Talk for UC Davis Host-Microbe Interactions Retreat 2015

1. Phylogeny driven approaches
to the study of microbiome diversity
November 5, 2015
UC Davis
Host-Microbe Interactions Retreat
Jonathan A. Eisen
@phylogenomics
University of California, Davis

2. The Rise of the Microbiome
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500
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4500
1956
1958
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1963
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1965
1966
1967
1968
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1981
1982
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1991
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2011
2012
2013
2014
Pubmed Hits to Microbiome vs. Year

3. 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.
Challenge 1: Complexity
Microbial Diversity
Microbial Diversity2 Fragmented Data
Host Variation
http://bit.ly/HumanMicrobiome
Functional
Diversity

4. Challenge 2: Public Understanding
Germophobia Microbiomania

5. Woese: Classification of Cultured Taxa by rRNA PCR
!6
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
EukaryotesBacteria ?????ArchaebacteriaArchaea

6. ACTGC
ACCTAT
CGTTCG
ACTCC
AGCTAT
CGATCG
ACCCC
AGCTCT
CGCTCG
AGGGG
AGCTCT
CGCTCG
AGGGG
AGCTCT
CGCTCG
ACTGC
ACCTAT
CGTTCG
Taxa Characters
B1 ACTGCACCTATCGTTCG
B2 ACTCCACCTATCGTTCG
E1 ACTCCAGCTATCGATCG
E2 ACTCCAGGTATCGATCG
A1 ACCCCAGCTCTCGCTCG
A2 ACCCCAGCTCTGGCTCG
New1 ACCCCAGCTCTGCCTCG
New2 ACTGCACCTATCGTTCG
New3 ACCCCAGCTCTCGCTCG
New4 AGGGGAGCTCTCGCTCG
Archaea EukaryotesBacteria
!7
rRNA
rRNA
PCR
rRNA
PCR
Isolate DNA
Phylotyping via rRNA PCR: Four Taxa

