Transcript Supporting the Microbiome - University of Colorado Denver

The Human Microbiome:
Its Impact on Our Lives & Health
Robert Rountree, MD
Strauss Lecture Series
October 19, 2016
Traditional Clinical Microbiology
• Microbes as agents of disease: pathogenic
“terrorists”
• Detected by microscopy and culture
• Characterized by growth on specific media,
sensitivity to antibiotics
“Computational” Microbiology
– 99% of all bacteria are unculturable, hence…
– Taxonomy is based on DNA sequencing
• 16S rRNA gene: ~1500 base pairs
(pioneered by Woese, Fox et al-1980s)
• Metagenomics (pioneered by Venter, et al)
• Whole genome sequencing: ~4 million bp
• Classified as “operational taxonomic units” (OTUs)
– Characterized by genetic expression
Human Microbiome:
The totality of microbes, their genomes and
environmental interactions in & on the
human organism
Joshua Lederberg, PhD (1925-2008)
American molecular biologist
1958 Nobel laureate
The Normal Microbiota
Humans are like mobile warm-blooded coral reefs, home to vast numbers
of microbial ecosystems that are rich in biodiversity.
The vast majority of microbes are harmless or beneficial.
The Normal Microbiota
Composition of the microbiota varies with each individual
– Most species fairly stable
– Some species transient
Each individual has a unique microbial “fingerprint”
Humans and Microbes
PLoS Computational Biology, 2010, Vol 6(2): e1000667
• Along with all other animals and plants, the
human condition is profoundly affected by
microbes, from the scourges of human, farm
animal, and crop pandemics, to the benefits in
agriculture, food industry, and medicine
• Given our intimate relationship with microbes,
sequencing the genomes of our own microbes is
essential for understanding the human condition
Types of Human Microbiota
• Viruses (acellular, “nonliving”)
• Prokaryotes (without a nucleus):
– Archaea (strict anaerobes)
– Bacteria (aerobes and anaerobes)
• Eukaryotes (possess nucleus + organelles)
– Microfungi (mycobiome)
– Protozoa
– Helminths (parasitic worms)
Bacteria colonizing the gut mucosa
The Microbiome: Comparative Mass
Humans vs. Bacteria
• Total # human cells (mainly RBCs)
10-37 trillion
• Total microbiota 10-100 trillion
approximate average
matching or outnumbering
human cells by 3:1
Sender, Fuchs, Milo: http://dx.doi.org/10.1101/036103
defection = loss of 1/3 of microbiome
• Human genes ~20,000
• Common microbial genes >3.3 million
– outnumbering human genes >150:1
• One of the most complex microbial ecosystems on the planet!
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
• Redefining what it means to be human!
Nat Rev
Genet. 2014,
Vol 15(9):
577–584.
Microbes occupy ecological niches
6-10 billion bacteria
archaea
protozoa
fungi
viruses
Shaping the oral microbiota through intimate kissing
• 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 less-frequent
kissers
• Similarity most pronounced for tongue surface
Microbiome, 2014, Vol 2:41
Acquisition of the Human Microbiome
• Initial inoculum from mother occurs during pregnancy
• 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
tract
PLoS Biol, 2013, Vol 11(8): e1001631
from mother’s GI
The microbes we acquire at
birth affect our health the rest
of our lives
Cesarian Sections and the Microbiome
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
• Each generation — particularly the 30% or so of infants born via Cesarian —
could be beginning life with a smaller endowment of ancient microbes than the
last
Cesarean Section Delivery Increases Child’s Risk of:
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Allergic Rhinitis
Asthma
Celiac Disease
Type I Diabetes
Inflammatory Bowel Disease
PLoS Biol, 2013, Vol 11(8): e1001631
Human Gut Microbiome:
Our Second Genome
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 approximately 3.3 million nonredundant genes
– the DNA of which is frequently transferred
via mobile genetic elements
What are the
ecosystem services
provided by microbial genes –
our “second” genome?
