Human Microbiome

Human Microbiome is the current project in Research field. The importance of Microorganisms in the human body, the importance and novel roe of the microorganisms on a human body is very effective and helpful. Fecal Transplantation is a unique and helpful technique to cure a dreadful disease naturally by means of microorganisms or introducing the normal flora in to the body again.

2. OUTLINE OF TALKOUTLINE OF TALK
What is meant by Human MicrobiomeWhat is meant by Human Microbiome
Describe the factors and processes that influence Describe the factors and processes that influence
community assembly and compositioncommunity assembly and composition
Importance of Human microbiomeImportance of Human microbiome
Gut Microbiota and its importanceGut Microbiota and its importance
Clostridium difficileClostridium difficile
Fecal TransplantationFecal Transplantation
ConclusionConclusion

3. •To make you all generally conversant in the
language of microbiomes and metagenomics
•To provide examples of how microbial
communities affect health and cure diseases
•To give practical examples of how medical
interventions interact with the microbiome and
change outcomes
Goal of my Talk

4. THE HUMAN THE HUMAN
MICROBIOMEMICROBIOME
The Human Microbiome: The
Undiscovered Country

5. What is the Human Microbiome
Microbe : Tiny living organism, such as
bacterium, fungus, protozoan, or virus
Microbiome : Collectively all the microbes in
the human body; a community of microbes
Biofilm : A community of microbes that live
together on a surface
A metagenome: the collection of genes/genomes
in an environmental

7. The Human Genome Project
started in 1990
Provides a basis to understand
how the human genome relates
to health and disease
However, the number of
microbial cells is 10 times
more than human cells in a
human being
The Problem :
Who am I Vs. Who are we

8. MICROBES ARE ALL OVER USMICROBES ARE ALL OVER US
There are millions of microbes
per square inch on your body
Thousands of different species on
the skin alone some thrive on dry
patches of the elbow, others thrive in
moist environment of armpit
It is estimated that there are more microbes
in your intestine there are human cells in
your body

9. Sites that harbor a normal floraSites that harbor a normal flora::
Skin and mucous Skin and mucous
membranesmembranes
Upper respiratory tractUpper respiratory tract
Gastrointestinal tractGastrointestinal tract
Outer opening of urethraOuter opening of urethra
External genitaliaExternal genitalia
VaginaVagina
External ear canalExternal ear canal
External eye (lids, External eye (lids,
conjunctiva)conjunctiva)

10. We are Covered with
Microbes ?
External Ear
Nose
Sinuses
Eyes
Mouth
Pharynx
Skin
Enteric tract
Vagina
How dense they are?
Who are they?
Where did they come from?
Do they all matter?
Democracy? Dictatorship?
Socialism
Can they be moved?
Transplanted? Adjusted?
Do they change when I am
sick?
When they change do they
make me sick?

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

12. Skin regions are like geographic regions of Earth

13. HOW MANY DIFFERENT ORGANISMS HOW MANY DIFFERENT ORGANISMS
ARE NORMALLY IN OUR BODY?ARE NORMALLY IN OUR BODY?
•Mouth ; > 600 SpeciesMouth ; > 600 Species
•Skin : > 600 SpeciesSkin : > 600 Species
•Intestine : (Cecum/ colon) : 8,000 Intestine : (Cecum/ colon) : 8,000
generagenera
•Vagina : > 200 SpeciesVagina : > 200 Species

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

15. 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.
Benefits of the normal flora

16. Yes
How? No
Why ?

17. •Microbes can communicate each other by chemical
language
•They interact each other by signals and respond to the
signals by using chemical language
•This Phenomenon is called “ Quorum Sensing”
• Quorum Sensing signals are called auto inducers
•All auto inducers are chemical language signals to one
another.
•Quorum Sensing is a system of stimulus and response
correlated to population density. Many species of
bacteria use quorum sensing to coordinate gene
expression according to the density of their local
population .(wiki)

22. GOALS OF THE HUMAN MICROBIOME GOALS OF THE HUMAN MICROBIOME
PROJECTPROJECT
•Determine if there are sets of microbes Determine if there are sets of microbes
common to each humancommon to each human
•Understand if changes in our microbiota Understand if changes in our microbiota
result in different states of health or diseaseresult in different states of health or disease
•Develop new technologies for studying Develop new technologies for studying
complex microbial and studying complex complex microbial and studying complex
microbial systems within their natural microbial systems within their natural
environments environments
•••Begin to deal with the legal ethical and Begin to deal with the legal ethical and
social complications that may arise with social complications that may arise with
human microbiome human microbiome

