Human body: Map where bacteria live
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
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
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
• 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/
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
Example of a condition dramatically decreasing quality of life,
with no good diagnostic tests nor effective treatments
Quality of Life
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
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
proteins, gluten (e.g.,
+Info on, preservatives,
sulfites, MSG (e.g.,
+Info on potential
poisoning or undeclared
La Yogurt Light Probiotic Blended Nonfat Yogurt Vanilla &
USDA: KRAFT BREYERS Smooth & Creamy Lowfat Strawberry
Yogurt (1% Milkfat)
In addition to micro and
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
We link it to strains - NCF-M
and clinical information
Nutrimirror: Black Cherry Yogurt, lowfat, organic, creamy
Australian style (Wallaby)
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)
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.
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
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
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.
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
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.
• 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
Examples of “Smelly” species (not among the early or prevalent)
amino acids Produces
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
iGEM competition: http://medgadget.com/archives/2006/11/would_e_coli_by_1.html
Q: Is heterogeneity of metabolic body odor sufferers hindering
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
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.
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.
Q: How often can we take antibiotic without
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.
Q: How does stress affect bacteria and enzyme deficiencies /
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.
Q: How does stress affect intestinal
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.
Q: Could a probiotic cleanse (sold on the
market) help to flush us help to populate
A: I am skeptical about it, but it may be helpful.
We need better studies, detailed stories from
people that claim it helped them.
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.
Q: How long will it take to see diet results?
A: 6 months on average, from 3 month to one
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
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: 790â€”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
Q: Why some IBS patients have no odor while
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.
Q: Can FMO3 be genetically engineered into a
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
Live discussion with Arun Nagrath,
pharmaceutical scientist, owner of
Sample Live Text Questions from the