Microbes and us


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Slides and Q&A transcript of the Live Online Webinar, "Microbes and us", Feb. 12, 2010

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Microbes and us

  1. 1. Aurametrix: Better Solutions for a Healthier World Irene Gabashvili, PhD Slides and Q&A transcript of the Live Online Webinar, Feb. 12, 2010 http://vokle.com/lineups/4194-microbes-and-us 1
  2. 2. 2
  3. 3. ~10 x ~3% of body mass 10-100μ 0.2-2μ 20μ/10ng 2½ to 5 pounds In the bowel 3
  4. 4. Human vs Bacterial Nations: 102 vs 106-109 E.Coli & Enterococci are among the first bacteria to colonize the neonatal gastrointestinal tract. 4
  5. 5. Human vs Bacterial Nations: 102 vs 106-109 Streptococci are also among the first bacteria to colonize the infants in large numbers 5
  6. 6. Types of Microbes: Bacteria … 6
  7. 7. Types of Microbes: Fungi 7
  8. 8. Types of Microbes: Protista 8
  9. 9. Types of Microbes All environmentally exposed human surfaces are home to bacteria, protists, algae, fungi (including yeast, molds, etc) and viruses. 9
  10. 10. Types of Microbes Wearing headphones for just an hour… Middle ear pathogens: Streptococcus pneumoniae, non-typeable Haemophilus influenzae, Branhamella catarrhalis Eyes: staphylococcus, streptococcus, diphtheroids, and Neisseria. Mouth: Streptococcus mutans causing cavities w/sticky foods , good: Strep sanguinis 10
  11. 11. The Normal Bacterial Flora of Humans Conjunctiva Bacterium Skin Nose Pharynx Mouth Lower GI Urethra Vagina Staphylococcus epidermidis ++ + ++ ++ ++ + ++ ++ Staphylococcus aureus* + +/- + + + ++ +/- + Streptococcus mitis + ++ +/- + + Streptococcus salivarius ++ ++ Streptococcus mutans* + ++ Enterococcus faecalis* +/- + ++ + + Streptococcus pneumoniae* +/- +/- + + +/- Streptococcus pyogenes* +/- +/- + + +/- +/- Neisseria sp. + + ++ + + + Neisseria meningitidis* + ++ + + Enterobacteriaceae*(E. coli) +/- +/- +/- + ++ + + Proteus sp. +/- + + + + + + Pseudomonas aeruginosa* +/- +/- + +/- Haemophilus influenzae* +/- + + + Bacteroides sp.* ++ + +/- Bifidobacterium bifidum ++ Lactobacillus sp. + ++ ++ ++ Clostridium sp.* +/- ++ Clostridium tetani +/- Corynebacteria ++ + ++ + + + + + Mycobacteria + +/- +/- + + Actinomycetes + + Spirochetes + ++ ++ Mycoplasmas + + + +/- + http://www.textbookofbacteriology.net/normalflora.html 11
  12. 12. Human body: Map where bacteria live http://aurametrix.blogspot.com/2009/11/human-body-map-of-where-bacteria-live.html 12
  13. 13. Types of Microbes • Bacterial phylotypes Clostridium cocleatum, Clostridium thermosuccinogenes, Coprobacillus catenaformis, Ruminococcus bromii-like, Ruminococcus torques and R. torques similar in IBS-C and IBS-D patients. C thermosuccinogenes - significantly different quantities depending on constipation or diarrhea-predominant cases. Bacteria similar to R. torques more prevalent in IBS-D patients' intestinal microbiota than in that of control subjects. a R. bromii-like phylotype was associated with IBS-C patients.. PMID: 17631127 13
  14. 14. Types of Microbes • For IBD, novel invasive species of Escherichia coli possibly replacing some Clostridiales were found in inflamed mucosa. The number of E.coli correlated with the severity of Crohn's disease involving the ileum. • Differences in microbiota may depend on genetics, metabolism, environmental exposures during childhood, state of health. Selective increase in novel invasive species of E.coli seems to be involved in the etiopathogenesis to Crohn's disease involving the ileum Other bacterial species specific to Crohn's are B. ovatus and B. vulgatus. Different species are implicated in UC. PMID: 18043660 ; PMID: 1840143; PMID: 11777829 14
  15. 15. The good microbes • Bacteria shown to be protective in inflammatory bowel disease includes Bacteroides fragilis , Lactobacillus casei, Lactobacillus plantarum, Lactobacillus salivarius, Lactobacillus acidophilus, Lactobacillus delbrueckii subspecies bulgaricus, Lactobacillus rhamnosus GG, Bifidobacterium longum, Bifidobacterium breve, Bifidobacterium infantis, Escherichia coli Nissle 1917, Streptococcus salivarius subspecies thermophilus, Bacteriodes thetaiotaomicron, Faecalibacterium prausnitzii, etc. PMID: 19343057 15
