E. coli • Vitamin K Lactobacillus acidophilus • Supports production of vitamins • Boosts immunity • Prevents pathogens Bifidobacterium Bifidum
- 36. The human microbiome market is expected to reach $658 million by 2023 from $294 million in 2019 growing at a CAGR of 22.3% Probiotics and gut health is a major market Probiotics can be helpful in some cases but there are relatively few studies to tell us if and when they are effective in adults.
- 37. Problems with many probiotics • NOT potent 50% of all products do not contain the type or numbers of bacteria they claim • NOT effective Many probiotic supplements do not ensure that they get through the stomach acids and survive • NOT natural Many products are processed and have too much added sugar
- 38. Pasteurization kills probiotics • Yogurt: best when “made with live, active cultures” • Avoid: “heat treated after culturing”
- 42. Fecal Microbiota Transplants • Currently a number of clinical trials evaluating FMT in Inflammatory Bowel Disease Results have been mixed so far • Have been used to treat C. difficile infections >90% efficacy compared to antibiotics (~50%)
- 43. Still many unknowns with FMT
- 44. Future of probiotic supplements • Genetically modified Lactobacillus • Lacto-ceuticals Using the fermentation process with different types of food, such as whey
- 45. CMiST will serve as a platform for connectivity, communication and collaboration for researchers, clinicians and our community at the UW, affiliated campuses and neighboring institutions and organizations.
- 46. Batch ID Services Batch ID is our comprehensive suite of microbiome research services
- 48. Add-on services: • Peptide Mass Profiling • Whole Genome Sequencing • Immuno-Phenotyping • Gnotobiotic Colonization • Microbiological Assays • 16s Profiling • Metabolic Analysis
- 49. If you are interested in supporting our research, and / or our art and public outreach initiatives, please visit us online: www.cmistuw.org/give Get involved Your investment in CMiST will be transformative.
Editor's Notes
- These bacteria reside on all surfaces and crevices of your body from the crease of your elbow to in between your toes… but the highest density is, of course, the gut
- Just because these bacteria reside within you and you are healthy wo disease does not mean you have all good bacteria… In fact all of us have many potentially harmful bacteria that call our intestines home. These include those that contaminate food, post surgical infections or one that you may have heard about C. diff
- Within the body, we actually have a “second brain” called the enteric nervous system (ENS). The ENS controls and regulates our intestinal tract and senses environmental threats. It reports information to the brain via the vagus nerve, the longest cranial nerve in the body. The vagus nerve links a number of organs with the brain, but about 90 percent of the signals passing alon There is other research on the topic of weight and gut flora as well, two of the more interesting and recent pieces being related to how gut bacteria influence which foods we crave. Here are a few more examples: Butyrate—one of the fatty acids produced by good gut bacteria—has been suggested to promote feelings of satiety (a feeling of fullness and satisfaction). (Nutr Rev 07;65(2):51–62) (Aliment Pharmacol Ther 08:27(2):104–119) This, obviously, can help prevent overeating. A Japanese company gave 87 overweight individuals 100 grams of fermented milk twice a day. The milk consumed by half the group contained the bacteria Lactobacillus gasseri. After 12 weeks, those individuals lost an average of 2.2 pounds—and there was no weight loss in the other group. (Eur J Clin Nutr 2010 March 10. [E-pub ahead of print PMID:20216555] Specifically, the participants lost 4.6 percent of their visceral fat (fat around the stomach) and 3.3 percent of their subcutaneous fat (fat just under the skin). Their hip circumference was reduced by 1.7 cm (almost ¾ of an inch) and their waist went down by 1.5 cm (just over ½ inch). Researchers feel that Lactobacillus gasseri somehow decreases the amount of fat absorbed from the intestines. Researchers evaluated the use of antibiotics in 11,532 children born in Britain’s Avon region in 1991 and 1992. Almost 30 percent of the infants were given antibiotics sometime during the first six months of their life. By age 38 months, the children in the antibiotic group had a 22 percent greater likelihood of being overweight. (Int J Obes (Lond) 21 October 2012 [Epub ahead of print]) Antibiotics. Doing it at such a critical period of development, such as early childhood, has long-lasting effects. g it are traveling from the gut to the brain.
