Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology

Challenges and Opportunities
in Microbiome Studies
and the Rise of Citizen Microbiology
FOGM15
Jonathan A. Eisen
@phylogenomics
University of California, Davis

0
350
700
1050
1400
00 01 02 03 04 05 06 07 08 09 10 11 12
Pubmed “Microbiome” Hits
The Rise of the Microbiome
http://microBE.net
microBEnet
microbiology of the Built
Environment
Network
Aquarium Microbiome
Project
Food Microbiome
DogMouth
Drosophila
Corn
Sea
Grass
Rice
Human Intestinal Transplants
Helicobacter pylori
microbiome

Culture Independent DNA Sequencing
DNA DNADNA
Taxa Characters
B1 ACTGCACCTATCGTTCG
B2 ACTCCACCTATCGTTCG
E1 ACTCCAGCTATCGATCG
E2 ACTCCAGGTATCGATCG
A1 ACCCCAGCTCTCGCTCG
A2 ACCCCAGCTCTGGCTCG
New1 ACCCCAGCTCTGCCTCG
New2 AGGGGAGCTCTGCCTCG

Challenge 1: Complexity
Microbial Diversity
Intraspeciﬁc Diversity 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
species of bacteria and other
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOING?
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?
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
Learn more about your microbiome
American Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
skinGI tractlungsmouth
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
human microbiome.
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
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HU
MICROBI
YOUR BODY: HUMAN AND M
Learn more about your micro
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
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
HOW DO WE GET OUR MICROB
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For t
will c
micro
s
p
n
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
WHAT IS THE MICROBIOME? WAIT ... WH
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%
human genome.
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HU
MICROBI
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% h
rest is many t
species of ba
microbes.
Cells in the
human body:
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For t
will c
micro
s
p
n
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
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%
human genome.
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUM
MICROBI
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
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%
human genome.
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUM
MICROBI
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
A microbe is a mic
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
human genome.
Genetic
Diversity

Challenge 1: Complexity
HUMA
MICROBIOM
YOUR BODY: HUMAN AND MICRO
fungal
bacterial
human
WHOʼS THERE?
A human body is actually on
species of bacteria and othe
microbes.
Cells in the
human body:
WHERE ARE THEY? WHAT ARE THEY DOIN
community.
Our microbiome helps us ex
and nutrients from the
and crowds out or inhibit
WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MI
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
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
and nutrients from the food we eat
and crowds out or inhibits pathogens
human microbiome.
Host Variation
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HU
MICROBI
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% h
rest is many t
species of ba
microbes.
Cells in the
human body:
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For t
will c
micro
s
p
n
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
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%
human genome.
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HU
MICROBI
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% h
rest is many t
species of ba
microbes.
Cells in the
human body:
community.
GI tractlungsmouth
Our microbi
and nu
and crowd
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For t
will c
micro
s
p
n
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
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%
human genome.
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUM
MICROBI
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
A microbe is a mic
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
human genome.
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUMAN
MICROBIOME
fungal
bacterial
human
WHOʼS THERE?
microbes.
Cells in the
human body:
community.
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENVIRONMENT:
microbes from:
soil and water
new and diverse
foods
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
2.5lb
2.5 LBS = WEIGHT
of the microbiome
3 PINTS = VOLUME
of the microbiome
by about 5:1.
5 1:99%
human genome.
urogenital
tract
HUM
MICROBI
fungal
bacterial
human
WHOʼS THERE?
A human bod
about 25% hu
rest is many t
species of bac
microbes.
Cells in the
human body:
community.
GI tractlungsmouth
Our microbio
and nut
and crowd
BIRTH:
A newborn gets its
microbes from:
BREAST MILK:
years to provide:
ENV
For th
will c
micro
so
pe
ne
fo
and antibodies
diverse microbes to
gut
canal
skin of its mother
and other care-
givers
human microbiome.
A microbe is a mic
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
human genome.
TranscriptomeSNPs, CNVs
Epigenetics
Environment

Challenge 2: Public Understanding
Germophobia Microbiomania

Opportunity 1: Better Reference Data

Genomes Poorly Sampled
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree

2002: TIGR Tree of Life Project

Genomic Encyclopedia of Bacteria & Archaea

GEBA Cyanobacteria
Shih et al. 2013. PNAS 10.1073/pnas.1217107110
0.3
B1
B2
C1
Paulinella
Glaucophyte
Green
Red
Chromalveolates
C2
C3
A
E
F
G
B3
D
A
B
Fig.
mum
noba