  16. 16. Diet Tidbits • The Specific Carbohydrate Diet created by Dr Sidney Haas and popularized by Elaine Gottschall, restricts the use of complex carbohydrates (disaccharides and polysaccharides) and eliminates refined sugar, gluten and starch from the diet; promoted as a way of reducing the symptoms of irritable bowel syndrome, Crohn's disease, Ulcerative Colitis and autism. Forgotten since the death of Dr Haas. /too restrictive/ • The most widely promoted prebiotics inulin and fructooligosaccharides (neither is absorbed in the upper gastrointestinal tract) have been suggested to increase the number of bifidobacteria. /could be increasing bad ones too/ 16
  17. 17. Conditions that may be linked to microbiota • Bad Breath (~20-40% population) • Acne (>6%) • Multiple Chemical Sensitivities (MCS, ~1%) • Depression (~5%, 20% lifetime risk for women) • Asthma (>6%) • Hyperhidrosis (~3 %) • Food intolerance (75%-100%) – IBS (~20%, 30% lifetime risk) – Celiac (~1%) – TMAU (~1%) – CFS (0.5-1%) Sources: CDC, WHO, National Center for Health Statistics , ACG, SATFMCS & other professional societies and publications 17
  18. 18. IBS Example of a condition dramatically decreasing quality of life, with no good diagnostic tests nor effective treatments http://aurametrix.blogspot.com/2009/05/ibs-resources.html Quality of Life Physical Mental Compiled from 8 sources by an IBS patient, Wikipedia, 2007 Mikocka-Walus et al. Clinical Practice and Epidemiology in Mental Health 2008 4:15 doi:10.1186/1745-0179-4-15 18
  19. 19. Aurametrix Nutrimirror >300 nutrients as provided by USDA & other research DBs (e.g. USDA DB choline/TMAU, glucose vs fructose & other specific Fitday carbohydrates to estimate GI (e.g., Diabetes, IBS, energy) TheCarrot +Information on specific allergenic proteins, gluten (e.g., Celiac, IBS) +Info on, preservatives, sulfites, MSG (e.g., headache, IBS) +Info on potential contamination (e.g. Salmonella, /food poisoning or undeclared milk/allergies) 19
  20. 20. La Yogurt Light Probiotic Blended Nonfat Yogurt Vanilla & Strawberry (TheCarrot) USDA: KRAFT BREYERS Smooth & Creamy Lowfat Strawberry Yogurt (1% Milkfat) Aurametrix In addition to micro and macro-nutrients, provides information on microbes incl. probiotic strains mapped to databases of genes, proteins and toxins. E.g.: Wallaby, lists 4 live cultures: L.acidophilus, L. bulgaricus, S. thermophilus and bifidobacteria We link it to strains - NCF-M and clinical information Nutrimirror: Black Cherry Yogurt, lowfat, organic, creamy 20 Australian style (Wallaby)
  21. 21. Thank You 21
  22. 22. Dr. Irene Gabashvili, founder of Aurametrix, answering questions from the audience. Maria de la Torre, Director of MeBO Research, and colleagues co-hosting and taking questions behind the scenes (Vokle live, chat, real-time e-mail) 22
  23. 23. Questions Q: Why do people have Bacterial Overgrowth? A: In addition to the presence of bacteria in atypical parts of the body (e.g., in small intestine that could be populated by colon bacteria if there are problems with immune system, nerves controlling the intestinal muscles, GI obstructions or intestinal lining damaged by toxins and stress), “overgrowth “ is often used to describe when rarer species are present in larger numbers than more prevalent ones. Why would “bad bacteria” grow faster than more beneficial types? Similar to ecology of endangered and overproducing animals, because of food, climate, failing competitors. 23
  24. 24. Questions Q: Why do people have Bacterial Overgrowth? (continued) A: Bacteria is fed by metabolites generated by our enzymes from our food & other chemicals. Accordingly if we have a certain genetic makeup, eat particular foods, are subjecting ourselves to specific stress hormones, our metabolic profile cultivates bacteria that likes it. There were studies showing how by changing diet you are squeezing out some bacteria and replacing it with other types, or reducing overall counts. Later you could reintroduce some of the problem foods back in your diet. Crowther, J. S., Drasar, B. S., Goddard, P., Hill, M. J., and Johnson, K. The effect of a chemically defined diet on the faecal flora and faecal steroid concentration. Gut, 14: 790-793,1973. Peltonen R, Kjeldsen-Kragh J, Haugen M, et al. Changes of faecal flora in rheumatoid arthritis during fasting and one-year vegetarian diet. Br J Rheumatol 1994;33:638–43 Rudi K, Zimonja M, Aasen IM, Knutsen SH, Sahlstrøm S. Novel 16S rRNA gene analyses reveal new in vitro effects of insoluble barley fibres on the human faecal microbiota. Lett Appl Microbiol. 2009 Apr;48(4):433-9. Epub 2009 Feb 2. See also PMID: 10479237;19160281,;20029525; 20101384; 20107147, 10831441 24
