Talk by Jonathan Eisen for UC Davis Medical Microbiology and Immunology department meeting with School of Medicine Dean

1. Jonathan Eisen Lab Topics

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Pubmed “Microbiome” Hits
The Rise of the Microbiome

3. Challenge 1: Complexity
Microbial Diversity
Microbial Diversity2 Fragmented Data
HUMA
MICROBIOM
YOUR BODY: HUMAN AND MICRO
fungal
bacterial
human
WHOʼS THERE?
A human body is actually on
about 25% human cells. The
rest is many thousands of
species of bacteria and othe
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOIN
Wherever the human body is exposed to
the outside world, there is a microbial
community.
Our microbiome helps us ex
and nutrients from the
and crowds out or inhibit
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MI
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organ
includes viruses, bacteria, and fun
Not all microbes make us sick - the
and on our bodies play many esse
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
Our microbiome helps us extract energy
and nutrients from the food we eat
and crowds out or inhibits pathogens
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
Host Variation
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HU
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% h
rest is many t
species of ba
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For t
will c
micro
s
p
n
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, b
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HU
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% h
rest is many t
species of ba
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For t
will c
micro
s
p
n
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, b
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUM
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, ba
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUM
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, ba
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
http://bit.ly/HumanMicrobiome
Functional
Diversity

4. Challenge 1: Complexity
HUMA
MICROBIOM
YOUR BODY: HUMAN AND MICRO
fungal
bacterial
human
WHOʼS THERE?
A human body is actually on
about 25% human cells. The
rest is many thousands of
species of bacteria and othe
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOIN
Wherever the human body is exposed to
the outside world, there is a microbial
community.
Our microbiome helps us ex
and nutrients from the
and crowds out or inhibit
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MI
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organ
includes viruses, bacteria, and fun
Not all microbes make us sick - the
and on our bodies play many esse
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
Our microbiome helps us extract energy
and nutrients from the food we eat
and crowds out or inhibits pathogens
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
Host Variation
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HU
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% h
rest is many t
species of ba
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For t
will c
micro
s
p
n
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, b
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HU
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% h
rest is many t
species of ba
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For t
will c
micro
s
p
n
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, b
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUM
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, ba
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human body is actually only
about 25% human cells. The
rest is many thousands of
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed to
the outside world, there is a microbial
community.
skinGI tractlungsmouth
Our microbiome helps us extract energy
and nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENVIRONMENT:
For the rest of the baby’s life, it
will continuously encounter new
microbes from:
soil and water
people, pets, plants
new and diverse
foods
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE?
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a microscopic organism - this
includes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes in
and on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
Viruses outnumber bacteria
by about 5:1.
5 1:99%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
urogenital
tract
HUM
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THE
Wherever the human body is exposed to
the outside world, there is a microbial
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
Breast milk has been fine-
tuned over millions of
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
nutrients, vitamins,
and antibodies
diverse microbes to
populate the baby’s
gut
its mother’s birth
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
The human body is home to
trillions of microbes. The
community of microbes
living in intimate association
with our bodies, and the genes
they contain, make up the
human microbiome.
A microbe is a mic
includes viruses, ba
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
Microbes contribute an extra
2,000,000 genes to the 20,000 gene
human genome.
http://bit.ly/HumanMicrobiome
TranscriptomeSNPs, CNVs
Epigenetics
Environment

5. Challenge 2: Public Understanding

6. Challenge 2: Public Understanding
Germophobia

7. Challenge 2: Public Understanding
Germophobia Microbiomania

8. Opportunity 1: Better Reference Data

9. Genomic Encyclopedia of Bacteria & Archaea
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree

10. JGI Dark Matter Project
environmental
samples (n=9)
isolation of single
cells (n=9,600)
whole genome
amplification (n=3,300)
SSU rRNA gene
based identification
(n=2,000)
genome sequencing,
assembly and QC (n=201)
draft genomes
(n=201)
SAK
HSM ETLTG
HOT
GOM
GBS
EPR
TAETL T
PR
EBS
AK E
SM G TATTG
OM
OT
seawater brackish/freshwater hydrothermal sediment bioreactor
GN04
WS3 (Latescibacteria)
GN01
+Gí
LD1
WS1
Poribacteria
BRC1
Lentisphaerae
Verrucomicrobia
OP3 (Omnitrophica)
Chlamydiae
Planctomycetes
NKB19 (Hydrogenedentes)
WYO
Armatimonadetes
WS4
Actinobacteria
Gemmatimonadetes
NC10
SC4
WS2
Cyanobacteria
:36í2
Deltaproteobacteria
EM19 (Calescamantes)
2FW6SDí )HUYLGLEDFWHULD