Haloarchaeal GEBA-like
Lynch et al. (2012) PLoS ONE 7(7): e41389. doi:10.1371/journal.pone.0041389

The Dark Matter of Biology
From Wu et al. 2009 Nature 462, 1056-1060

Uncultured Lineages: Methods
• Get into culture
• Enrichment cultures
• If abundant in low diversity ecosystems
• Flow sorting
• Microbeads
• Microfluidic sorting
• Single cell amplification

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

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

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

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

NSF Geneology of Life
• Ramunas
Stepanauskas
• Tanja Woyke
• Jonathan Eisen
• Duane Moser
• Tullis Onstott

A Genomic Encyclopedia of Microbes (GEM)

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

Opportunity 2: Methods Development

Better Computational Methods
DNA DNADNA
Taxa Characters

DNA DNADNA
Taxa Characters
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
LAST
search input against references
hmmalign
multiple alignment
hmmalign
multiple alignment
Infernal
multiple alignment
LAST
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

DNA DNADNA
Taxa Characters
PhyEco
Markers

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

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

Long Read Sequencing (Moleculo Pacbio)
rhodopsin
w/ Susumu Yoshizawa
Lizzy Wilbanks
@lizzywilbanks

Value of Model Systems: Rice Microbiomes
Joseph
Edwards
@Bulk_Soil
Sundar
@sundarlab
Cameron
Johnson
Srijak
Bhatnagar
@srijakbhatnagar
Edwards et al. 2015. Structure, variation,
and assembly of the root-associated
microbiomes of rice. PNAS
Supplementary Figures1
2
Fig. S1 Map depicting soil collection locations for greenhouse experiment.3
10
234
Fig. S2. Sampling and collection of the rhizocompartments. Roots are collected from rice235
plants and soil is shaken off the roots to leave ~1mm of soil around the roots. The ~1 mm of soil236

Rice Microbiome: Variation w/in Plant
Joseph
Edwards
@Bulk_Soil
Sundar
@sundarlab
Cameron
Johnson
Srijak
Bhatnagar
@srijakbhatnagar
growth. For our study, the rhizosphere compartment was com-
the un
sitive t
zocomp
indicat
microb
and SI
ration
the ext
terior o
(PERM
talizati
microb
P 0.0
howeve
the sec
P 0.0
perform
(CAP)
iance a
Materia
PCoA
analysi
terest t
on the
soil typ
quenci
agreem
Fig. 1. Root-associated microbial communities are separable by rhizo-
compartment and soil type. (A) A representation of a rice root cross-section
depicting the locations of the microbial communities sampled. (B) Within-
sample diversity (α-diversity) measurements between rhizospheric compart-
ments indicate a decreasing gradient in microbial diversity from the rhizo-
sphere to the endosphere independent of soil type. Estimated species

Rice Genotype Affects Microbiome
rhizocompartments were analyzed as before. Unfortunately,
collection of bulk soil controls for the field experiment was not
Fig. 3. Host plant genotype significantly affects microbial communities in
the rhizospheric compartments. (A) Ordination of CAP analysis using the
WUF metric constrained to rice genotype. (B) Within-sample diversity
measurements of rhizosphere samples of each cultivar grown in each soil.
Estimated species richness was calculated as eShannon_entropy
. The horizontal

Rice: Cultivation Site Effects
Edwards et al. 2015.
Structure, variation, and
assembly of the root-
associated
microbiomes of rice.
PNAS
the field plants again showed that the rhizosphere had the
highest microbial diversity, whereas the endosphere had the least
found to be enriche
greenhouse plants (S
OTUs were classifiabl
sisted of taxa in the fa
and Myxococcaceae, al
bidopsis root endosphe
Cultivation Practice Result
The rice fields that we
practices, organic farmi
tion called ecofarming
farming in that chemica
are all permitted but g
harvest fumigants are n
itself does significantly
partments overall (P =
a significant interaction
the rhizocompartments
indicating that the α-d
affected differentially by
the rhizosphere compa
practice, with the mean
zospheres than organic
Dataset S14), whereas
crobial communities (P
tests; Dataset S14). Un
practices are separable a
the WUF metric (Fig.

