Aurametrix: Better Solutions for a Healthier World

Irene Gabashvili, PhD

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Slides and Q&A transcript of the Live Online Webinar, Feb. 12, 2010http://vokle.com/lineups/4194-microbes-and-us

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~10 x ~3% of body mass

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10-100μ 0.2-2μ

20μ/10ng 2½ to 5 poundsIn the bowel

Human vs Bacterial Nations: 102 vs 106-109

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E.Coli & Enterococci are among the first bacteria to colonize the neonatal gastrointestinal tract.

Human vs Bacterial Nations: 102 vs 106-109

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Streptococci are also among the first bacteria to colonize the infants in large numbers

Types of Microbes: Bacteria

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…

Types of Microbes: Fungi

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Types of Microbes: Protista

Types of Microbes

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All environmentally exposed human surfaces are home to bacteria, protists, algae, fungi (including yeast, molds, etc) and viruses.

Types of Microbes

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Middle ear pathogens: Streptococcus pneumoniae, non-typeable Haemophilusinfluenzae, Branhamella catarrhalisEyes: staphylococcus, streptococcus, diphtheroids, and Neisseria. Mouth: Streptococcus mutans causing cavities w/sticky foods , good: Strep sanguinis

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The Normal Bacterial Flora of Humans

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Bacterium Skin Conjunctiva 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

Human body: Map where bacteria live

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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

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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. ovatusand B. vulgatus. Different species are implicated in UC.PMID: 18043660 ; PMID: 1840143; PMID: 11777829

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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, Bifidobacteriumlongum, Bifidobacterium breve, Bifidobacteriuminfantis, Escherichia coli Nissle 1917, Streptococcus salivarius subspecies thermophilus, Bacteriodes thetaiotaomicron, Faecalibacteriumprausnitzii, etc. PMID: 19343057

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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/

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• 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 publications17

Conditions that may be linked to microbiota

IBS

Physical Mental

Quality of Life

Mikocka-Walus et al. Clinical Practice and Epidemiology in Mental Health 2008 4:15 doi:10.1186/1745-0179-4-15

Compiled from 8 sources by an IBS patient, Wikipedia, 200718

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

Nutrimirror

USDA DB

Fitday

TheCarrot

>300 nutrients as provided by USDA & other research DBs (e.g. choline/TMAU, glucose vsfructose & other specific carbohydrates to estimate GI (e.g., Diabetes, IBS, energy)

+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)

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Aurametrix

Nutrimirror: Black Cherry Yogurt, lowfat, organic, creamy Australian style (Wallaby)

La Yogurt Light Probiotic Blended Nonfat Yogurt Vanilla & Strawberry (TheCarrot)USDA: KRAFT BREYERS Smooth & Creamy Lowfat Strawberry Yogurt (1% Milkfat)

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. thermophilusand bifidobacteria

We link it to strains - NCF-M and clinical information

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Aurametrix

Thank You

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Dr. Irene Gabashvili, founder of Aurametrix, answering questions from the audience. Maria de la Torre, Director of MeBOResearch, and colleagues co-hosting and taking questions behind the scenes (Vokle live, chat, real-time e-mail)

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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.

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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 faecalsteroid 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

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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.

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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

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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.

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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

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Examples of “Smelly” species (not among the early or prevalent)

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Produces hydrogen sulfide(rotten eggs)from sulfur-containing amino acids Produces

TMA(dead fish) from choline

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

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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.

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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

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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.

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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.

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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.

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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.

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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.

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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.

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Questions

Q: How long will it take to see diet results?

A: 6 months on average, from 3 month to one year

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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

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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.

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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

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Live discussion with Arun Nagrath, pharmaceutical scientist, owner of

bodyodorsupport.com

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Sample Live Text Questions from the Audience

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Maria is concluding the webinar

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