11. GAL35
Aquificae
EM3
Thermotogae
Dictyoglomi
SPAM
GAL15
CD12 (Aerophobetes)
OP8 (Aminicenantes)
AC1
SBR1093
Thermodesulfobacteria
Deferribacteres
Synergistetes
OP9 (Atribacteria)
:36í2
Caldiserica
AD3
Chloroflexi
Acidobacteria
Elusimicrobia
Nitrospirae
49S1 2B
Caldithrix
GOUTA4
6$5 0DULQLPLFURELD

12. Chlorobi
)LUPLFXWHV
Tenericutes
)XVREDFWHULD
Chrysiogenetes
Proteobacteria
)LEUREDFWHUHV
TG3
Spirochaetes
WWE1 (Cloacamonetes)
70
ZB3
093í
'HLQRFRFFXVí7KHUPXV
OP1 (Acetothermia)
Bacteriodetes
TM7
GN02 (Gracilibacteria)
SR1
BH1
OD1 (Parcubacteria)
:6
OP11 (Microgenomates)
Euryarchaeota
Micrarchaea
DSEG (Aenigmarchaea)
Nanohaloarchaea
Nanoarchaea
Cren MCG
Thaumarchaeota
Cren C2
Aigarchaeota
Cren pISA7
Cren Thermoprotei
Korarchaeota
pMC2A384 (Diapherotrites)
BACTERIA ARCHAEA
archaeal toxins (Nanoarchaea)
lytic murein transglycosylase
stringent response
(Diapherotrites, Nanoarchaea)
ppGpp
limiting
amino acids
SpotT RelA
(GTP or GDP)
+ PPi
GTP or GDP
+ATP
limiting
phosphate,
fatty acids,
carbon, iron
DksA
Expression of components
for stress response
sigma factor (Diapherotrites, Nanoarchaea)
ı4
ȕ ȕ¶
ı2ı3 ı1
-35 -10
Į17'
Į7'
51$ SROPHUDVH
oxidoretucase
+ +e- donor e- acceptor
H
1
Ribo
ADP
+
1+2
O
Reduction
Oxidation
H
1
Ribo
ADP
1+
O
2H
1$' + H 1$'++ + -
HGT from Eukaryotes (Nanoarchaea)
Eukaryota
O
+2+2
OH
1+
2+3
O
O
+2+2
1+
2+3
O
tetra-
peptide
O
+2+2
OH
1+
2+3
O
O
+2+2
1+
2+3
O
tetra-
peptide
murein (peptido-glycan)
archaeal type purine synthesis
(Microgenomates)
PurF
PurD
3XU1
PurL/Q
PurM
PurK
PurE
3XU
PurB
PurP
?
Archaea
adenine guanine
O
+ 12
+
1
1+2
1
1
H
H
1
1
1
H
H
H1 1
H
PRPP )$,$5
IMP
$,$5
A
GUA
G U
G
U
A
G
U
A U
A U
A U
Growing
AA chain
W51$*O

13. recognizes
UGA
P51$
UGA recoded for Gly (Gracilibacteria)
ribosome
Woyke et al. Nature 2013.