- Within the body, we actually have a “second brain” called the enteric nervous system (ENS). The ENS controls and regulates our intestinal tract and senses environmental threats. It reports information to the brain via the vagus nerve, the longest cranial nerve in the body. The vagus nerve links a number of organs with the brain, but about 90 percent of the signals passing along There is other research on the topic of weight and gut flora as well, two of the more interesting and recent pieces being related to how gut bacteria influence which foods we crave. Here are a few more examples: Butyrate—one of the fatty acids produced by good gut bacteria—has been suggested to promote feelings of satiety (a feeling of fullness and satisfaction). (Nutr Rev 07;65(2):51–62) (Aliment Pharmacol Ther 08:27(2):104–119) This, obviously, can help prevent overeating. A Japanese company gave 87 overweight individuals 100 grams of fermented milk twice a day. The milk consumed by half the group contained the bacteria Lactobacillus gasseri. After 12 weeks, those individuals lost an average of 2.2 pounds—and there was no weight loss in the other group. (Eur J Clin Nutr 2010 March 10. [E-pub ahead of print PMID:20216555] Specifically, the participants lost 4.6 percent of their visceral fat (fat around the stomach) and 3.3 percent of their subcutaneous fat (fat just under the skin). Their hip circumference was reduced by 1.7 cm (almost ¾ of an inch) and their waist went down by 1.5 cm (just over ½ inch). Researchers feel that Lactobacillus gasseri somehow decreases the amount of fat absorbed from the intestines. Researchers evaluated the use of antibiotics in 11,532 children born in Britain’s Avon region in 1991 and 1992. Almost 30 percent of the infants were given antibiotics sometime during the first six months of their life. By age 38 months, the children in the antibiotic group had a 22 percent greater likelihood of being overweight. (Int J Obes (Lond) 21 October 2012 [Epub ahead of print]) Antibiotics. Doing it at such a critical period of development, such as early childhood, has long-lasting effects. g it are traveling from the gut to the brain.
- Within the body, we actually have a “second brain” called the enteric nervous system (ENS). The ENS controls and regulates our intestinal tract and senses environmental threats. It reports information to the brain via the vagus nerve, the longest cranial nerve in the body. The vagus nerve links a number of organs with the brain, but about 90 percent of the signals passing along There is other research on the topic of weight and gut flora as well, two of the more interesting and recent pieces being related to how gut bacteria influence which foods we crave. Here are a few more examples: Butyrate—one of the fatty acids produced by good gut bacteria—has been suggested to promote feelings of satiety (a feeling of fullness and satisfaction). (Nutr Rev 07;65(2):51–62) (Aliment Pharmacol Ther 08:27(2):104–119) This, obviously, can help prevent overeating. A Japanese company gave 87 overweight individuals 100 grams of fermented milk twice a day. The milk consumed by half the group contained the bacteria Lactobacillus gasseri. After 12 weeks, those individuals lost an average of 2.2 pounds—and there was no weight loss in the other group. (Eur J Clin Nutr 2010 March 10. [E-pub ahead of print PMID:20216555] Specifically, the participants lost 4.6 percent of their visceral fat (fat around the stomach) and 3.3 percent of their subcutaneous fat (fat just under the skin). Their hip circumference was reduced by 1.7 cm (almost ¾ of an inch) and their waist went down by 1.5 cm (just over ½ inch). Researchers feel that Lactobacillus gasseri somehow decreases the amount of fat absorbed from the intestines. Researchers evaluated the use of antibiotics in 11,532 children born in Britain’s Avon region in 1991 and 1992. Almost 30 percent of the infants were given antibiotics sometime during the first six months of their life. By age 38 months, the children in the antibiotic group had a 22 percent greater likelihood of being overweight. (Int J Obes (Lond) 21 October 2012 [Epub ahead of print]) Antibiotics. Doing it at such a critical period of development, such as early childhood, has long-lasting effects.
- Lets start off by simply defining the term …probiotic. Translates to FOR LIFE. But now we know it defined as …. Pretty vague, huh? Well this is because Food and Drug administration does not regulate probiotics.
- Here are a few other words you may hear used interchangeably with probiotics
- The first mention of probiotics was actually the bible At the start of the 20th century, Russian noble prize winner and father of modern immunology, Elie Metchnikoff, a scientist at the Pasteur institute, was the first conceptualize “probiotics”. In 1907 Metchnokoff proposed that the acid producing bacteria in fermented milk products could prevent “fouling” in the large intestine and if consumed regularly, lead to a longer, healthier life In early 1930’s, in Japan, Minoru shirota developed a fermented milk product called Yakult (probiotic yogurt like product made by fermenting a mixture of skimmed milk with a special strain of Lactobacillus casei shirota). It was first used by Lilly and Stillwell in 1965 to describe “substances secreted by one microorganism which stimulates the growth of another
