The Human Microbiome : Its Impact on Our Lives & Health

1. The Human Microbiome:Its Impact on Our Lives & Health Robert Rountree, MD Strauss Lecture Series October 19, 2016

2. Traditional Clinical Microbiology • Microbes as agents of disease: pathogenic “terrorists” • Detected by microscopy and culture • Characterized by growth on specific media, sensitivity to antibiotics

3. “Computational” Microbiology • 99% of all bacteria are unculturable, hence… • Taxonomy is based on DNA sequencing • 16S rRNA gene: ~1500 base pairs (pioneered by Woese, Fox et al--1980s) • Metagenomics (pioneered by Venter, et al) • Whole genome sequencing: ~4 million bp • Classified as “operational taxonomic units” (OTUs) • Characterized by genetic expression

4. Human Microbiome: The totality of microbes, their genomes and environmental interactions in & on the human organism Joshua Lederberg, PhD (1925-2008) American molecular biologist1958 Nobel laureate

5. The Normal Microbiota Humans are like mobile warm-blooded coral reefs, home to vast numbers of microbial ecosystems that are rich in biodiversity. The vast majority of microbes are harmless or beneficial.

6. The Normal Microbiota Composition of the microbiota varies with each individual • Most species fairly stable • Some species transient Each individual has a unique microbial “fingerprint”

7. Humans and MicrobesPLoS Computational Biology, 2010, Vol 6(2): e1000667 • Along with all other animals and plants, the human condition is profoundly affected by microbes, from the scourges of human, farm animal, and crop pandemics, to the benefits in agriculture, food industry, and medicine • Given our intimate relationship with microbes, sequencing the genomes of our own microbes is essential for understanding the human condition

8. Types of Human Microbiota • Viruses (acellular, “nonliving”) • Prokaryotes (without a nucleus): • Archaea (strict anaerobes) • Bacteria (aerobes and anaerobes) • Eukaryotes (possess nucleus + organelles) • Microfungi (mycobiome) • Protozoa • Helminths (parasitic worms)

9. Bacteria colonizing the gut mucosa

10. The Microbiome: Comparative Mass

11. Humans vs. Bacteria • Total # human cells (mainly RBCs) approximate average 10-37 trillion • Total microbiota 10-100 trillion matching or outnumbering human cells by 3:1 Sender, Fuchs, Milo: http://dx.doi.org/10.1101/036103defection = loss of 1/3 of microbiome • Human genes ~20,000 • Common microbial genes >3.3 million • outnumbering human genes >150:1 • One of the most complex microbial ecosystems on the planet!

12. Humans as Superorganisms • The mammalian microbiome has evolved over millions of years to its current state of symbiosis • The human metagenome results from an amalgamation of microbial and human genes • Redefining what it means to be human!

13. Nat Rev Genet. 2014, Vol 15(9): 577–584. Microbes occupy ecological niches

14. 6-10 billion bacteria archaea protozoa fungi viruses

15. Shaping the oral microbiota through intimate kissing • Kissing for 10 seconds transfers an average of 80 million bacteria • Couples who reported they kissed more often ended up having more similar microbiota than less-frequent kissers • Similarity most pronounced for tongue surface Microbiome, 2014, Vol 2:41

16. PLoSBiol, 2013, Vol 11(8): e1001631 Acquisition of the Human Microbiome • Initial inoculum from mother occurs during pregnancy • Vaginal delivery – • microbiome develops species similar to mother’s vagina • Cesarean section – • microbiome develops predominant species similar to skin flora of mother and hospital attendants • Breast feeding provides bacteria from mother’s GI tract

17. The microbes we acquire at birth affect our health the rest of our lives

18. Cesarian Sections and the MicrobiomeBlaser; Nature, 2011, Vol 476: 393-394 • Bacteria have lived in and on animals—constituting their microbiome—since multicellular life evolved about 1 billion years ago • Babies acquire their founding bacterial populations from their mothers while passing through the vagina at birth • Each generation — particularly the 30% or so of infants born via Cesarian — could be beginning life with a smaller endowment of ancient microbes than the last

19. Cesarean Section Delivery Increases Child’s Risk of: • Allergic Rhinitis • Asthma • Celiac Disease • Type I Diabetes • Inflammatory Bowel Disease PLoS Biol, 2013, Vol 11(8): e1001631

20. Human Gut Microbiome: Our Second GenomeMarchesi, Environ Microbiol (2011) • After the age of 2.5, the distal gut microbiotais stable and colonized predominantly by two phyla: Firmicutesand Bacteroidetes, which comprise 90% of the species found • Current estimates are that the microbiome encodes approximately 3.3 million non-redundant genes • the DNA of which is frequently transferred via mobile genetic elements

21. What are theecosystem services provided by microbial genes –our “second” genome?

22. Functions of the Gut Metagenome • Digestion/metabolism: energy and nutrient extraction • Production of vitamins & metabolites • Protection against infection • Maintenance of gut barrier • Immune modulation • Influences on mood & behavior

23. “It is reasonable to propose that the composition of the microbiome and its activities are involved in most, if not all, of the biological processes that constitute human health and disease” Martin J Blaser, MDJ Clin Invest. 2014;124(10):4162-4165

24. Major Influences on Individual Microbiomes • Host genotype • Type of birth (vaginal vs C-section) • Excessive hygiene • Diet (macronutrients, fiber, phytochemicals, alcohol) • Stress (social, emotional)

25. Major Influences on Individual Microbiomes • Medications • Antibiotics • Non-steroidal anti-inflammatory drugs • Proton pump inhibitors • Environmental toxins • Chronic disease • Aging • Surgery

26. We are what we eat: • Our diet determines which bacterial species and strains thrive in our intestines • This effects the composition of our second genome and therefore our health