14. Microbial Dark Matter Part 2
• Ramunas
Stepanauskas
• Tanja Woyke
• Jonathan Eisen
• Duane Moser
• Tullis Onstott

15. Microbial Dark Matter Part 2
• Ramunas
Stepanauskas
• Tanja Woyke
• Jonathan Eisen
• Duane Moser
• Tullis Onstott

16. Same Thing Needed for Protein Families
A
B
C
Representative
Genomes
Extract
Protein
Annotation
All v. All
BLAST
Homology
Clustering
(MCL)
SFams
Align
Build
HMMs
HMMs
Screen for
Homologs
New
Genomes
Extract
Protein
Annotation
Figure 1

17. Opportunity 2: Methods Development

18. General Workflow
DNA DNADNA
Taxa Characters
B1 ACTGCACCTATCGTTCG
B2 ACTCCACCTATCGTTCG
E1 ACTCCAGCTATCGATCG
E2 ACTCCAGGTATCGATCG
A1 ACCCCAGCTCTCGCTCG
A2 ACCCCAGCTCTGGCTCG
New1 ACCCCAGCTCTGCCTCG
New2 AGGGGAGCTCTGCCTCG

19. Phylosift
DNA DNADNA
Taxa Characters
B1 ACTGCACCTATCGTTCG
B2 ACTCCACCTATCGTTCG
E1 ACTCCAGCTATCGATCG
E2 ACTCCAGGTATCGATCG
A1 ACCCCAGCTCTCGCTCG
A2 ACCCCAGCTCTGGCTCG
New1 ACCCCAGCTCTGCCTCG
New2 AGGGGAGCTCTGCCTCG
Input Sequences
rRNA workflow
protein workflow
profile HMMs used to align
candidates to reference alignment
Taxonomic
Summaries
parallel option
hmmalign
multiple alignment
LAST
fast candidate search
pplacer
phylogenetic placement
LAST
fast candidate search
LAST
fast candidate search
search input against references
hmmalign
multiple alignment
hmmalign
multiple alignment
Infernal
multiple alignment
LAST
fast candidate search
600 bp
600 bp
Sample Analysis
Comparison
Krona plots,
Number of reads placed
for each marker gene
Edge PCA,
Tree visualization,
Bayes factor tests
eachinputsequencescannedagainstbothworkflows

20. PhyEco Markers
DNA DNADNA
Taxa Characters
B1 ACTGCACCTATCGTTCG
B2 ACTCCACCTATCGTTCG
E1 ACTCCAGCTATCGATCG
E2 ACTCCAGGTATCGATCG
A1 ACCCCAGCTCTCGCTCG
A2 ACCCCAGCTCTGGCTCG
New1 ACCCCAGCTCTGCCTCG
New2 AGGGGAGCTCTGCCTCG
PhyEco
Markers