7. Automation is Critical

8. STAP (for rRNA)
An Automated Phylogenetic Tree-Based Small Subunit
rRNA Taxonomy and Alignment Pipeline (STAP)
Dongying Wu1
*, Amber Hartman1,6
, Naomi Ward4,5
, Jonathan A. Eisen1,2,3
1 UC Davis Genome Center, University of California Davis, Davis, California, United States of America, 2 Section of Evolution and Ecology, College of Biological Sciences,
University of California Davis, Davis, California, United States of America, 3 Department of Medical Microbiology and Immunology, School of Medicine, University of
California Davis, Davis, California, United States of America, 4 Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America,
5 Center of Marine Biotechnology, Baltimore, Maryland, United States of America, 6 The Johns Hopkins University, Department of Biology, Baltimore, Maryland, United
States of America
Abstract
Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know
about the phylogenetic diversity of both cultured and uncultured microorganisms. As sequencing costs continue to decline
and throughput increases, sequences of ss-rRNA genes are being obtained at an ever-increasing rate. This increasing flow of
data has opened many new windows into microbial diversity and evolution, and at the same time has created significant
methodological challenges. Those processes which commonly require time-consuming human intervention, such as the
preparation of multiple sequence alignments, simply cannot keep up with the flood of incoming data. Fully automated
methods of analysis are needed. Notably, existing automated methods avoid one or more steps that, though
computationally costly or difficult, we consider to be important. In particular, we regard both the building of multiple
sequence alignments and the performance of high quality phylogenetic analysis to be necessary. We describe here our fully-
automated ss-rRNA taxonomy and alignment pipeline (STAP). It generates both high-quality multiple sequence alignments
and phylogenetic trees, and thus can be used for multiple purposes including phylogenetically-based taxonomic
assignments and analysis of species diversity in environmental samples. The pipeline combines publicly-available packages
(PHYML, BLASTN and CLUSTALW) with our automatic alignment, masking, and tree-parsing programs. Most importantly,
this automated process yields results comparable to those achievable by manual analysis, yet offers speed and capacity that
are unattainable by manual efforts.
Citation: Wu D, Hartman A, Ward N, Eisen JA (2008) An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP). PLoS
ONE 3(7): e2566. doi:10.1371/journal.pone.0002566
multiple alignment and phylogeny was deemed unfeasible.
However, this we believe can compromise the value of the results.
For example, the delineation of OTUs has also been automated
via tools that do not make use of alignments or phylogenetic trees
(e.g., Greengenes). This is usually done by carrying out pairwise
comparisons of sequences and then clustering of sequences that
have better than some cutoff threshold of similarity with each
other). This approach can be powerful (and reasonably efficient)
but it too has limitations. In particular, since multiple sequence
alignments are not used, one cannot carry out standard
phylogenetic analyses. In addition, without multiple sequence
alignments one might end up comparing and contrasting different
regions of a sequence depending on what it is paired with.
The limitations of avoiding multiple sequence alignments and
phylogenetic analysis are readily apparent in tools to classify
sequences. For example, the Ribosomal Database Project’s
Classifier program [29] focuses on composition characteristics of
each sequence (e.g., oligonucleotide frequency) and assigns
taxonomy based upon clustering genes by their composition.
Though this is fast and completely automatable, it can be misled in
cases where distantly related sequences have converged on similar
composition, something known to be a major problem in ss-rRNA
sequences [30]. Other taxonomy assignment systems focus
primarily on the similarity of sequences. The simplest of these is
classification tools it does have some limitations. For example,
the generation of new alignments for each sequence is both
computational costly, and does not take advantage of available
curated alignments that make use of ss-RNA secondary structure
to guide the primary sequence alignment. Perhaps most
importantly however is that the tool is not fully automated. In