28. Diet rapidly and reproducibly alters the human gut microbiome David, Turnbaugh, et al, Nature 2014 Vol 505: 559–563 • 9 Volunteers placed on two extreme diets x 5 days: (1) meat, egg and cheese, then switched to (2) grains, vegetables and legumes • Within 1-2 days: major alterations in microbiome (measured by 16S rRNA sequencing) • Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation

29. Diet rapidly and reproducibly alters the human gut microbiomeTurnbaugh, et al, Nature 2014 Vol 505: 559–563 • Animal diet: • increased abundance & activity of bile-tolerant organisms (eg Biophila wadsworthia – toxic H2S producer, linked to colitis in animal studies) • decreased Firmicutes species that metabolize plant polysaccharides • Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and viruses

30. What Does a Three Day Dietary Cleanse do to Your Gut Microbiome?Luke Thompson, PhD: www.americangut.org • Dr. Oz 3 day cleanse = smoothies of fruits & vegetables, plus a multivitamin & probiotic • Cleanse resulted in increase in the microbial groups Akkermansia and Enterobacteriaceae

31. What Does a Three Day Dietary Cleanse do to Your Gut Microbiome?Luke Thompson, PhD: www.americangut.org • Akkermansia is thought to help prevent metabolic diseases like diabetes by aiding mucin turnover and production, causing thickening of the gut wall • However, within a week after returning to “normal” or “Western” food, the microbiome returns to original state

32. Changes in microbial taxa with 3-day Dr. Oz fruit & vegetable cleanse + VSL#3 (www.americangut.com)

33. Burkina Faso diet & lifestyle

34. Gut Microbiota: European vs. rural Burkino Fasan ChildrenPNAS, 2010, Vol 107(33): 14691-14696 • Exposure to the large variety of environmental microbes associated with a high-fiber diet could increase the potentially beneficial bacterial genomes, enriching the microbiome • Reduction in microbial richness is possibly one of the undesirable effects of globalization and of eating generic, nutrient-rich, uncontaminated foods

35. Internal Diversity:The Human Microbiome • A lack of microbial species richness and phylogenetic diversity are associated with poor health • Excessively sterile environments, diets low in plant fiber, repeated exposure to antibiotics, and aging all decrease microbial diversity • Hunter-foragers have much greater microbial diversity than Westerners • (http://humanfoodproject.com)

36. Diversity Association and Relative Abundance

37. http://news.sciencemag.org/biology/2015/04/resistance-antibiotics-found-isolated-amazonian-tribehttp://news.sciencemag.org/biology/2015/04/resistance-antibiotics-found-isolated-amazonian-tribe

38. The microbiome of uncontacted Amerindians Gloria Dominguez-Bello, et al, Sci Adv. 2015 Apr 3;1(3) • The uncontacted Yanomami harbor “significantly higher diversity than other populations,” including high amounts of Prevotella, Helicobacter, Oxalobacter, and Spirochaeta that are absent or significantly reduced in industrialized humans

39. The microbiome of uncontacted Amerindians Sci Adv. 2015 Apr 3;1(3) • The Yanomami had high levels of parasites but were healthy and did not suffer from autoimmune disorders, diabetes, high blood pressure, or heart disease

40. Resistance to antibiotics found in isolated Amazonian tribenews.sciencemag.org April 15, 2015 • Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, the Yanomami gut bacteria had nearly 60 unique genes that could turn on and rally to fend off antibiotics, including a half-dozen genes that could protect the bacteria from synthetic antibiotics

41. Regulation of the immune system by biodiversity from the natural environment: An ecosystem service essential to health Rook, G, PNAS 2013 Vol 110(46): 18360–18367 • Numerous studies demonstrate that living close to the natural rural or coastal environment, often denoted “green space or “blue space,” respectively, is beneficial for human health • The requirement for microbial input from the environment to drive immunoregulation is a major component of the beneficial effect of green space, and a neglected ecosystem service that is essential for our well-being

42. Rook, G, PNAS 2013

43. Regulation of the immune system by biodiversity from the natural environment: An ecosystem service essential to health Rook, G, PNAS 2013 Vol 110(46): 18360–18367 • Immigration from a developing country to a high-income urban center leads to a loss of exposure to microbial biodiversity • In such immigrant populations, there are large increases in autoimmunity, inflammatory bowel disease, depression, and allergic disorders

44. Richness of human gut microbiome correlates with metabolic markers Nature 2013, Vol 500: 541-549 • Individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals • The obese individuals among the lower bacterial richness group also gain more weight over time

45. Major Influences on the Gut Microbiome in Developed Countries J Clin Invest. 2014;124(10):4190–4196 • Lifestyle factors: diet, stress, and sleep disorders; sterile environment • Environmental pollutants and xenobiotics (glyphosate) • Wide and indiscriminate use of antibiotics by livestock producers and in medical practice

47. Antibiotic overuse: Stop the killing of beneficial bacteriaBlaser; Nature, 2011, Vol 476: 393-394 • Evidence is accumulating that our welcome residents do not recover completely from antibiotics or are replaced in the long term by resistant organisms • Overuse of antibiotics could be fueling the dramatic increase in conditions such as obesity, type 1 diabetes, inflammatory bowel disease, allergies and asthma, which have more than doubled in many populations

48. “Independent of well-known asthma risk factors, asthma was significantly more likely to develop at age 7 years in children who had received antibiotics in the first year of life.” Chest, 2007, Vol 131: 1753-1759

49. Blaser; Nature, 2011, Vol 476: 393-394

50. 40% of all adults and 70% of all children in the U.S. take one or more courses of antibiotics every year (CDC)80% of antibiotics in U.S. are given to animals for non-therapeutic purposes The Pew Charitable Trusts