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 ( ) American molecular biologist 1958 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. Each individual has a unique microbial “fingerprint”
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 Microbes PLoS 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 trillion
Total microbiota trillion matching or outnumbering human cells by 3:1 Sender, Fuchs, Milo: defection = 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!
We temporarily become more human after each elimination!

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. Microbes occupy ecological niches
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. 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
PLoS Biol, 2013, Vol 11(8): e

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

18. Cesarian Sections and the Microbiome Blaser; 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): e

20. Human Gut Microbiome: Our Second Genome Marchesi, Environ Microbiol (2011)
After the age of 2.5, the distal gut microbiota is stable and colonized predominantly by two phyla: Firmicutes and 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 the ecosystem 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, MD J Clin Invest. 2014;124(10):

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 microbiome Turnbaugh, 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
What Does a Three Day Dietary Cleanse do to Your Gut Microbiome? Luke Thompson, PhD:
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
What Does a Three Day Dietary Cleanse do to Your Gut Microbiome? Luke Thompson, PhD:
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
Changes in microbial taxa with 3-day Dr. Oz fruit & vegetable cleanse + VSL#3 (

33. Burkina Faso diet & lifestyle

34. Gut Microbiota: European vs
Gut Microbiota: European vs. rural Burkino Fasan Children PNAS, 2010, Vol 107(33):
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 (

36. Diversity Association and Relative Abundance

37. http://news. sciencemag

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 tribe news
Resistance to antibiotics found in isolated Amazonian tribe news.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. Environmental pollutants and xenobiotics (glyphosate)
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 bacteria Blaser; 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
Martin Blaser, NYU Langon medicat center

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:

49. Blaser; Nature, 2011, Vol 476:

50. 40% of all adults and 70% of all children in the U. S
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 trust had this graphic
The Pew Charitable Trusts

51. Dysbiosis
Microbial imbalance, most commonly in the gastrointestinal tract
Associated with chronic intestinal symptoms: gas, bloating, diarrhea, constipation
May predispose to a chronic diseases
Contributes to “leaky gut” syndrome (hyperpermeable tight junctions)

52. Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness
Prolonged stays in ICU leads to “complete ecological collapse” with the emergence of ultra- low (1–4 taxa) multi-drug resistant pathogenic bacteria communities in 30% of patients;
~75% of cases C albicans & C glabrata overgrowth
These limited communities keep each other in check until triggered by acute stressful events (opioids) which can lead to life-threatening sepsis
University of Chicago mBio 2014 Vol 5(5): e

54. Dysbiotic Events in Gut Microbiota: Impact on Human Health Nutrients 2014, 6, 5786-5805
Dybiosis (gut microbial imbalance) has been linked with important human diseases, including autoimmune and/or autoinflammatory disorders, such as IBD, metabolic disorders, such as, obesity, type 2 diabetes, allergies, and neurological disorders

55. Supporting the Microbiome (from the Human Microbiome Project)
Get adequate sleep
Exercise frequently
Eat a wide variety of fresh plant foods
Minimize:
Refined carbohydrates
NSAIDs
Alcohol
Antibiotics

56. Supporting The Microbiome
Consume prebiotic fibers:
pectin, inulin, fructo-oligosaccharides, hydrolyzed guar, larch arabinogalactan, gum arabic, beta glucans, boabab, chicory root, asparagus, dandelion greens, garlic, onions, leeks, wheat bran, bananas
Eat fermented foods: fresh sauerkraut, kimchi
Take probiotics
Yogurt (homemade)
Lactobacilli (multiple species)
Bifidobacteria (multiple species)
Saccharomyces boulardii

57. Conclusions
Research into the microbiome using DNA sequencing has redefined what it means to be human
Humans are superorganisms that represent a blend of genetic traits from human & microbial cells
Our microbiomes have a major impact on our digestion, metabolism, neurology & immunology

58. Conclusions
The vast majority of our interactions with bacteria are either neutral or mutually beneficial: maintaining tolerance is essential to health
Alteration of the microbiome by our modern lifestyle (diet, stress, excessive hygiene and antibiotics) may be responsible for many chronic diseases
Dietary changes, prebiotics and probiotics may help to maintain a healthy microbiome