addition, it does not generate multiple sequence alignments for all
sequences in a dataset which would be necessary for doing many
analyses.
Automated methods for analyzing rRNA sequences are also
available at the web sites for multiple rRNA centric databases,
such as Greengenes and the Ribosomal Database Project (RDPII).
Though these and other web sites offer diverse powerful tools, they
do have some limitations. For example, not all provide multiple
sequence alignments as output and few use phylogenetic
approaches for taxonomy assignments or other analyses. More
importantly, all provide only web-based interfaces and their
integrated software, (e.g., alignment and taxonomy assignment),
cannot be locally installed by the user. Therefore, the user cannot
take advantage of the speed and computing power of parallel
processing such as is available on linux clusters, or locally alter and
potentially tailor these programs to their individual computing
needs (Table 1).
Given the limited automated tools that are available for
Table 1. Comparison of STAP’s computational abilities relative to existing commonly-used ss-RNA analysis tools.
STAP ARB Greengenes RDP
Installed where? Locally Locally Web only Web only
User interface Command line GUI Web portal Web portal
Parallel processing YES NO NO NO
Manual curation for taxonomy assignment NO YES NO NO
Manual curation for alignment NO YES NO* NO
Open source YES** NO NO NO
Processing speed Fast Slow Medium Medium
It is important to note, that STAP is the only software that runs on the command line and can take advantage of parallel processing on linux clusters and, further, is
more amenable to downstream code manipulation.
*
Note: Greengenes alignment output is compatible with upload into ARB and downstream manual alignment.
**
The STAP program itself is open source, the programs it depends on are freely available but not open source.
doi:10.1371/journal.pone.0002566.t001
ss-rRNA Taxonomy Pipeline
STAP database, and the query sequence is aligned to them using
the CLUSTALW profile alignment algorithm [40] as described
above for domain assignment. By adapting the profile alignment
algorithm, th
while gaps ar
sequence ac
Figure 1. A flow chart of the STAP pipeline.
doi:10.1371/journal.pone.0002566.g001
STAP database, and the query sequence is aligned to them using
the CLUSTALW profile alignment algorithm [40] as described
above for domain assignment. By adapting the profile alignment
algorithm, the alignments from the STAP database remain intact,
while gaps are inserted and nucleotides are trimmed for the query
sequence according to the profile defined by the previous
alignments from the databases. Thus the accuracy and quality of
the alignment generated at this step depends heavily on the quality
of the Bacterial/Archaeal ss-rRNA alignments from the
Greengenes project or the Eukaryotic ss-rRNA alignments from
the RDPII project.
Phylogenetic analysis using multiple sequence alignments rests on
the assumption that the residues (nucleotides or amino acids) at the
same position in every sequence in the alignment are homologous.
Thus, columns in the alignment for which ‘‘positional homology’’
cannot be robustly determined must be excluded from subsequent
analyses. This process of evaluating homology and eliminating
questionable columns, known as masking, typically requires time-
consuming, skillful, human intervention. We designed an automat-
ed masking method for ss-rRNA alignments, thus eliminating this
bottleneck in high-throughput processing.
First, an alignment score is calculated for each aligned column
by a method similar to that used in the CLUSTALX package [42].
Specifically, an R-dimensional sequence space representing all the
possible nucleotide character states is defined. Then for each
aligned column, the nucleotide populating that column in each of
the aligned sequences is assigned a score in each of the R
dimensions (Sr) according to the IUB matrix [42]. The consensus
‘‘nucleotide’’ for each column (X) also has R dimensions, with the
Figure 2. Domain assignment. In Step 1, STAP assigns a domain to
each query sequence based on its position in a maximum likelihood
tree of representative ss-rRNA sequences. Because the tree illustrated
here is not rooted, domain assignment would not be accurate and
Figure 1. A flow chart of the STAP pipeline.
doi:10.1371/journal.pone.0002566.g001
ss-rRNA Taxonomy Pipeline
Dongying
Wu
Amber
Hartman
Naomi Ward

