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The Human Microbiome:
Its Impact On Our Lives and Our Health
Robert Rountree, M.D.
Boulder, Colorado
Christine Stubbe, ND
Medical Education Specialist - Asheville
Dr. Robert Rountree, M.D.
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The Human Microbiome:
Its Impact On Our Lives and Our Health
Robert Rountree, M.D.
Boulder, Colorado
Learning Objectives
• Review
– How DNA sequencing has redefined what it means
to be human
– How gut microbiomes impact on our digestion,
metabolism, neurology & immunology
– The impact of our modern lifestyle on our
microbiome and its correlation with chronic diseases
– How prebiotics and probiotics may help to maintain
a healthy microbiome
The Normal Microbiota
Humans are like mobile
warm-blooded coral
reefs, home to vast
numbers of microbial
ecosystems that are
rich in biodiversity
The Normal Microbiota
Composition of
microbiota varies
with each individual
– most fairly stable
– some species
transient
Each individual has a
unique microbial
“fingerprint”
Types of Human Microbiota
• Viruses (acellular)
• Prokaryotes (no nucleus)
– Archaea (strict anaerobes)
– Bacteria (aerobes and anaerobes)
• Eukaryotes (nucleus + organelles)
– Microfungi (yeasts)
– Protozoa
– Helminths (parasitic worms)
Archaea in the Human Microbiome
• Initially thought to be extremophiles
that only lived in harsh
environments, now known to
colonize humans
• Strict anaerobes – difficult to culture
– Identified by PCR of DNA sequences
(16S rRNA gene)
– or by breath testing
• Usually thought to be commensals
or mutualists that aid digestion, but
now implicated in oral & GI disorders
Methanogens in Human Health and Disease
Pimentel et al, Am J Gastroenterol Supp, 2012, Vol 1: 28-33
• Evidence has linked overabundance of
methanogenic archaea to constipation & IBS
• Methane may influence intestinal transit & pH &
facilitate development of constipation
• Methanogens ensure more complete
fermentation of carbohydrates, leading to higher
production & absorption of SCFAs, which may
lead to obesity
Methanobrevibacter smithii
• Dominant archaeon in GI tract:
– 10% of prokaryotes
• Not detected in about 50% of people
• Produces methane from H2, CO2, or
SCFAs (acetate):
– a major source of flatulence in cows
(cause of global warming ?) and in humans
• Implicated in constipation predominant
IBS, SIBO, obesity, T2DM
Am J Gastroenterol Suppl 2012 1:28–33
“A positive methane breath test
is synonymous to the presence
of methanogenic archaea”
World J Gastroenterol 2014 Vol 20(43): 16062-16078
The Bacterial Microbiome:
By the Numbers
• Every bodily surface hosts a myriad
of microorganisms:
– Skin = 1012 (one trillion) resident bacteria
– Mouth = 1010 (ten billion)
– Gut (especially distal) = 1014 (100 trillion)
with total weight ~ 2-5 lbs. Mostly anaerobes
The Bacterial Microbiome:
By the Numbers
• Current estimates for oral and intestinal microbiota:
– up to 500–1000 different species
• 30–40 species make up 99% of total population
• Biodiversity defined by
– Species richness (number of species)
– Relative species abundance
Dominant Bacterial Phyla in Human Habitats
(Mucosal & Cutaneous)
•
•
•
•
Bacteroidetes
Firmicutes
Actinobacteria
Proteobacteria
The Microbiome: Comparative Mass
Meet your microbiome – The bacteria that call you home
NOSE
•
•
Mass of microbes 10 g
Typical resident Streptococcus
MOUTH
•
•
Mass of microbes 20 g
Typical resident Streptococcus (cheek),
Neisseria (teeth)
VAGINA
•
•
•
•
Mass of microbes 1000 g
Typical resident Bacteroidetes
Mass of microbes 20 g
Typical resident Lactobacillus
SKIN
•
•
•
GUT
Mass of microbes 200 g
Typical resident Staphylococcus (oily areas),
Corynebacteria (moist areas)
MICROBIAL CELLS
OUTNUMBER YOUR
OWN CELLS 10 TO 1 AND
HAVE A TOTAL MASS OF
> 1.2 kg
Humans vs Bacteria
• Human somatic & germ cells:
– Approximate average = 1013 (10 trillion)
• Total microbiota > 100 trillion
– Outnumbering human cells by 10:1
• One of the most complex microbial
ecosystems on the planet!