- Natto - is prepared with soybeans and is fermented so it forms the beneficial bacteria Bacillus. It’s an excellent source of calcium, iron, dietary fiber, and vitamin K2. You may not have heard a lot about it, but K2 is essential for heart health as it keeps calcium out of your arteries and gets it to your bones where it’s needed. Natto also contains nattokinase, a powerful anti-clotting agent that protects your heart and brain and lowers your blood pressure. Kefir - s a bit like yogurt, except that it’s more of a drinkable consistency. Researchers report kefir may reduce irritation in the intestines, preventing toxins and other pathogens from getting into the blood.[2] If you’re choosing to drink dairy kefir, make sure it’s organic and isn’t loaded with refined sugar. Kombucha Made from tea, clean water, sugar, yeast, and bacteria, kombucha has become popular recently for its probiotic qualities. Its fizzy bite is also popular among those used to drinking soda. Research finds this fermented tea fights off E. coli and Staph bacteria in the digestive tract, possibly protecting against illness and aiding digestion Sauerkraut & kimchi & pickles. Traditional sauerkraut preparation uses water, salt, and cabbage, and very little heat is applied to the final product in order to prevent killing off beneficial microbes. The sour taste comes from lacto-fermentation, or the breakdown of lactose by the probiotic bacteria native to the cabbage. A serving gives you a powerful dose of healthy probiotics that aid digestion, and research has found raw sauerkraut prevents cancer cells from forming.[4] Tempeh: This Indonesian ‘cake’ has a nutty flavor and chewy texture, and because of this, it is often used as a replacement for meat in many vegan recipes. Traditionally made from soybeans and a yeast starter, it undergoes controlled fermentation that makes it a great source of probiotic bacteria. Tempeh is also a great source of calcium, iron, and magnesium. Lassi Yogurt and fermented dairy play an important role in Indian cuisine. Lassi is made by combining yogurt and milk (or water) and sometimes fruit and spices to create a great probiotic-rich drink. It digests quickly, helps restore friendly gut bacteria, and soothes irritation in the colon
- Antagonism – compete for food Lactobacillus produces lactic acid which affects pH Produce antimicorbial peptides
- Consumer Lab, an independent agency that tests vitamins and supplements, found that 30 percent of probiotic products didn’t contain the amount of viable bacteria claimed on the label. The full report is available for $18 and includes cost value as well, which can be helpful, considering probiotics are one of the most expensive supplements out there, averaging nearly $1 per day and as much as $6 per day.
- Many products list only the genus and species, but different strains provide different benefits (more on that later).
- Many products list only the genus and species, but different strains provide different benefits (more on that later).
- Lactose intolerant Strains that help produce lactase Irritable bowel syndrome – more research needed, bacteria listed have been shown to help with bloat and gas
- Added sugar bad b/c bad bacteria can use it to grow as well
- The heat treated or pasteurization process kills the lactase, which would have made the diary more digestible (2) Heat treating also kills the live active cult Kefir - Kefir is still the leader in nutrition when compared to yogurt. While traditional recipes for yogurt contained live active cultures, the bacteria were transient beneficial bacteria
- Here are a few other words you may hear used interchangeably with probiotics
- Natto - is prepared with soybeans and is fermented so it forms the beneficial bacteria Bacillus. It’s an excellent source of calcium, iron, dietary fiber, and vitamin K2. You may not have heard a lot about it, but K2 is essential for heart health as it keeps calcium out of your arteries and gets it to your bones where it’s needed. Natto also contains nattokinase, a powerful anti-clotting agent that protects your heart and brain and lowers your blood pressure. Kefir - s a bit like yogurt, except that it’s more of a drinkable consistency. Researchers report kefir may reduce irritation in the intestines, preventing toxins and other pathogens from getting into the blood.[2] If you’re choosing to drink dairy kefir, make sure it’s organic and isn’t loaded with refined sugar. Kombucha Made from tea, clean water, sugar, yeast, and bacteria, kombucha has become popular recently for its probiotic qualities. Its fizzy bite is also popular among those used to drinking soda. Research finds this fermented tea fights off E. coli and Staph bacteria in the digestive tract, possibly protecting against illness and aiding digestion Sauerkkraut & kimchi & picklesTraditional sauerkraut preparation uses water, salt, and cabbage, and very little heat is applied to the final product in order to prevent killing off beneficial microbes. The sour taste comes from lacto-fermentation, or the breakdown of lactose by the probiotic bacteria native to the cabbage. A serving gives you a powerful dose of healthy probiotics that aid digestion, and research has found raw sauerkrau prevents cancer cells from forming.[4] Tempeh: This Indonesian ‘cake’ has a nutty flavor and chewy texture, and because of this, it is often used as a replacement for meat in many vegan recipes. Traditionally made from soybeans and a yeast starter, it undergoes controlled fermentation that makes it a great source of probiotic bacteria. Tempeh is also a great source of calcium, iron, and magnesium. Lassi Yogurt and fermented dairy play an important role in Indian cuisine. Lassi is made by combining yogurt and milk (or water) and sometimes fruit and spices to create a great probiotic-rich drink. It digests quickly, helps restore friendly gut bacteria, and soothes irritation in the colon Fermentation is an inconsistent process, and is more of an art than a science. Commercial food processors developed techniques to help standardize more consistent yields. These include pasteurization, which effectively destroys the naturally occurring probiotics. Simply put, some pickles are simply packed in salt, vinegar, and are pasteurized. Beware of some "probiotic" yogurts, too. Most of them that you find in the grocery are NOT recommended for many reasons: they are pasteurized (and are linked to the problems of pasteurized milk products), and typically contain added sugars, high-fructose corn syrup, dyes, and/or artificial sweeteners, which can be detrimental to your health.
- This base service enables further studies (using CMiST add-on services)
- Ultimately our goal is simple.