The Human Microbiome

2. The Human Microbiome With great thanks to Dr. Jess Maher for making a lot of these community slides

3. Objectives 11/27/12 • Describe the factors and processes that influence community assembly and composition • Describe how community composition impacts function • Compare species diversity in different communities • Apply ecological concepts to a new system

4. A microbe’s view of us Bacterial cells outnumber your body cells 10:1 and comprise up to 4-6 lbs of your body mass Skin

5. Sites that harbor a normal flora: Skin and mucous membranes Upper respiratory tract Gastrointestinal tract Outer opening of urethra External genitalia Vagina External ear canal External eye (lids, conjunctiva)

6. Benefits of the normal flora 1. Synthesize and excrete vitamins Vitamin K and Vitamin B12 2. Prevent colonization by pathogens competing for attachment sites or for essential nutrients  3. May antagonize other bacteria the production of substances which inhibit or kill non-indigenous species(nonspecific fatty acids, peroxides, bacteriocins). 4. Stimulate the development of certain tissues i.e., intestines, certain lymphatic tissues, capillary density 5. Stimulate the production of cross-reactive antibodies. Low levels of antibodies produced against components of the normal flora are known to cross react with certain related pathogens, and thereby prevent infection or invasion.

7. A healthy microbial community is essential Mice raised in a germ-free environment display: Decreased nutrient absorption Less developed intestines Vitamin deficiency Underdeveloped immune system Heighted sensitivity to pathogens (Hooper et al. 2001 Science)

8. (Fierer et al 2012)

9. Dethlefsen, McFall-Ngai and Relman 2007

10. http://www.genome.gov

11. A belly button microbial 'portrait' http://www.wildlifeofyourbody.org/

12. What factors determine the species composition of normal flora in the human body?

13. What abiotic conditions might differ between areas of the human body that are normally colonized by microbes?

14. What biotic factors might differ between areas of the human body that are normally colonized by microbes?

15. Skin regions are like geographic regions of Earth

16. Individuals have different microbial communities. Why?

17. abiotic biotic Although multiple scenarios are likely to apply to any real-world setting, one may dominate. For example, differences between body habitats may be best explained by environmental selection (abiotic), differences between siblings for the same habitat may be best explained by historical contingency (biotic), differences between monozygotic twins prior to weaning highlight the role of stochasticity (random), and differences between neonates born by cesarean section versus vaginal delivery are likely to be explained by dispersal limitation (dispersal). dispersal

18. Let’s focus on the microbial community in the gut: • How is the community assembled? • How does community composition affect function?

19. Families have more similar microbiomes

20. Families have more similar microbiomes Think-Pair-Share: Why?(remember that the uterus is a sterile environment, so babies are not born with their bacteria)

21. Community Assembly: How do we acquire our resident flora? Dispersal 1. From delivery: The gut flora of vaginally-delivered babies differs from babies delivered by C-section The vaginal microbial community of pregnant women contains bacteria involved in digesting milk (Lactobacillus) 2. From feeding: The nature of the flora colonizing the intestines changes depending on whether the baby is bottle- or breast-fed (The skin, gastrointestinal tract, respiratory, and urogenital system all continue to be colonized as contact with other humans continues)

22. Disturbance and succession: As the gut environment changes, so does the microbial communityWhy? Switch to solid foods

23. How does community composition impact function?Hypothesis: Gut microbial communities can impact risk for obesity

24. Different gut microbial community structure in obese mice % Sequences Firmicutes Bacteroidetes Ley et al., PNAS 102: 11070-5 (2006)

25. Effects of dieting • Ley et al. Nature 444: 1022 (2006)

26. Microbiota fecal transplantation ob wt Conventionally raised donors wt wt Germ-free Wild type recipients Donor Turnbaugh et al., Nature 444: 1027-1031

27. Mice that receive a fecal transplant from obese donors not only become obese, but do so while eating less food… Conventionalized mice (CONV-D) are formerly germ-free (GF) recipients of a gut microbiota transplant from conventionally-raised (CONV-R) donors

28. T-P-S: What might be functionally different about the gut communities in the lean donor and the obese donor? Donor

29. Energy extraction efficiency could be a function of the gut community composition Metagenomic analysis of obese/lean mouse gut microbiotas Obese gut microbiome contains more genes predicted to harvest energy from polysaccharides Hypothesis: Differences in gut microbial ecology among humans affects the efficiency of their energy harvest/storage when consuming a given diet Turnbaugh et al., Nature 444: 1027-1031

30. Little-known fecal transplant cures woman's bacterial infection “After surviving a near-fatal car accident, Kaitlin Hunter found herself battling a devastating bacterial infection in her colon that also threatened her life. The persistent infection was beaten through a little-known technique involving the transplant of fecal matter from Hunter's mother... Following the July procedure, "I've been so happy," said Hunter, 20, of Marietta, Georgia. "I'm cured." Why did this work? What happened in Katie’s colon?