Functions of the Gut Metagenome
• Digestion/metabolism:
extraction
• Production of vitamins & metabolites
• Protection against infection
• Maintenance of gut barrier
• Immune modulation
• Influences on mood & behavior
energy and nutrient
“It is reasonable to propose that the composition of the
microbiome and its activities are involved in most, if not all,
of the biological processes that constitute human health and
disease”
Martin J Blaser, MD
J Clin Invest. 2014;124(10):4162-4165
Major Influences on Individual Microbiomes
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Host genotype
Type of birth (vaginal vs C-section)
Excessive hygiene
Diet (macronutrients, fiber, phytochemicals, alcohol)
Stress (social, emotional)
Major Influences on Individual Microbiomes
• Medications
– Antibiotics
– Non-steroidal anti-inflammatory drugs
– Proton pump inhibitors
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Environmental toxins
Chronic disease
Aging
Surgery
We are what we eat:
• Our diet determines which bacterial species and strains thrive
in our intestines
• This effects the composition of our second genome and
therefore our health
Diet rapidly and reproducibly alters the human gut microbiome
David, Turnbaugh, et al, 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: 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
Turnbaugh, et al, Nature 2014 Vol 505: 559–563
• Animal diet:
– increased abundance & activity of bile-tolerant organisms (eg Biophila
wadsworthia – toxic H2S producer, 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
What Does a Three Day Dietary Cleanse do to Your Gut
Microbiome?
Luke Thompson, PhD: www.americangut.org
• Dr. Oz 3 day cleanse = smoothies of fruits & vegetables, plus a
multivitamin & probiotic
• Cleanse resulted in increase in the microbial groups Akkermansia and
Enterobacteriaceae
What Does a Three Day Dietary Cleanse do to Your Gut
Microbiome?
Luke Thompson, PhD: www.americangut.org
• Akkermansia is thought to help prevent metabolic
diseases like diabetes by aiding mucin turnover
and production, causing thickening of the gut
wall
• However, within a week after returning to
“normal” or “Western” food, the microbiome
returns to original state
Changes in microbial taxa with 3-day Dr. Oz fruit &
vegetable cleanse + VSL#3
(www.americangut.com)
Burkina Faso diet & lifestyle
Gut Microbiota: European vs. rural Burkino Fasan Children
PNAS, 2010, Vol 107(33): 14691-14696
• Exposure to the large variety of environmental microbes associated with a highfiber diet could increase the potentially beneficial bacterial genomes, enriching the
microbiome
• Reduction in microbial richness is possibly one of the undesirable effects of
globalization and of eating generic, nutrient-rich, uncontaminated foods
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Internal 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
• Hunter-foragers have much greater microbial diversity than
Westerners
– (http://humanfoodproject.com)
Diversity Association and
Relative Abundance
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http://news.sciencemag.org/biology/2015/04/resistance-antibiotics-found-isolated-amazonian-tribe
The microbiome of uncontacted Amerindians
Gloria Dominguez-Bello, et al, Sci Adv. 2015 Apr 3;1(3)
• The uncontacted Yanomami harbor
“significantly higher diversity than other
populations,” including high amounts of
Prevotella, Helicobacter, Oxalobacter, and
Spirochaeta that are absent or significantly
reduced in industrialized humans
The microbiome of uncontacted Amerindians Sci Adv. 2015 Apr 3;1(3)
• The Yanomami had high levels of parasites but were healthy and did
not suffer from autoimmune disorders, diabetes, high blood pressure,
or heart disease
Resistance to antibiotics found in isolated Amazonian tribe
news.sciencemag.org April 15, 2015
• Despite their isolation, presumably for >11,000 years since their
ancestors arrived in South America, the Yanomami gut bacteria had
nearly 60 unique genes that could turn on and rally to fend off
antibiotics, including a half-dozen genes that could protect the bacteria