23. THE CONCEPT OF A CORE THE CONCEPT OF A CORE
MICROBIOMEMICROBIOME

24. WHAT DO THE MICROBES DO WHAT DO THE MICROBES DO
FOR US? FOR US?
•Provide the ability to harvest nutrients and Provide the ability to harvest nutrients and
•Produce additional energy otherwise Produce additional energy otherwise
inaccessible to the host.inaccessible to the host.
•Produce vitaminsProduce vitamins
•Metabolize xenobiotics Metabolize xenobiotics
•Provide resistance to tumor and cancer leading Provide resistance to tumor and cancer leading
neoplasms neoplasms
•Assist in developing a mature immune systemAssist in developing a mature immune system

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

26. INTESTINAL MICROBIOMEINTESTINAL MICROBIOME
•
>>1,000 species but most in adults are 1,000 species but most in adults are
from 2 phyla: Firmicutes and from 2 phyla: Firmicutes and
BacteroidetesBacteroidetes
•Outnumber human somatic cells by Outnumber human somatic cells by
factor of 10factor of 10
22
• Total Weight: 1-2 kg Total Weight: 1-2 kg
•60% of total fecal content60% of total fecal content
• Concentration: ~1012/gram in colon Concentration: ~1012/gram in colon
•••Total #: ~1014Total #: ~1014

27. O’Hara and Shanahan (2006) EMBO Reports
Where are all the organisms?

28. THE HUMAN GUT FLORATHE HUMAN GUT FLORA
DiBiase, et al. Mayo Clin Proc 2008;83:460-469

29. When Microbes entered in the
humans body?
Is it starts in the Mother’s
Womb?
Or? after the birth ?

30. THE MICROBIOME: WHO’S THERE?THE MICROBIOME: WHO’S THERE?
•Early gut colonization has four phasesEarly gut colonization has four phases
•Phase 1: Sterile gut Phase 1: Sterile gut
•Phase 2: Initial acquisition: vagina, feces, hospitalPhase 2: Initial acquisition: vagina, feces, hospital
•Phase 3: Breast feeding or bottle-feeding (different)Phase 3: Breast feeding or bottle-feeding (different)
•Breast fed more bifidobacteria (up to 90% of flora)Breast fed more bifidobacteria (up to 90% of flora)
•Bottle fed more diverse; more Bottle fed more diverse; more BacteroidesBacteroides , and , and
Clostridial speciesClostridial species
•Phase 4: Start of solids; move to adult flora Phase 4: Start of solids; move to adult flora
•Bifidobacteria remain key flora into adulthoodBifidobacteria remain key flora into adulthood
Ley, Peterson, Gordon. Cell 2006 ;124:837
Ley, et al. PNAS. 2005, 102: 11070
Edwards, et al. Br J Nutr. 2002

32. The gut environment selects its microbiota
Primary Succesion in the
Lina.et,al 2012

33. MATURATION OF THE MICROBIOME MATURATION OF THE MICROBIOME
DURING THE 1DURING THE 1
STST
YEAR OF LIFE YEAR OF LIFE
Development of the Human Infant Intestinal Microbiota
Palmer C,Bik EM,DiGiulio DB,Relman

34. THE MICROBIOME: WHO’S THERE?THE MICROBIOME: WHO’S THERE?
•Adult Microbiome:Adult Microbiome:
−Increasing diversity of flora as we ageIncreasing diversity of flora as we age
−In some newer PCR (16S rRNA) studies, up to 92% In some newer PCR (16S rRNA) studies, up to 92%
of the flora in adults were “novel” speciesof the flora in adults were “novel” species
•Serial stool collections show remarkable stability by Serial stool collections show remarkable stability by
an individualan individual
−Greatest concordance with twinsGreatest concordance with twins
−Less concordance with householdsLess concordance with households
−Host genetic influence unexploredHost genetic influence unexplored..
McCartney and Gibson in Gastrointestinal
Microbiology, 51-73, 2006