9. Hartman et al. BMC Bioinformatics 2010, 11:317
http://www.biomedcentral.com/1471-2105/11/317
Open AccessSOFTWARE
Software
Introducing W.A.T.E.R.S.: a Workflow for the
Alignment, Taxonomy, and Ecology of Ribosomal
Sequences
Amber L Hartman†1,3, Sean Riddle†2, Timothy McPhillips2, Bertram Ludäscher2 and Jonathan A Eisen*1
Abstract
Background: For more than two decades microbiologists have used a highly conserved microbial gene as a
phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is
encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over
time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive
collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of
data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA
sequence analysis has increased correspondingly.
Results: We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16
S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera
removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological
analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-
source Kepler system as a platform.
Conclusions: By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA
analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like
some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying
out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One
advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result
interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the
workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-
to-combine tools for asking increasingly complex microbial ecology questions.
Background
Microbial communities and how they are surveyed
Microbial communities abound in nature and are crucial
for the success and diversity of ecosystems. There is no
end in sight to the number of biological questions that
can be asked about microbial diversity on earth. From
animal and human guts to open ocean surfaces and deep
sea hydrothermal vents, to anaerobic mud swamps or
boiling thermal pools, to the tops of the rainforest canopy
and the frozen Antarctic tundra, the composition of
microbial communities is a source of natural history,
intellectual curiosity, and reservoir of environmental
health [1]. Microbial communities are also mediators of
insight into global warming processes [2,3], agricultural
success [4], pathogenicity [5,6], and even human obesity
[7,8].
In the mid-1980 s, researchers began to sequence ribo-
somal RNAs from environmental samples in order to
characterize the types of microbes present in those sam-
ples, (e.g., [9,10]). This general approach was revolution-
ized by the invention of the polymerase chain reaction
(PCR), which made it relatively easy to clone and then
* Correspondence: jaeisen@ucdavis.edu
1 Department of Medical Microbiology and Immunology and the Department
of Evolution and Ecology, Genome Center, University of California Davis, One
Shields Avenue, Davis, CA, 95616, USA
† Contributed equally
Full list of author information is available at the end of the article
WATERS - Kepler Workflow for rRNA
matics 2010, 11:317
.com/1471-2105/11/317
Page 2 of 14
genes for ribosomal RNA) in partic-
ubunit ribosomal RNA (ss-rRNA).
ed a large amount of previously
l diversity [1,11-13]. Researchers
all subunit rRNA gene not only
ith which it can be PCR amplified,
has variable and highly conserved
to be universally distributed among
nd it is useful for inferring phyloge-
4,15]. Since then, "cultivation-inde-
" have brought a revolution to the
by allowing scientists to study a
mount of diversity in many different
ments [16-18]. The general premise
Figure 1 Overview of WATERS. Schema of WATERS where white
boxes indicate "behind the scenes" analyses that are performed in WA-
Align
Check
chimeras
Cluster Build
Tree
Assign
Taxonomy
Tree w/
Taxonomy
Diversity
statistics &
graphs
Unifrac
files
Cytoscape
network
OTU table
Hartman et al. BMC Bioinformatics 2010, 11:317
http://www.biomedcentral.com/1471-2105/11/317
Page 3 of 14
Motivations
As outlined above, successfully processing microbial
sequence collections is far from trivial. Each step is com-
plex and usually requires significant bioinformatics
expertise and time investment prior to the biological
interpretation. In order to both increase efficiency and
ensure that all best-practice tools are easily usable, we
sought to create an "all-inclusive" method for performing
all of these bioinformatics steps together in one package.
To this end, we have built an automated, user-friendly,
workflow-based system called WATERS: a Workflow for
the Alignment, Taxonomy, and Ecology of Ribosomal
Sequences (Fig. 1). In addition to being automated and
simple to use, because WATERS is executed in the Kepler
scientific workflow system (Fig. 2) it also has the advan-
tage that it keeps track of the data lineage and provenance
of data products [23,24].
Automation
The primary motivation in building WATERS was to
minimize the technical, bioinformatics challenges that
arise when performing DNA sequence clustering, phylo-
genetic tree, and statistical analyses by automating the 16
S rDNA analysis workflow. We also hoped to exploit
additional features that workflow-based approaches
entail, such as optimized execution and data lineage
tracking and browsing [23,25-27]. In the earlier days of 16
S rDNA analysis, simply knowing which microbes were
present and whether they were biologically novel was a
noteworthy achievement. It was reasonable and expected,
therefore, to invest a large amount of time and effort to
get to that list of microbes. But now that current efforts
are significantly more advanced and often require com-
parison of dozens of factors and variables with datasets of
thousands of sequences, it is not practically feasible to
process these large collections "by hand", and hugely inef-
ficient if instead automated methods can be successfully
employed.
Broadening the user base
A second motivation and perspective is that by minimiz-
ing the technical difficulty of 16 S rDNA analysis through
the use of WATERS, we aim to make the analysis of these
datasets more widely available and allow individuals with
Figure 2 Screenshot of WATERS in Kepler software. Key features: the library of actors un-collapsed and displayed on the left-hand side, the input
and output paths where the user declares the location of their input files and desired location for the results files. Each green box is an individual Kepler
actor that performs a single action on the data stream. The connectors (black arrows) direct and hook up the actors in a defined sequence. Double-
clicking on any actor or connector allows it to be manipulated and re-arranged.
Hartman et al. BMC Bioinformatics 2010, 11:317
http://www.biomedcentral.com/1471-2105/11/317
Page 9 of
default is 97% and 99%), and they are also generated for
every metadata variable comparison that the user
includes.
Data pruning
To assist in troubleshooting and quality contro
WATERS returns to the user three fasta files of sequenc
Figure 3 Biologically similar results automatically produced by WATERS on published colonic microbiota samples. (A) Rarefaction curves sim
ilar to curves shown in Eckburg et al. Fig. 2; 70-72, indicate patient numbers, i.e., 3 different individuals. (B) Weighted Unifrac analysis based on phylo
genetic tree and OTU data produced by WATERS very similar to Eckburg et al. Fig. 3B. (C) Neighbor-joining phylogenetic tree (Quicktree) representing
the sequences analyzed by WATERS, which is clearly similar to Fig. S1 in Eckburg et al.
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10. Similarity vs. Phylogeny
!11