31. Bacteriotherapy Clostridium difficile-associated diarrhea (CDAD) - usually results from prior antibiotic treatment and persistant disruption of gut microbiota - can be severe, even causing death J Clin Gastroenterology (2010) 44:354-360

32. Patient: • 61 year old woman • Chronic diarrhea • (8 mos, every 15 min) • Confined to wheelchair • Lost 60 lbs • Donor: • Husband Patient Day 0 Donor

33. T-P-S: Describe the differences between the gut communities from the patient and the donor. Patient Day 0 Donor

34. Species Diversity Richness = number of species present Evenness = relative abundance of each species Diversity measures both richness and evenness 26 Species 21 Species

35. Fecal transplant = assisted colonization • Patient: • Diarrhea subsided within 2 days • Gut flora similar to donor within 14 days Patient Day 0 Donor Patient Day 14

36. T-P-S: What might have been preventing the women from having a “healthy” gut community? (Think about the factors that can influence species composition in a community)

37. How can you use the Human Microbiome in your teaching about Ecology?

38. Evolution in the Human Microbiome: Gonorrhea! • Clap, Drip • Sexually transmitted infection caused by the bacterium Neisseria gonorrhoeae • Can be detected by microscopy, culturing, or DNA testing

39. Who gets gonorrhea? • Spread by sexual contact • Those at highest risk are young adults (women 15 – 19 and men 20 – 24) • Can be passed from mother to newborn

40. United States Gonorrhea Infection Statistics • Second most-frequently reported STD • ~700,000 Americans are infected annually • Treatment of gonorrhea costs $1 billion/year

41. What are the symptoms? • Most men who get gonorrhea experience extremely painful urination and pus release from the urethra • Many women do not experience noticeable symptoms

42. Why is proper detection and treatment of gonorrhea important? This is serious! • Co-infection can cause increased transmission of other STDs including HIV • If untreated, the bacteria can spread to other sites in the body • Pelvic Inflammatory Disease • Ectopic pregnancy • Infertility • Meningitis • Arthritis • Blindness • Death

43. What are some of the difficulties in treating the disease? • Some people do not know that they are infected • Can be a difficult topic for some to talk about/embarrassment • Many isolates of N. gonorrhoeae are resistant to antibiotics commonly used to treat gonorrhea • The CDC announced in August 2012 we're down to our last effective antibiotic • injected ceftriaxone

44. Journalist Dan Avery argues "the AIDS epidemic is what might help us prevent a catastrophe" “Before AIDS, if you got a STD, your doctor gave you the cure and told you to tell your partners (wink, wink). But as AIDS cut a swath through society, learning how to tracking disease vectors became a life-or-death issue. ... Before AIDS, medical professionals were not always diligent about sterility—and nobody bothered putting on gloves unless you were getting a prostate exam. Now, the importance placed on antibacterial soap, latex protection and other tools will help control the spread of gonorrhea, which can transfer from a patient’s genitals to a nurse’s hands to her eye. That’s where some experts say we’re headed: working to control the spread of gonorrhea instead of administering a simple cure.“

45. How have the gonorrhea populations of the world developed resistance to most of our antibiotics?

46. Antibiotics disrupt essential cell processes • Antibiotics help cure infections by decreasing the bacterial population to a level that the human immune system can handle • Gonorrhea is treated with antibiotics Antibiotic treatment

47. Cell processes of Gonorrhea Replication DNA Transcription RNA Translation • Enzymes • Cell structure • Signaling Protein

48. What is the target of one specific antibiotic, Ciprofloxacin? • Ciprofloxacin binds to the DNA/enzyme complex that forms during DNA replication • This forms a physical barrier that prevents movement of the replication fork and replicating enzymes down the DNA strand • The result: no DNA replication

49. Cell processes of Gonorrhea Replication DNA Transcription RNA Translation • Enzymes • Cell structure • Signaling Protein

50. Mechanisms of Ciprofloxacin Resistance in N. gonorrhoeae • Deactivation of drug by a bacterial enzyme digesting it • Less drug enters the bacterium • Changes to pore proteins in bacterial cell walls • Concentration of drug within a bacterium is lowered • Protein pumps that pump out drugs • Molecular target of drug is changed