Acquisition of the Human Microbiome
PLoS Biol, 2013, Vol 11(8): e1001631
• Initial inoculum from mother occurs during
pregnancy (womb is not sterile)
• Vaginal delivery –
– microbiome develops species similar
to mother’s vagina
• Cesarean section –
– microbiome develops predominant
species similar to skin flora of mother
and hospital attendants
• Breast feeding provides bacteria from
mother’s GI tract (breast milk is not sterile)
The microbes we acquire
at birth affect our health
throughout our lives
We are born 99% human
but we die 90% microbial
Cesarean Section Delivery
Increases Child’s Risk
PLoS Biol, 2013, Vol 11(8): e1001631
•
•
•
•
•
Allergic rhinitis
Asthma
Celiac disease
Type I diabetes
Inflammatory bowel disease
Bacterial Community Variation in Human
Body Habitats Across Space & Time
Science 2009: Vol. 326 no. 5960 pp. 1694-1697
• Bacterial community composition is primarily determined by
microecology of body habitat (gut, oral cavity, skin region)
• For each specific habitat:
– High levels of interpersonal variability:
• Each individual has a unique microbial fingerprint
– Minimal temporal variability within individuals
6–10 BILLION BACTERIA
Archaea
Protozoa
Fungi
Viruses
Shaping the oral microbiota
through intimate kissing
Microbiome, 2014, Vol 2:41
• Kissing for 10 seconds transfers an
average of 80 million bacteria
• Couples who reported they kissed
more often ended up having more
similar microbiota than lessfrequent kissers
• The similarity was most
pronounced for the tongue surface
The oral microbiome in
health and disease
Pharmacol Res 2013, Vol 69(1): 137-143
• 40–60% of oral bacteria have not been
cultivated or phenotypically characterized
• Periodontitis appears to result from an
inappropriate inflammatory reaction to the
normal microbiota, exacerbated by the
presence of some disease-associated
bacterial species
Continuing on
to the GI tract…
Total Bacteria in the Human Gut:
Approximately 100 TRILLION
• Over 98% of the bacteria in
the colon are strict
anaerobes
• Approx. 1010 bacteria/gm
• Anaerobes greatly out
number aerobes
• Closer to the ileocecal
valve, the number and
variety of organisms
increases to 105 – 6 /gm
• Anaerobes increase
significantly, including:
• Clostridium
• Bacteroides
• Fusobacterium
The stomach contains
103 – 5 acid resistant
organisms per gram:
• Helicobacter
• Streptococci
• Lactobacilli
• Staphylococci
There are 1012 – 13 bacteria
per gm in stool
• The small intestine starts
with organisms similar to
the stomach, at amounts of
103 – 5 /gm
• Anaerobes only slightly
outnumber facultative
organisms
Cell densities in the colon
(1011–1012/ml contents) are
the highest recorded for
any known ecosystem.