11. Automation is Critical

12. alignment used to build the profile, resulting in a multiple
sequence alignment of full-length reference sequences and
metagenomic reads. The final step of the alignment process is a
quality control filter that 1) ensures that only homologous SSU-
rRNA sequences from the appropriate phylogenetic domain are
included in the final alignment, and 2) masks highly gapped
alignment columns (see Text S1).
We use this high quality alignment of metagenomic reads and
references sequences to construct a fully-resolved, phylogenetic
tree and hence determine the evolutionary relationships between
the reads. Reference sequences are included in this stage of the
analysis to guide the phylogenetic assignment of the relatively
short metagenomic reads. While the software can be easily
extended to incorporate a number of different phylogenetic tools
capable of analyzing metagenomic data (e.g., RAxML [27],
pplacer [28], etc.), PhylOTU currently employs FastTree as a
PD versus PID clustering, 2) to explore overlap between PhylOTU
clusters and recognized taxonomic designations, and 3) to quantify
the accuracy of PhylOTU clusters from shotgun reads relative to
those obtained from full-length sequences.
PhylOTU Clusters Recapitulate PID Clusters
We sought to identify how PD-based clustering compares to
commonly employed PID-based clustering methods by applying
the two methods to the same set of sequences. Both PID-based
clustering and PhylOTU may be used to identify OTUs from
overlapping sequences. Therefore we applied both methods to a
dataset of 508 full-length bacterial SSU-rRNA sequences (refer-
ence sequences; see above) obtained from the Ribosomal Database
Project (RDP) [25]. Recent work has demonstrated that PID is
more accurately calculated from pairwise alignments than multiple
sequence alignments [32–33], so we used ESPRIT, which
Figure 1. PhylOTU Workflow. Computational processes are represented as squares and databases are represented as cylinders in this generalize
workflow of PhylOTU. See Results section for details.
doi:10.1371/journal.pcbi.1001061.g001
Finding Metagenomic OTUs
Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer
JP, Green JL, Eisen JA, Pollard KS. (2011) PhylOTU: A High-
Throughput Procedure Quantifies Microbial Community
Diversity and Resolves Novel Taxa from Metagenomic Data.
PLoS Comput Biol 7(1): e1001061. doi:10.1371/journal.pcbi.
1001061
OTUs via Phylogeny (PhylOTU)
Tom
Sharpton
Katie
Pollard
Jessica
Green
Finding Metagenomic OTUs

13. Opportunity 2: Dealing w/ rRNA Issues

14. rRNA Gene Copy # Variation
Vetrovsky T, Baldrian P (2013) The Variability of the 16S rRNA Gene in Bacterial Genomes and Its
Consequences for Bacterial Community Analyses. PLoS ONE 8(2): e57923. doi:10.1371/journal.pone.
0057923

15. Copy # Affects Relative Abundance Estimates
Kembel SW, Wu M, Eisen JA, Green JL (2012)
Incorporating 16S Gene Copy Number
Information Improves Estimates of Microbial
Diversity and Abundance. PLoS Comput Biol
8(10): e1002743. doi:10.1371/journal.pcbi.
1002743
Steven
Kembel
Jessica
Green
Martin
Wu

16. rRNA Copy # vs. Phylogeny
Steven
Kembel
Jessica
Green
Martin
Wu
Kembel SW, Wu M, Eisen JA, Green JL (2012)
Incorporating 16S Gene Copy Number
Information Improves Estimates of Microbial
Diversity and Abundance. PLoS Comput Biol
8(10): e1002743. doi:10.1371/journal.pcbi.
1002743

17. rRNA Phylogeny Copy # Correction
Steven
Kembel
Jessica
Green
Martin
Wu
Phylogeny-Independent Contrasts
method of Felsenstein can be
used to estimate copy number
based on tree
Kembel SW, Wu M, Eisen JA, Green JL (2012)
Incorporating 16S Gene Copy Number
Information Improves Estimates of Microbial
Diversity and Abundance. PLoS Comput Biol
8(10): e1002743. doi:10.1371/journal.pcbi.
1002743