35. METABOLOMICSMETABOLOMICS
•Study of the metabolites and small molecules Study of the metabolites and small molecules
that the body and that the body and gut bacteria producegut bacteria produce..
•New area of science New area of science
•Broader than Broader than proteomicsproteomics
•Includes bacteria products with our own genetic Includes bacteria products with our own genetic
productsproducts
•Pioneered by Jeremy Nicholson and Jeff GordonPioneered by Jeremy Nicholson and Jeff Gordon

36. GUT FLORA AND GUT FLORA AND
METABOLISMMETABOLISM
•Microbial genomes enhance our metabolic Microbial genomes enhance our metabolic
activityactivity
•May indirectly or directly effect our May indirectly or directly effect our
metabolismmetabolism
•The colon is very active metabolicallyThe colon is very active metabolically
•20-70 gms of carbons and 5-20 gms of 20-70 gms of carbons and 5-20 gms of
protein/dayprotein/day
•Over 100 kcal per day!Over 100 kcal per day!
•Mass of colonic microbiome = single kidneyMass of colonic microbiome = single kidney
•Metabolically as active as the liverMetabolically as active as the liver
Hooper, et al. Annu Rev Nutr, 2002

37. GUT FLORA AND THE BRAINGUT FLORA AND THE BRAIN
Collins and Bercik in GASTRO 2009;136:2003–2014

38. Fecal Microbiota TransplantsFecal Microbiota Transplants
(FMT)(FMT)

39. Clostridium difficile also known as "CDF/cdf", or "C. diff",
is a species of Gram-positive spore-forming bacterium that
is best known for causing antibiotic-associated
diarrhea(AAD).
While it can be a minor normal component of colonic flora,
the bacterium is thought to cause disease when competing
bacteria in the gut have been wiped out by antibiotic
treatment.
In severe cases, C. difficile can cause "pseudomembranous
colitis," a severe inflammation of the colon.

40. Inflammation is part of the complex biological response of vascular tissues
to harmful stimuli, such as pathogens, damaged cells, or irritants
The classical signs of acute inflammation are pain, heat, redness, swelling,
and loss of function. Inflammation is a protective attempt by the organism to
remove the injurious stimuli and to initiate the healing process.
Inflammation

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

42. FMTFMT
Procedure:
 Donar History (Similar to blood donation )
Obtain stool sample, homogenize with saline and filter
 How to Administer
 Nasogastric Tube
 Enema
 Colonoscope
 Perform 6-24 hrs of obtaining the sample
 Future: Frozen Samples, Lyophilized Powders, Capsules..??
TJ.BOOD ET.AL

43. •FecalFecal microbiota transplantationmicrobiota transplantation ( (FMTFMT) also ) also
known as a known as a stool transplantstool transplant is the process of is the process of
transplantation of fecal bacteria from a healthy transplantation of fecal bacteria from a healthy
individual into a recipient. It has been proven to be a individual into a recipient. It has been proven to be a
highly effective treatment for patients suffering from highly effective treatment for patients suffering from
ClostridiumClostridium difficiledifficile infection (CDI) infection (CDI),, which which
produces effects ranging from diarrhea to produces effects ranging from diarrhea to
pseudomembranous colitis.pseudomembranous colitis.

44. BACTERIOTHERAPYBACTERIOTHERAPY
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

45. CONCLUSIONSCONCLUSIONS
•The human microbiome and the Microbiome The human microbiome and the Microbiome
Project: research just beginning…Project: research just beginning…
•Gut flora by their genes, by-products, and Gut flora by their genes, by-products, and
metabolic activity influence our metabolism, metabolic activity influence our metabolism,
weight, activity, immunity, health and weight, activity, immunity, health and
disease.disease.
•Manipulation of gut flora may be an integral Manipulation of gut flora may be an integral
part of weight loss programs and different part of weight loss programs and different
disease treatments in the future.disease treatments in the future.

46. CONCLUSIONSCONCLUSIONS
•Future studies must focus on the mechanisms Future studies must focus on the mechanisms
that influence of our gut flora.that influence of our gut flora.
•Studies must be place to controlled and high Studies must be place to controlled and high
quality research should be done.quality research should be done.
•Truly need translational science to work at Truly need translational science to work at
the levels of the petri dish, genomics, and the levels of the petri dish, genomics, and
clinical outcomes.clinical outcomes.
•Hope much much more to come!Hope much much more to come!