The Genome Institute at Washington University
Small Intestinal Bacterial Overgrowth
• Expansion of archaea & coliforms (E coli, Klebsiella) from
colon into small intestine (Pimentel hypothesis)
• Predisposed by
– Loss of antibacterial mechanisms: achlorhydria (PPIs),
pancreatic exocrine deficiency, immunodeficiency syndromes
– Anatomical abnormalities
– Motility disorders
Human Distal Gut Microbiome
Marchesi, Environ Microbiol (2011)
• After the age of 2.5, the distal gut microbiota is
stable and colonized predominantly by two phyla:
– Firmicutes and Bacteroidetes, which comprise 90% of
the species found
• Current estimates are that the microbiome
encodes from 3–10 million unique genes…the
DNA of which is frequently transferred via phage,
plasmids, transposons and other mobile genetic
elements (MGEs)
Humans as Superorganisms
• The mammalian microbiome has
evolved over millions of years to its
current state of symbiosis
• The human metagenome results
from an amalgamation of microbial
and human genes
Although there is a staggering
diversity of genes in the
human microbiome, many
perform similar functions in
different individuals
What are the functions
of proteins made by
these genes?
(The Metagenome)
Functions of Gut Microfloral Metagenome
• Digestion and energy harvesting
• Detoxification / biotransformation (hormones, toxins)
• Chemical synthesis: SCFAs, amino acids,
neurotransmitters, vitamins
• Colonization resistance against pathogens (C.R.A.P.)
• Systemic immune modulation
Gut Microbiota, Immunity, & Disease
Frontiers in Microbiology, 2011, Vol 2: 1-11
• The gut microbiota has a significant impact on
the systemic immune response
• …these data suggest that gut microbiota
influence the development of
inflammatory/autoimmune diseases…
• Commensal bacteria belonging to the
Bifidobacterium, Bacteroides, Clostridium and
Lactobacillus genera are associated with
inflammatory/autoimmune disease protection
Faecalibacterium prausnitzii
and human intestinal health
Current Opinion in Microbiology 2013, 16:1–7
• The most abundant bacterium in the
human intestinal microbiota of
healthy adults
– 5–15% of the total bacterial population
• One of the most abundant
butyrate producing bacteria
• Anti-inflammatory / mucosal
protective properties
Faecalibacterium prausnitzii
and human intestinal health
Current Opinion in Microbiology 2013, 16:1–7
• Extremely sensitive to oxygen & oxidative stress
• Relative abundance can serve as an indicator or
biomarker of intestinal health in adults
• Very low levels could be predictive for Crohn’s Disease
Major Influences on
Individual Microbiomes
• Host genotype
• Type of birth (vaginal vs C-section)
• Hygiene (excessive)
– PLoS One. 2011;6(12):e28284
• Diet
– Macronutrients, fiber, phytochemicals, alcohol
• Probiotics and prebiotics
Major Influences on
Individual Microbiomes
• Medications:
– Antibiotics, nonsteroidal anti-inflammatory drugs, etc.
• Stress (social, emotional)
• Chronic disease
• Aging
• Surgery (gastric bypass)
• Fecal bacteriotherapy transplants
Chowing down on meat, dairy alters
gut bacteria a lot, and quickly
Diet rapidly and reproducibly alters
the human gut microbiome
Turnbaugh, et al (Harvard Medical School), Nature 2014 Vol 505: 559–563
9 Volunteers placed on two extreme diets x 5 days:
•
1) meat, egg and cheese, then switched to
•
2) grains, vegetables and legumes
• Within 1–2 days saw major alterations in microbiome
measured by 16S rRNA sequencing
• Microbial activity mirrored differences between herbivorous
and carnivorous mammals, reflecting trade-offs between
carbohydrate and protein fermentation
Diet rapidly and reproducibly alters
the human gut microbiome
Nature 2014 Vol 505: 559–563
• Animal diet
– Increased abundance & activity of bile-tolerant organisms
(eg biophila wadsworthia – linked to colitis in animal studies)
– Decreased Firmicutes species that metabolize plant
polysaccharides
• Foodborne microbes from both diets transiently
colonized the gut, including bacteria, fungi, and viruses
Dysbiosis, Reduced
Microbial Diversity
and Disease
Diversity Association and
Relative Abundance Graphics
51
Internal Exposure to Diversity
The Human Microbiome