18. Corrected Copy Number Changes Inferences
Steven
Kembel
Jessica
Green
Martin
Wu
Kembel SW, Wu M, Eisen JA, Green JL (2012)
Incorporating 16S Gene Copy Number
Information Improves Estimates of Microbial
Diversity and Abundance. PLoS Comput Biol
8(10): e1002743. doi:10.1371/journal.pcbi.
1002743

19. AMPHORA
Martin
Wu

20. Automated Accurate Genome Tree
Lang JM, Darling AE, Eisen JA (2013) Phylogeny of
Bacterial and Archaeal Genomes Using Conserved
Genes: Supertrees and Supermatrices. PLoS ONE
8(4): e62510. doi:10.1371/journal.pone.0062510
Jenna
Lang
Aaron
Darling

21. Opportunity 3: Interpreting Metagenomes

22. Metagenomics
metagenomics
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaea

23. Culture Independent “Metagenomics”
DNA DNADNA
!24
Taxa Characters
B1 ACTGCACCTATCGTTCG
B2 ACTCCACCTATCGTTCG
E1 ACTCCAGCTATCGATCG
E2 ACTCCAGGTATCGATCG
A1 ACCCCAGCTCTCGCTCG
A2 ACCCCAGCTCTGGCTCG
New1 ACCCCAGCTCTGCCTCG
New2 AGGGGAGCTCTGCCTCG
New3 ACTCCAGCTATCGATCG
New4 ACTGCACCTATCGTTCG
RecA RecARecA
http://genomebiology.com/2008/9/10/R151 Genome Biology 2008, Volume 9, Issue 10, Article R151 Wu and Eisen R151.7
Genome Biology 2008, 9:R151
sequences are not conserved at the nucleotide level [29]. As a
result, the nr database does not actually contain many more
protein marker sequences that can be used as references than
those available from complete genome sequences.
Comparison of phylogeny-based and similarity-based phylotyping
Although our phylogeny-based phylotyping is fully auto-
mated, it still requires many more steps than, and is slower
than, similarity based phylotyping methods such as a
MEGAN [30]. Is it worth the trouble? Similarity based phylo-
typing works by searching a query sequence against a refer-
ence database such as NCBI nr and deriving taxonomic
information from the best matches or 'hits'. When species
that are closely related to the query sequence exist in the ref-
erence database, similarity-based phylotyping can work well.
However, if the reference database is a biased sample or if it
contains no closely related species to the query, then the top
hits returned could be misleading [31]. Furthermore, similar-
ity-based methods require an arbitrary similarity cut-off
value to define the top hits. Because individual bacterial
genomes and proteins can evolve at very different rates, a uni-
versal cut-off that works under all conditions does not exist.
As a result, the final results can be very subjective.
In contrast, our tree-based bracketing algorithm places the
query sequence within the context of a phylogenetic tree and
only assigns it to a taxonomic level if that level has adequate
sampling (see Materials and methods [below] for details of
the algorithm). With the well sampled species Prochlorococ-
cus marinus, for example, our method can distinguish closely
related organisms and make taxonomic identifications at the
species level. Our reanalysis of the Sargasso Sea data placed
672 sequences (3.6% of the total) within a P. marinus clade.
On the other hand, for sparsely sampled clades such as
Aquifex, assignments will be made only at the phylum level.
Thus, our phylogeny-based analysis is less susceptible to data
sampling bias than a similarity based approach, and it makes
Major phylotypes identified in Sargasso Sea metagenomic dataFigure 3
Major phylotypes identified in Sargasso Sea metagenomic data. The metagenomic data previously obtained from the Sargasso Sea was reanalyzed using
AMPHORA and the 31 protein phylogenetic markers. The microbial diversity profiles obtained from individual markers are remarkably consistent. The
breakdown of the phylotyping assignments by markers and major taxonomic groups is listed in Additional data file 5.
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Alphaproteobacteria
Betaproteobacteria
G
am
m
aproteobacteria
D
eltaproteobacteria
Epsilonproteobacteria
U
nclassified
proteobacteria
Bacteroidetes
C
hlam
ydiae
C
yanobacteria
Acidobacteria
Therm
otogae
Fusobacteria
ActinobacteriaAquificae
Planctom
ycetes
Spirochaetes
Firm
icutes
C
hloroflexiC
hlorobi
U
nclassified
bacteria
dnaG
frr
infC
nusA
pgk
pyrG
rplA
rplB
rplC
rplD
rplE
rplF
rplK
rplL
rplM
rplN
rplP
rplS
rplT
rpmA
rpoB
rpsB
rpsC
rpsE
rpsI
rpsJ
rpsK
rpsM
rpsS
smpB
tsf
Relativeabundance
RpoB RpoBRpoB
Rpl4 Rpl4Rpl4 rRNA rRNArRNA
Hsp70 Hsp70Hsp70
EFTu EFTuEFTu
Many other genes
better than rRNA