  25. 25. Questions Q: Do bacterial populations in human body depend on genetics, environment? A: Yes, it’s a combination of environment and genetics. By environment I mean food, stress, hormones. It’s a combination. 25
  26. 26. Questions Q: What kinds of bacteria are TMA-producing? A: Proteobacteria, distant relatives of E.coli, E.coli could do it too. I do not think anybody isolated and sequenced microbes from TMAU sufferers, so nobody knows for sure what the particular species and sub-types are. Handbook of Hydrocarbon and Lipid Microbiology: Methylotrophic Bacteria in Trimethylaminuria and Bacterial Vaginosis ISBN978-3-540-77584-3 26
  27. 27. Questions Q: I heard that Solobacteria causes halitosis. Is it really so? A: There are thousands of bacterial types in the body, Solobacterium could be one of dozens that cause halitosis. It’s a distant relative of clostridium - some of its types are found in SIBO, others associated with botulism; it’s also a distant relative of streptococci some of which produce fetid smell. 27
  28. 28. Halitosis-related bacteria • Streptococcus salivarius • Prevotella melaninogenica • Streptococcus parasanguinis • Campylobacter concisus • Streptococcus mitis • Veillonella atypica • Streptococcus sanguinis - Note that it protects from cavities! So is it good or ugly? • Veillonella parvula • Actinomyces odontolyticus • Solobacterium moorei • Streptococcus oralis • Granulicatella adiacens 28
  29. 29. Examples of “Smelly” species (not among the early or prevalent) Produces hydrogen sulfide (rotten eggs) from sulfur- containing amino acids Produces TMA (dead fish) from choline 29
  30. 30. Questions Q: What bacteria smell? A: All of them. The question is which ones produce odors offensive to human nose. Note also that it depends not only on the type of bacteria but also its food. Example: E.coli - that usually produces fecal odors - smells like rotten fish when fed trimethylamine-N-oxide. It is becoming a popular subject for high-school and even middle-school projects to engineer rain-, mint- or banana-smelling bacteria iGEM competition: http://medgadget.com/archives/2006/11/would_e_coli_by_1.html http://openwetware.org/wiki/IGEM:MIT/2006/System_brainstorming/Smell-o-Rama http://www.dnaindia.com/bangalore/report_a-whiff-of-sweet-smelling-rain-in-a-science-lab_1341426 30
  31. 31. Questions Q: Is heterogeneity of metabolic body odor sufferers hindering research? A: Yes, it’s a big problem that diversity is so large. Knowledge has started to emerge about differences of bacterial make-ups in people. We may want to invite some of researchers working on it for our next seminars. Some scientists are skeptical about the feasibility of studies at this stage of our knowledge - although technically feasible, this would be time consuming and expensive. We could already start collecting samples, skin swabs, for example – and freezing them. Cost of sequencing is decreasing, large and small companies are working on it: Illumina/Solexa, Roche/454, Applied Biosystems, Helicos Biosciences and many others. Microbiota microarrays were also developed albeit for research purposes. 31
  32. 32. Questions Q: The collection of microbes for study must be a problem. Cross- contamination, etc. How do you get them? A: Biospecimen collection can be a problem. NIH is sponsoring the development of new technologies for obtaining samples of individual microbial isolates, let me know if you have suggestions on how to do it. For skin microbes, I am considering using q-tips to wipe sweat (on the forehead, for example), placing it in a small sterile tube and freezing it. For intestinal microbiota, it may require specific diets and time collections (preferably mornings). Oral samples should be collected from particular sites like dorsum of the tongue, lateral sides of the tongue, buccal fold, hard palate, soft palate, labial gingiva and tonsils of soft tissue surfaces, supragingival and subgingival plaques from tooth surfaces – with swab brushes or sterile Gracey curette. http://www.grants.nih.gov/grants/guide/rfa-files/RFA-CA-09-004.html 32