21. HiC Crosslinking Sequencing
Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore
RW, Eisen JA, Darling AE. (2014) Strain- and plasmid-
level deconvolution of a synthetic metagenome by
sequencing proximity ligation products. PeerJ 2:e415
http://dx.doi.org/10.7717/peerj.415
Table 1 Species alignment fractions. The number of reads aligning to each replicon present in the
synthetic microbial community are shown before and after filtering, along with the percent of total
constituted by each species. The GC content (“GC”) and restriction site counts (“#R.S.”) of each replicon,
species, and strain are shown. Bur1: B. thailandensis chromosome 1. Bur2: B. thailandensis chromosome
2. Lac0: L. brevis chromosome, Lac1: L. brevis plasmid 1, Lac2: L. brevis plasmid 2, Ped: P. pentosaceus,
K12: E. coli K12 DH10B, BL21: E. coli BL21. An expanded version of this table can be found in Table S2.
Sequence Alignment % of Total Filtered % of aligned Length GC #R.S.
Lac0 10,603,204 26.17% 10,269,562 96.85% 2,291,220 0.462 629
Lac1 145,718 0.36% 145,478 99.84% 13,413 0.386 3
Lac2 691,723 1.71% 665,825 96.26% 35,595 0.385 16
Lac 11,440,645 28.23% 11,080,865 96.86% 2,340,228 0.46 648
Ped 2,084,595 5.14% 2,022,870 97.04% 1,832,387 0.373 863
BL21 12,882,177 31.79% 2,676,458 20.78% 4,558,953 0.508 508
K12 9,693,726 23.92% 1,218,281 12.57% 4,686,137 0.507 568
E. coli 22,575,903 55.71% 3,894,739 17.25% 9,245,090 0.51 1076
Bur1 1,886,054 4.65% 1,797,745 95.32% 2,914,771 0.68 144
Bur2 2,536,569 6.26% 2,464,534 97.16% 3,809,201 0.672 225
Bur 4,422,623 10.91% 4,262,279 96.37% 6,723,972 0.68 369
Figure 1 Hi-C insert distribution. The distribution of genomic distances between Hi-C read pairs is
shown for read pairs mapping to each chromosome. For each read pair the minimum path length on
the circular chromosome was calculated and read pairs separated by less than 1000 bp were discarded.
The 2.5 Mb range was divided into 100 bins of equal size and the number of read pairs in each bin
was recorded for each chromosome. Bin values for each chromosome were normalized to sum to 1 and
plotted.
E. coli K12 genome were distributed in a similar manner as previously reported (Fig. 1;
(Lieberman-Aiden et al., 2009)). We observed a minor depletion of alignments spanning
the linearization point of the E. coli K12 assembly (e.g., near coordinates 0 and 4686137)
due to edge eVects induced by BWA treating the sequence as a linear chromosome rather
than circular.
10.7717/peerj.415 9/19
Figure 2 Metagenomic Hi-C associations. The log-scaled, normalized number of Hi-C read pairs
associating each genomic replicon in the synthetic community is shown as a heat map (see color scale,
blue to yellow: low to high normalized, log scaled association rates). Bur1: B. thailandensis chromosome
1. Bur2: B. thailandensis chromosome 2. Lac0: L. brevis chromosome, Lac1: L. brevis plasmid 1, Lac2:
L. brevis plasmid 2, Ped: P. pentosaceus, K12: E. coli K12 DH10B, BL21: E. coli BL21.
reference assemblies of the members of our synthetic microbial community with the same
alignment parameters as were used in the top ranked clustering (described above). We first
Figure 3 Contigs associated by Hi-C reads. A graph is drawn with nodes depicting contigs and edges
depicting associations between contigs as indicated by aligned Hi-C read pairs, with the count thereof
depicted by the weight of edges. Nodes are colored to reflect the species to which they belong (see legend)
with node size reflecting contig size. Contigs below 5 kb and edges with weights less than 5 were excluded.
Contig associations were normalized for variation in contig size.
typically represent the reads and variant sites as a variant graph wherein variant sites are
represented as nodes, and sequence reads define edges between variant sites observed in
the same read (or read pair). We reasoned that variant graphs constructed from Hi-C
data would have much greater connectivity (where connectivity is defined as the mean
path length between randomly sampled variant positions) than graphs constructed from
mate-pair sequencing data, simply because Hi-C inserts span megabase distances. Such
Figure 4 Hi-C contact maps for replicons of Lactobacillus brevis. Contact maps show the number of
Hi-C read pairs associating each region of the L. brevis genome. The L. brevis chromosome (Lac0, (A),
Chris Beitel
@datscimed
Aaron Darling
@koadman

22. 12
C, 12
C14
N, 32
S
Wilbanks, E.G. et al (2014). Environmental Microbiology
Transfer of 34
S from SRB to PSB
Lizzy Wilbanks
@lizzywilbanks
34S-incorporation Biomass
NanoSIMS to Localize Processes