24. AMPHORA
AMPHORA

25. Phylotyping w/ Protein Markers
AMPHORA
http://genomebiology.com/2008/9/10/R151 Genome Biology 2008, Volume 9, Issue 10, Article R151 Wu and Eisen R151.7
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Alphaproteobacteria
Betaproteobacteria
G
am
m
aproteobacteria
D
eltaproteobacteria
Epsilonproteobacteria
U
nclassified
proteobacteria
Bacteroidetes
C
hlam
ydiae
C
yanobacteria
Acidobacteria
Therm
otogae
Fusobacteria
ActinobacteriaAquificae
Planctom
ycetes
Spirochaetes
Firm
icutes
C
hloroflexiC
hlorobi
U
nclassified
bacteria
dnaG
frr
infC
nusA
pgk
pyrG
rplA
rplB
rplC
rplD
rplE
rplF
rplK
rplL
rplM
rplN
rplP
rplS
rplT
rpmA
rpoB
rpsB
rpsC
rpsE
rpsI
rpsJ
rpsK
rpsM
rpsS
smpB
tsf
Relativeabundance
Martin Wu

26. GOS 1
GOS 2
GOS 3
GOS 4
GOS 5
Phylogenetic ID of Novel Lineages
Dongying
Wu
Wu D, Wu M, Halpern A, Rusch DB,
Yooseph S, Frazier M, et al. (2011)
Stalking the Fourth Domain in
Metagenomic Data: Searching for,
Discovering, and Interpreting Novel, Deep
Branches in Marker Gene Phylogenetic
Trees. PLoS ONE 6(3): e18011. doi:
10.1371/journal.pone.0018011

27. Phylosift
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
Aaron Darling
@koadman
Erik Matsen
@ematsen
Holly Bik
@hollybik
Guillaume Jospin
@guillaumejospin
Darling AE, Jospin G, Lowe E,
Matsen FA IV, Bik HM, Eisen JA.
(2014) PhyloSift: phylogenetic
analysis of genomes and
metagenomes. PeerJ 2:e243
http://dx.doi.org/10.7717/peerj.
243
Erik Lowe

28. Eisen et al.
1992
Phylotyping vs. Function
Genomic Variation w/in Species

29. Proteorhodopsin Functional Diversity
Venter et al., Science 304: 66. 2004

30. Shotmap
Simulate)
metagenomic)
library)
Translate)
metagenomic)
reads)
Search)
metagenomic)
pep6des)
Classify)
metagenomic)
pep6des)
Es6mate)
protein)family)
abundance)
Taxonomic)
profiles)from)real)
metagenomes)
Protein)family)
database)
IMG/ER)
reference)
genomes)
Construct))
mock))
community)
1"
Annotate)
genes)in)
genomes)
2"
Expected)
abundance)of)
gene)families)
3"
4"
5"
Protein)family)
database)
Evaluate)
es6ma6on)
accuracy)
6" 7"
8"
9"
Tom Sharpton
Katie Pollardhttps://github.com/sharpton/shotmap

31. Opportunity 4: Linking Function and Phylogeny

32. HiC
From Belton JM1, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Methods.
2012 Nov;58(3):268-76. doi: 10.1016/j.ymeth.2012.05.001. Hi-C: a comprehensive
technique to capture the conformation of genomes.

33. 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

34. Pink Berries
PB-PSB1
(Purple sulfur bacteria)
PB-SRB1
(Sulfate reducing bacteria)
(sulfate)
(sulfide)
Wilbanks, E.G. et al (2014). Environmental Microbiology
Lizzy Wilbanks
@lizzywilbanks

35. Long Reads Help, A Lot

36. Long Reads Help, A Lot
Moleculo
2-20 kb
Micky Kertesz,
Tim Blauwcamp

37. Long Reads Help, A Lot
Moleculo
2-20 kb
Micky Kertesz,
Tim Blauwcamp
Illumina-based
“synthetic long
reads”

38. Long Reads Help, A Lot
Hiseq & Miseq
100-250 bp
Moleculo
2-20 kb
Micky Kertesz,
Tim Blauwcamp
Illumina-based
“synthetic long
reads”

39. Long Reads Help, A Lot
Hiseq & Miseq
100-250 bp
Moleculo
2-20 kb
Pacbio RSII
2-20kb
Micky Kertesz,
Tim Blauwcamp
Meredith Ashby
Cheryl Heiner
Illumina-based
“synthetic long
reads”
Real-time single
molecule
sequencing
(p4-c2, p5-c3)

40. Long Reads Help, A Lot
Hiseq & Miseq
100-250 bp
Moleculo
2-20 kb
Pacbio RSII
2-20kb
Micky Kertesz,
Tim Blauwcamp
Meredith Ashby
Cheryl Heiner
Illumina-based
“synthetic long
reads”
Real-time single
molecule
sequencing
(p4-c2, p5-c3)
295 Megabases 474 Megabases61 Gigabases

41. Light-responsive sulfate reducer?
rhodopsin
w/ Susumu Yoshizawa

42. Transfer of 34
S from SRB to PSB
12
C, 12
C14
N, 32
S
Biomass
(RGB composite)
Wilbanks, E.G. et al (2014). Environmental Microbiology

43. Transfer of 34
S from SRB to PSB
12
C, 12
C14
N, 32
S
Biomass
(RGB composite)
0.044 0.080
34S-incorporation
(34S/32S ratio)
Wilbanks, E.G. et al (2014). Environmental Microbiology

44. Opportunity 5: Better Reference Data

45. PhyEco Markers
Phylogenetic group Genome Number Gene Number Maker Candidates
Archaea 62 145415 106
Actinobacteria 63 267783 136
Alphaproteobacteria 94 347287 121
Betaproteobacteria 56 266362 311
Gammaproteobacteria 126 483632 118
Deltaproteobacteria 25 102115 206
Epislonproteobacteria 18 33416 455
Bacteriodes 25 71531 286
Chlamydae 13 13823 560
Chloroflexi 10 33577 323
Cyanobacteria 36 124080 590
Firmicutes 106 312309 87
Spirochaetes 18 38832 176
Thermi 5 14160 974
Thermotogae 9 17037 684
Wu D, Jospin G, Eisen JA (2013) Systematic Identification of Gene Families
for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological
Studies of Bacteria and Archaea and Their Major Subgroups. PLoS ONE
8(10): e77033. doi:10.1371/journal.pone.0077033

46. Better Protein Families
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
Sharpton et al. 2012.BMC bioinformatics,
13(1), 264.
A
B
C

47. Diverse Reference Genomes

49. Need More Cultures w/ Genomes

50. Opportunity 6: Whole Systems

51. Mom The Microbes We Eat
PetsBuilt
Environment
Other People
Many Taxa
Opportunity 6: Whole Systems

52. Opportunity 7:
Outreach and Community Engagement At
Every Level is Critical

53. Engage Other Fields

54. Eisen Lab Citizen Microbiology
Kitty Microbiome
Georgia Barguil
Jack Gilbert
Project MERCCURI
Phone
and
Shoes
tinyurl/kittybiome
Holly Ganz
David Coil

55. 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