  33. 33. Questions Q: What’s the most effective treatment to eliminate the desired bacteria: food or antibiotics? A: Unfortunately food Is not always an alternative, bugs may need drugs. Keep in mind, however, that antibiotics may wipe out all the bacteria in the gut. Or, worse, they are specific to certain types of bacteria and not necessarily to the ones you need to get rid of. Even if your overall counts of bacteria are increased and antibiotics are the only remedy, be careful with your during- and after-antibiotic diet as you need to re-grow the right types of bacteria. 33
  34. 34. Questions Q: How often can we take antibiotic without causing harm? A: I would say twice a year, although some take them 4-5 times a year. You do not want your bacteria to grow stronger and turn into multi- drug resistant superbugs. 34
  35. 35. Questions Q: How does stress affect bacteria and enzyme deficiencies / pathways? A: Stress hormones trigger multiple biochemical reactions perturbing metabolic pathways, causing alterations in the pattern of gene and protein expression, causing macro- changes in the temperature of the body and heart rate. This could be stressing our bacteria too. It responds to changes in their chemical environment by creating more proteins, chemicals even by mutating (bacterial equivalent of panic, if you will). This could also decrease the body’s ability to produce digestive enzymes. 35
  36. 36. Questions Q: How does stress affect intestinal permeability? A: Stress affects gut motility, mucus, and permeability. Several studies demonstrated this for a variety of stresses applied to humans and animals. Social stress too increases permeability and secretion and triggers disturbances in intestinal motility. Low-grade stress could cause temporary changes. 36
  37. 37. Questions Q: Could a probiotic cleanse (sold on the market) help to flush us help to populate good bacteria A: I am skeptical about it, but it may be helpful. We need better studies, detailed stories from people that claim it helped them. 37
  38. 38. Questions Q: For many of us the diet is confusing would it be difficult to customize a diet for us A: I truly believe that we need better health management tools, digital food and symptom diary analyzing patterns and generating individual advice – Aurametrix is working on such a system. 38
  39. 39. Questions Q: How long will it take to see diet results? A: 6 months on average, from 3 month to one year 39
  40. 40. Questions Q: What would be the ideal diet .. Are proteins beneficial? A: It depends , some people could benefit from protein-rich diet, while others won’t. Generally proteins are the substrates for odor – white meat is better than red meat. Excess sugar and starch makes microbes grow faster. Examples of studies: Healthy adults fed a chemically defined residue-free (elemental, soluble) diet experience a reduction in in the number of anaerobic organisms, and a reduction in some particular species of bacteria. Crowther, J. S., Drasar, B. S., Goddard, P., Hill, M. J., and Johnson, K. The effect of a chemically defined diet on the faecal flora and faecal steroid concentration. Gut, 14: 790—793,1973. ( Bran-enriched diet favors Roseburia spp., E. rectale and Clostridium hathewayi like species, while resistant starch-based diet favored Ruminococcus bromii and Bifidobacterium adolescentis Nutrition Bulletin, 2008) Animal studies – concentrated diet (increased protein, fat, and fiber, decreased starch, minerals exceeding daily values) increased odorants and extended the persistence of E. coli species PMID: 1867671 40
  41. 41. Questions Q: Why some IBS patients have no odor while others do? A: Sometimes minimal genetic differences cause significant metabolic difference, it was shown on metabolomic studies of mouse fed similar diets, for example. Different IBS patients can harbor different bacteria, even though these bacteria may be close relatives of each other. 41
  42. 42. Questions Q: Can FMO3 be genetically engineered into a probiotic? A: Enzymes could be easily added to plant genomes – would you like an orange with FMO3? Too much controversy about genetically engineered food though. Bacteria supplying FMO3 could be also created but it would take more work to make it harmless and beneficial for humans 42
  43. 43. Live discussion with Arun Nagrath, pharmaceutical scientist, owner of bodyodorsupport.com 43
  44. 44. Sample Live Text Questions from the Audience 44
  45. 45. Maria is concluding the webinar 45