23. Opportunity 3: Whole Systems
Mom The Microbes We Eat
PetsBuilt
Environment
Other People
All Taxa

24. Opportunity 4: Outreach, Training, Community

25. Opportunity 5: Citizen Science
Kitty Microbiome

26. UCD Microbiome Center
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Everything (or, at least a lot) about Microbiology at UC Davis
Posted on May 31, 2014 by Jonathan Eisen
So – getting lots of calls and emails and having local meetings with people interested in microbiology at UC
Davis. Rather than continuing to answer each person separately I am just going to put everything together on
this page. Departments and groups with a major focus on microbiology.
Microbiology and Molecular Genetics in the College of Biological Sciences
Pathology, Microbiology and Immunology in the School of Veterinary Medicine
Medical Microbiology and Immunology in the School of Medicine
Plant Pathology
Department of Pathology in the School of Medicine
Department of Internal Medicine Division of Infectious Diseases in the School of Medicine
USDA ARS Crop Pathology and Genetics Group
Departments with a lot of people working on microbiology
Food Science Technology
Viticulture and Enology
Graduate Groups with a Major Focus on Microbiology
Microbiology
Plant Pathology
Epidemiology
Soils and Biogeochemistry
Food Science and Technology
Educational Programs and Courses
Microbiology Major
UC Davis Chapter of ASM
Medical Microbiology and Immunology Courses
Plant Pathology Courses
Microbiology Courses
Vetmed: Pathology, Microbiology and Immunology Courses
UC Davis iGEM
Other related entitites
Coccidioidomycosis Serology Laboratory
Clinical Laboratory – UC Davis Health System
Faculty Studying Host Microbe Interactions
Host-Microbe Interactions Retreat
Center for Vectorborne Diseases
Host-Microbe Systems Biology Core
Seminars
Emerging Challenges in Microbiology and Immunology Seminars
Plant Pathology Seminar Series
Microbiology and Molecular Genetics Seminars
MIC291 Seminars
Individual People / Faculty / Groups with an Emphasis on Something Microbial (I am including people who
have expressed interest in microbial related work even if they may not yet be doing much).
1. Jason Adams. Pulmonary and Critical Care, SOM.
2. John Adaska. Pathology, Microbiology Immunology, SVM.
3. Mark Anderson. Pathology, Microbiology Immunology, SVM.
4. Charles Bamforth. Food Science and Technology, CAES.
5. Nicole Baumgarth. Pathology, Microbiology Immunology, SVM.
6. Kendra Baumgartner. Crops Pathology and Genetics Research, USDA ARS.
7. Andreas Baumler. Medical Microbiology and Immunology, SOM.
8. Danielle Barille. Food Science and Technology. CAES.
9. Jacqueline Barlow.
10. Peter Barry.
11. Ramie Begum. Medical Microbiology and Immunology, SOM.
12. Alison Berry. Plant Sciences, CAES.
13. Alan Bennett, Plant Sciences, CAES.
14. Charles Bevins. Medical Microbiology and Immunology, SOM.
15. Linda Bisson, Viticulture and Enology.
16. David Block, Department of Chemical Engineering and Materials Science, COE.
17. Dori Borjesson. Pathology, Microbiology Immunology, SVM.
18. Richard Bostock. Plant Pathology. CAES.
19. Kyria Boundary-Mills. Food Science and Technology. CAES.
20. Walter Boyce. Pathology, Microbiology Immunology, SVM.
21. C. Titus Brown. Population, Health, and Reproduction, SVM.
22. Greg Browne. Crops Pathology and Genetics Research, USDA ARS.
23. Barbara Byrne. Pathology, Microbiology Immunology, SVM.
24. Silvia Carrasco
25. Claire Casteel. Plant Pathology. CAES.
26. Kristen Clothier. Pathology, Microbiology Immunology, SVM.
27. Gitta Coaker. Plant Pathology. CAES.
28. Sean Collins. Microbiology and Molecular Genetics. CBS.
29. Pat Conrad. Pathology, Microbiology Immunology, SVM.
30. Doug Cook. Plant Pathology. CAES.
31. Abhaya Dandekar. Plant Sciences. CAES.
32. Satya Dandekar. Medical Microbiology and Immunology, School of Medicine
33. Michael Davis. Plant Pathology. CAES.
34. Scott Dawson. Microbiology and Molecular Genetics. CBS.
35. Jason DeJong. Civil and Environmental Engineering.
36. Kathy DeRiemer. Medical Microbiology and Immunology, School of Medicine
37. Savithram Dinesh-Kumar. Plant Biology. CBS.
38. Jonathan Eisen. Evolution and Ecology, CBS. Medical Microbiology and Immunology, SOM.
39. Lynn Epstein. Plant Pathology. CAES.
40. Marc Facciotti. Biomedical Engineering. SOE.
41. Bryce Falk. Plant Pathology. CAES.
42. Julia Fan. Biological and Agricultural Engineering. SOE.
43. Janet Foley. Medicine Epidemiology. SVM.
44. Heather Fritz. Pathology, Microbiology Immunology, SVM.
45. Amelie Gaudin, Plant Sciences,
46. Angie Gelli. Pharmacology. SOM.
47. Michael George. Medical Microbiology and Immunology, SOM.
48. J. Bruce German. Food Science and Technology. CAES.
49. Laurel Gershwin. Pathology, Microbiology Immunology, SVM.
50. M. Eric Gershwin. Rheumatology. SOM.
51. Thomas R. Gordon. Plant Pathology. CAES.
52. W. Douglas Gubler. Plant Pathology. CAES.
53. Linda Harris. Food Science and Technology. CAES.
54. Dennis J Hartigan. Medical Microbiology and Immunology, SOM.
55. Volkmar Heinrich. Biomedical Engineering. SOE.
56. Wolf-Dietrich Heyer. Microbiology and Molecular Genetics. CBS.
57. James Hildreth. Molecular and Cellular Biology. CBS.
58. Neil Hunter. Microbiology and Molecular Genetics. CBS.
59. Michele Igo. Microbiology and Molecular Genetics. CBS.
60. Louise Jackson. Department of Land, Air, and Water Resources.
61. Kevin Keel. Pathology, Microbiology Immunology, SVM.
62. Hailu Kinde. Pathology, Microbiology Immunology, SVM.
63. Bruce C. Kirkpatrick. Plant Pathology. CAES.
64. Steve Kowalczykowski. Microbiology and Molecular Genetics. CBS.
65. Dan Kluepfel. Crops Pathology and Genetics Research, USDA ARS.
66. John Labavitch. Plant Sciences. CAES.
67. Michael Lairmore. Pathology, Microbiology Immunology, SVM.
68. Gregory Lanzaro. Pathology, Microbiology Immunology, SVM.
69. Rance LeFebvre. Pathology, Microbiology Immunology, SVM.
70. Patrick Leung. Rheumatology, Allergy and Clinical Immunology. SOM.
71. Johan Leveau. Plant Pathology. CAES.
72. Michael Liebowitz. Medical Microbiology and Immunology, SOM.
73. Su-Ju Lin. Microbiology and Molecular Genetics. CBS
74. Bo Liu. Plant Biology. CBS.
75. Frank Loge. Department of Civil and Environmental Engineering, SOE.
76. Paul Luciw. Medical Pathology and Laboratory Medicine. SOM.
77. Shirley Luckhart. Medical Microbiology and Immunology, SOM.
78. N. James MacLachlan. Pathology, Microbiology Immunology, SVM.
79. Elizabeth Maga. Animal Sciences.
80. Maria Marco. Food Science and Technology. CAES.
81. Neil McRoberts. Plant Pathology. CAES.
82. Stephen Mcsorley.
83. Asli Mete. Pathology, Microbiology Immunology, SVM.
84. Jack Meeks. Microbiology and Molecular Genetics. CBS.
85. Themis Michailides.
86. Richard Michelmore.
87. Christopher J. Miller. Pathology, Microbiology Immunology, SVM.
88. Woutrina A. Miller. Pathology, Microbiology Immunology, SVM.
89. David Mills. Food Science and Technology. CAES.
90. Robert Moeller. Pathology, Microbiology Immunology, SVM.
91. Brian Murphy. Pathology, Microbiology Immunology, SVM.
92. Lorena Navarro. Microbiology and Molecular Genetics. CBS.