from synthetic antibiotics
Regulation of the immune system by
biodiversity from the natural environment:
An ecosystem service essential to health
Rook, G, PNAS 2013 Vol 110(46): 18360–18367
• Numerous studies demonstrate that living close to the natural rural or coastal
environment, often denoted “green space or “blue space,” respectively, is beneficial
for human health
• The requirement for microbial input from the environment to drive
immunoregulation is a major component of the beneficial effect of green space,
and a neglected ecosystem service that is essential for our well-being
Rook, G, PNAS 2013
Regulation of the immune system by
biodiversity from the natural environment:
An ecosystem service essential to health
Rook, G, PNAS 2013 Vol 110(46): 18360–18367
• Immigration from a developing country to a high-income urban center
leads to a loss of exposure to microbial biodiversity
• In such immigrant populations, there are large increases in
autoimmunity, inflammatory bowel disease, depression, and allergic
disorders
Richness of human gut microbiome correlates with metabolic
markers
Nature 2013, Vol 500: 541-549
• Individuals with a low bacterial richness (23% of the population) are
characterized by more marked overall adiposity, insulin resistance and
dyslipidemia and a more pronounced inflammatory phenotype when
compared with high bacterial richness individuals
• The obese individuals among the lower bacterial richness group also
gain more weight over time
Major Influences on the Gut Microbiome in Developed Countries
J Clin Invest. 2014;124(10):4190–4196
• Lifestyle factors: diet, stress, and sleep disorders; sterile
environment
• Environmental pollutants and xenobiotics (glyphosate)
• Wide and indiscriminate use of antibiotics by livestock
producers and in medical practice
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Antibiotic overuse: Stop the killing of
beneficial bacteria
Blaser; Nature, 2011, Vol 476: 393-394
• Evidence is accumulating that our welcome residents 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
“Independent of well-known asthma risk factors, asthma was
significantly more likely to develop at age 7 years in children
who had received antibiotics in the first year of life.”
Chest, 2007, Vol 131: 1753-1759
Blaser; Nature, 2011, Vol 476: 393-394
40% of all adults and 70% of all children in the U.S. take one or more courses of
antibiotics every year (CDC)
80% of antibiotics in U.S. are given to animals for non-therapeutic purposes
The Pew Charitable Trusts
Dysbiosis
• Microbial imbalance, most commonly in the gastrointestinal
tract
• Associated with chronic intestinal symptoms: gas, bloating,
diarrhea, constipation
• May predispose to a chronic diseases
• Contributes to “leaky gut” syndrome (hyperpermeable tight
junctions)
Membership and Behavior of Ultra-Low-Diversity Pathogen Communities
Present in the Gut of Humans during Prolonged Critical Illness
• 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
University of Chicago mBio 2014 Vol 5(5): e01361-14
Dysbiotic Events in Gut Microbiota: Impact on Human Health
Nutrients 2014, 6, 5786-5805
Dybiosis (gut microbial imbalance) has been linked with important
human diseases, including autoimmune and/or autoinflammatory
disorders, such as IBD, metabolic disorders, such as, obesity, type 2
diabetes, allergies, and neurological disorders
Supporting the Microbiome
(from the Human Microbiome Project)
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Get adequate sleep
Exercise frequently
Eat a wide variety of fresh plant foods
Minimize:
– Refined carbohydrates
– NSAIDs
– Alcohol
– Antibiotics
Supporting The Microbiome
• Consume prebiotic fibers:
– pectin, inulin, fructo-oligosaccharides, hydrolyzed guar, larch
arabinogalactan, gum arabic, beta glucans, boabab, chicory root,
asparagus, dandelion greens, garlic, onions, leeks, wheat bran, bananas
• Eat fermented foods: fresh sauerkraut, kimchi
• Take probiotics
– Yogurt (homemade)
– Lactobacilli (multiple species)
– Bifidobacteria (multiple species)
– Saccharomyces boulardii
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