• A lack of microbial species richness and phylogenetic diversity
are associated with poor health
• Excessively sterile environments, diets low in plant fiber,
repeated exposure to antibiotics, and aging all decrease
microbial diversity
• The Hazda (Tanzanian hunter-foragers) have much great
microbial diversity than Westerners
humanfoodproject.com
52
Martin Blaser is chair of the
Department of Medicine, New York
University Langone Medical Center,
New York, NY
“Antibiotic overuse: Stop the killing
of beneficial bacteria”
Blaser; Nature, 2011, Vol 476: 393-394
• Bacteria have lived in and on animals—constituting their
microbiome — since multicellular life evolved about
1 billion years ago
• Babies acquire their founding bacterial populations from
their mothers while passing through the vagina at birth
• So each generation — particularly the 30% or so of infants
born via Caesarian — could be beginning life with a
smaller endowment of ancient microbes than the last
“Antibiotic overuse: Stop the killing
of beneficial bacteria”
Blaser; Nature, 2011, Vol 476: 393-394
• Evidence is accumulating that beneficial commensals
do not recover completely from antibiotics or are
replaced in the long term by resistant organisms
• Overuse of antibiotics could be fueling the dramatic
increase in conditions such as obesity, type 1 diabetes,
inflammatory bowel disease, allergies and asthma,
which have more than doubled in many populations
J Allergy Clin Immunol, 2011, Vol 128: 646-652
Reduced bacterial diversity of the infant’s intestinal flora
was associated with increased risk of allergic sensitization,
allergic rhinitis and peripheral blood eosinophilia…
Membership and Behavior of Ultra-LowDiversity Pathogen Communities Present in the
Gut of Humans during Prolonged Critical Illness
University of Chicago
mBio 2014 Vol 5(5): e01361-14
• Prolonged stays in ICU leads to “complete ecological collapse”
with the emergence of ultra-low (1–4 taxa) multi-drug
resistant pathogenic bacteria communities in 30% of patients;
• ~75% of cases C albicans & C glabrata overgrowth
• These limited communities keep each other in check until
triggered by acute stressful events (opioids) which can lead to
life-threatening sepsis
Gut Microbiota Disruption
Disease Risk Associations
• Acne
• Allergies & Asthma
• Autoimmune Disease
–
–
–
–
Diabetes
Reactive arthritis
Rheumatoid arthritis
Ankylosing spondylitis)
• Autism
Gut Microbiota Disruption
Disease Risk Associations
•
•
•
•
•
•
•
Colorectal cancer
Cardiovascular Disease
Irritable bowel syndrome
Inflammatory Bowel Disease
Fatty Liver Disease
Obesity
Aging
Fecal Bacteriotherapy
Human Probiotic Infusion
• Fecal transplants also being successfully
used for inflammatory bowel disease
• Does transplanting an entire ecosystem
impact the core microbiome in ways that
prebiotics and probiotics do not?
Conclusions
• Research into the microbiome using DNA sequencing
has redefined what it means to be human
• Humans are superorganisms that represent a blend
of genetic traits from human & microbial cells
• Our microbiomes have a major impact on our
digestion, metabolism, neurology & immunology
Conclusions
• The vast majority of our interactions with bacteria
are either neutral or mutually beneficial: maintaining
tolerance is essential to health
• Alteration of the microbiome by our modern lifestyle
(diet, stress, excessive hygiene and antibiotics) may
be responsible for many chronic diseases
• Dietary changes, prebiotics and probiotics may help
to maintain a healthy microbiome
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The views and opinions expressed herein are solely those of the presenter and do not necessarily represent those of Genova Diagnostics.
Thus, Genova Diagnostics does not accept liability for consequences of any actions taken on the basis of the information provided.
The Human Microbiome:
Its Impact On Our Lives and Our Health
Robert Rountree, M.D.
Boulder, Colorado
The views and opinions expressed herein are solely those of the presenter and do not
necessarily represent those of Genova Diagnostics. Thus, Genova Diagnostics does not accept
liability for consequences of any actions taken on the basis of the information provided.