93. Doug Nelson. Microbiology and Molecular Genetics. CBS.
94. Edward Panacek. Emergency Medicine. SOM.
95. Becky Parales. Microbiology and Molecular Genetics. CBS.
96. Demosthenes Pappagianis. Medical Microbiology and Immunology, SOM.
97. Niels Pedersen. Medicine and Epidemiology, SVM.
98. Patricia Pesavento. Pathology, Microbiology Immunology, SVM.
99. Chris Polage. Medical Pathology and Laboratory Medicine. SOM
100. Chester Price.
101. Katherine Ralston, Microbiology and Molecular Genetics, CBS
102. William Reisen. Pathology, Microbiology Immunology, SVM.
103. David Rizzo. Plant Pathology. CAES.
104. Jorge Rodrigues, Department of Land, Air, and Water Resources.
105. Pamela Ronald.
106. Jeff Ross-Ibarra. Plant Sciences.
107. John Roth. Microbiology and Molecular Genetics. CBS.
108. Sumathi Sankaran. Medical Microbiology and Immunology, SOM.
109. Michael Savageau. Biomedical Engineering. SOE.
110. Jeffrey L. Scott. Pathology, Microbiology Immunology, SVM.
111. Thomas W. Scott. Entomology.
112. Kate Scow. Department of Land, Air, and Water Resources.
113. Barbara Shacklett. Medical Microbiology and Immunology, SOM.
114. Kaz Shiozaki. Microbiology and Molecular Genetics. CBS.
115. Christopher Simmons. Food Science and Technology. CAES.
116. Mitch Singer. Microbiology and Molecular Genetics. CBS.
117. Jay Solnick. Medical Microbiology and Immunology, SOM.
118. Athena Soulika. Dermatology. SOM.
119. Ellen E. Sparger.
120. Charles Stephensen. Immunity and Disease Prevention Research Unit. USDA ARS.
121. Ioannis (Yiannis) Stergiopoulos. Plant Pathology. CAES.
122. Valley Stewart. Microbiology and Molecular Genetics. CBS.
123. Jeffrey Stott. Pathology, Microbiology Immunology, SVM.
124. Sharon Strauss. Evolution and Ecology, CBS.
125. Dawn Y Sumner. Earth and Planetary Sciences.
126. Mysore Sudarshana. Plant Pathology. CAES.
127. Venketesan Sundaresan, Plant Biology, CBS.
128. Michael Syvanen. Medical Microbiology and Immunology, SOM.
129. Ilias Tagkopoulos. Computer Science. SOE.
130. George Thompson. Medical Microbiology and Immunology, SOM.
131. Jose Torres. Medical Microbiology and Immunology, SOM.
132. Renee Tsolis. Medical Microbiology and Immunology, SOM.
133. Michael Turelli. Evolution and Ecology, CBS.
134. Diane Ullman. Entomology and Nematology.
135. Mark Underwood. Pediatrics. SOM.
136. Francisco Uzal. Pathology, Microbiology Immunology, SVM.
137. Neal Van Alfen. Plant Pathology. CAES.
138. Mariel Vasquez. Microbiology and Molecular Genetics. CBS. Also in Mathematics.
139. Bart Weimer. Pathology, Microbiology Immunology, SVM.
140. Andrew Whitehead.
141. Carl Winter. Food Science and Technology. CAES.
142. Leslie Woods. Pathology, Microbiology Immunology, SVM
143. Stefan Wuertz. Civil and Environmental Engineering. SOE.
144. Tilahun Yilma. Medical Microbiology and Immunology, SOM.
145. Glenn Young. Food Science and Technology. CAES.
146. Ruihong Zhang. Biological and Agricultural Engineering. SOE.
147. Huaijun Zhou. Animal Science.
148. Xiangdong Zhu. Physics.
149. Angela Zivcovik. Food Science and Technology. CAES.
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27. Acknowledgements
DOE JGI Sloan GBMF NSF
DHS DARPA
Aaron Darling
Lizzy
Wilbanks
Jenna Lang Russell
Neches
Rob Knight
Jack Gilbert Tanja Woyke Rob Dunn
Katie Pollard
Jessica
Green
Darlene
Cavalier
Eddy RubinWendy Brown
Dongying Wu
Phil
Hugenholtz
DSMZ
Sundar
Srijak
Bhatnagar David Coil
Alex Alexiev
Hannah
Holland-Moritz
Holly Bik
John Zhang
Holly
Menninger
Guillaume
Jospin
David Lang
Cassie
Ettinger
Tim HarkinsJennifer Gardy
Holly Ganz