Rice: Functional Enrichment x Genotype
and mitochondrial) reads to analyze microbial abundance in
the endosphere over time (Fig. 6A). Using this technique, we
confirmed the sterility of seedling roots before transplantation.
(13 d) approach the endosphere and rhizoplane microbiome
compositions for plants that have been grown in the green-
house for 42 d.
Fig. 5. OTU coabundance network reveals modules of OTUs associated with methane cycling. (A) Subset of the entire network corresponding to 11
modules with methane cycling potential. Each node represents one OTU and an edge is drawn between OTUs if they share a Pearson correlation of
greater than or equal to 0.6. (B) Depiction of module 119 showing the relationship between methanogens, syntrophs, methanotrophs, and other
methane cycling taxonomies. Each node represents one OTU and is labeled by the presumed function of that OTU’s taxonomy in methane cycling. An
edge is drawn between two OTUs if they have a Pearson correlation of greater than or equal to 0.6. (C) Mean abundance profile for OTUs in module 119
across all rhizocompartments and field sites. The position along the x axis corresponds to a different field site. Error bars represent SE. The x and y axes
represent no particular scale.
Edwards et al. 2015. Structure, variation, and assembly of the root-associated

Rice Developmental Time Series
of magnitude greater than in any single plant species
Under controlled greenhouse conditions, the rhizocomp
described the largest source of variation in the microb
munities sampled (Dataset S5A). The pattern of separ
tween the microbial communities in each compar
consistent with a spatial gradient from the bulk soil a
rhizosphere and rhizoplane into the endosphere (F
Similarly, microbial diversity patterns within samples
same pattern where there is a gradient in α-diversity
rhizosphere to the endosphere (Fig. 1B). Enrichment
pletion of certain microbes across the rhizocompartme
cates that microbial colonization of rice roots is not a
process and that plants have the ability to select for ce
crobial consortia or that some microbes are better at f
root colonizing niche. Similar to studies in Arabidopsis, w
that the relative abundance of Proteobacteria is increas
endosphere compared with soil, and that the relative abu
of Acidobacteria and Gemmatimonadetes decrease from
to the endosphere (9–11), suggesting that the distrib
different bacterial phyla inside the roots might be simil
land plants (Fig. 1D and Dataset S6). Under controlle
house conditions, soil type described the second large
of variation within the microbial communities of each
However, the soil source did not affect the pattern of se
between the rhizospheric compartments, suggesting
rhizocompartments exert a recruitment effect on micro
sortia independent of the microbiome source.
By using differential OTU abundance analysis in t
partments, we observed that the rhizosphere serves an
ment role for a subset of microbial OTUs relative to
(Fig. 2). Further, the majority of the OTUs enriche
rhizosphere are simultaneously enriched in the rhizoplan
endosphere of rice roots (Fig. 2B and SI Appendix, Fig
consistent with a recruitment model in which factors pro
the root attract taxa that can colonize the endosphere. W
that the rhizoplane, although enriched for OTUs that
enriched in the endosphere, is also uniquely enriched for
of OTUs, suggesting that the rhizoplane serves as a sp
Edwards et al. 2015.
Structure, variation, and
assembly of the root-
associated
microbiomes of rice.
PNAS

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

Opportunity 4: Engage Other Fields

Opportunity 5: Public Participation

The Rise of Citizen Microbiology
Darlene Cavalier

Example 1: American Gut
$800,000
8450 56
www.americangut.org

Example 2: Phones at Public Events
Georgia Barguil
Georgia Barguil
Jack Gilbert

Example 4: Wild Life of Your Home
Slide from Holly Menninger, CoPI on the project
Holly Meninger
Rob Dunn

Wild Life of Your Home
4 locations: interior and exterior trim,
pillowcase, kitchen counter
Microbes: fungi (ITS), bacteria (16S)
1430 homes
Dunn et al. 2013, PLOS ONE

Example 5: Seagrass Microbiome
An in-depth look at the community composition
dgments

Zostera Experimental Network
Example 5: Seagrass Microbiome

Sampling Kits
3-D
printed
base for
Aeropress
~ $100 per
kit

Citizen Microbiology is Fun, Really Fun
AP Bio class at Bodega Bay

Example 6: Kitty Microbiome Project
A citizen
science
project to
advance cat
health by
studying the
gut
microbiome of
cats in health
and disease
https://catbiome.com

Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Viewers also liked

Viewers also liked (20)

Similar to Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology

Similar to Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology (20)

More from Jonathan Eisen

More from Jonathan Eisen (20)

Recently uploaded

Recently uploaded (20)

Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology