Jonathan Eisen talk at #UCDavis 10/19/15 on "Microbiomes in Food and Agriculture"

Microbiomes in Food and Agriculture
IFAL
October 19, 2015
Jonathan A. Eisen
@phylogenomics
University of California, Davis

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Pubmed “Microbiome” Hits
The Rise of the Microbiome

microBIOME or microbiOME?
• microbi-OME
• collection of genomes of microbes from a
community (emphasis on OME)
• micro-BIOME
• a community of microbes (emphasis on
BIOME)
• see http://tinyurl.com/definemicrobiome

Why Now I: Appreciation of Microbial Diversity

Diversity of Form

Diversity of Form
Phylogenetic Diversity

Functional Diversity
Diversity of Form

Functional Diversity
Diversity of Form
MICROBES
RUN THE
PLANET

Why Now II: Post Genome Blues
Overselling the Human Genome?

Transcriptome

Transcriptome
Epigenome

Transcriptome
VariomeEpigenome

The Microbiome
Transcriptome
VariomeEpigenome

Why Now III: Sequencing Has Gone Crazy

Why Now III: Culture Independent Studies

Observation

Culturing Observation

CountCount

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DNA

Turnbaugh et al Nature. 2006 444(7122):1027-31.
Why Now IV: Microbiome Functions

Challenge 1: Complexity
http://bit.ly/HumanMicrobiome

Microbial Diversity

Microbial Diversity
Microbial Diversity2

Microbial Diversity
Microbial Diversity2
Functional
Diversity

Microbial Diversity
Microbial Diversity2 Fragmented Data
Functional
Diversity

HUMAN
MICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiome
American Academy of Microbiology:
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
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
includes viruses, ba
Not all microbes m
and on our bodies
2.5lb
2.5 LBS = WEIGHT
of the microbiome
Viru
599%
human genome.
Microbial Diversity
Microbial Diversity2 Fragmented Data
Host Variation
Functional
Diversity

Challenge 2: Public Understanding

Germophobia

Germophobia Microbiomania

Dealing w/ Complexity 1: 
 
rRNA Surveys

Worse Classification of Cultured Taxa by rRNA
Carl
Woese

rRNA rRNArRNA
Carl
Woese

rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Carl
Woese

rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Carl
Woese

Archaea
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
EukaryotesBacteria
Carl
Woese

rRNA Phylotyping: One Taxon
DNA
ACTGC
ACCTAT
CGTTCG
ACTGC
ACCTAT
CGTTCG
ACTGC
ACCTAT
CGTTCG
Taxa Characters
B1 ACTGCACCTATCGTTCG
B2 ACTCCACCTATCGTTCG
E1 ACTCCAGCTATCGATCG
E2 ACTCCAGGTATCGATCG
A1 ACCCCAGCTCTCGCTCG
A2 ACCCCAGCTCTGGCTCG
New1 ACTGCACCTATCGTTCG
EukaryotesBacteria Archaea
Many
sequences
from one
sample all
point to the
same branch
on the tree
Norm
Pace

DNA
ACTGC
ACCTAT
CGTTCG
ACTGC
ACCTAT
CGTTCG
ACCCC
AGCTCT
CGCTCG
Taxa Characters
New1 ACCCCAGCTCTGCCTCG
One can
estimate cell
counts from
the number of
times each
sequence is
seen.
rRNA Phylotyping: Two Taxa

DNA
Taxa Characters
New2 AGGGGAGCTCTGCCTCG
New3 ACTCCAGCTATCGATCG
ACTGC
ACCTAT
CGTTCG
ACTCC
AGCTAT
CGATCG
ACCCC
AGCTCT
CGCTCG
AGGGG
AGCTCT
CGCTCG
AGGGG
AGCTCT
CGCTCG
ACTGC
ACCTAT
CGTTCG
Even with
more taxa it
still works
rRNA Phylotyping: Many Taxa

rRNA Phylotyping: Relative Abundance
DNA
Taxa Characters
ACTGC
ACCTAT
CGTTCG
ACTCC
AGCTAT
CGATCG
ACCCC
AGCTCT
CGCTCG
AGGGG
AGCTCT
CGCTCG
AGGGG
AGCTCT
CGCTCG
ACTGC
ACCTAT
CGTTCG
Even with
more taxa it
still works

DNA DNADNA
ACTGC
ACCTAT
CGTTCG
ACTCC
AGCTAT
CGATCG
ACCCC
AGCTCT
CGCTCG
Taxa Characters
New2 ACGGCAGCTCTGCCTCG
rRNA PCR: Community Comparisons

Uses of rRNA Example: Rice Microbiome

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- sitive
zocom
indica
microb
and SI
ration
the ex
terior
(PERM
talizat
microb
P < 0.
howev
the se
P < 0.
perfor
(CAP)
iance
Materi
PCoA
analys
terest
on the
soil ty
quenc
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
Shannon_entropy
Edwards et al. 2015. Structure, variation, and assembly of the
root-associated microbiomes of rice. PNAS 24;112(8):E911-20.
doi: 10.1073/pnas.1414592112

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.
Edwards et al. 2015. Structure, variation, and assembly of the
root-associated microbiomes of rice. PNAS 24;112(8):E911-20.
doi: 10.1073/pnas.1414592112

Rice: Cultivation Site Effects
highest microbial diversity, whereas the endosphere had the least greenhouse plants (S
OTUs were classifiab
sisted of taxa in the f
and Myxococcaceae, a
bidopsis root endosph
Cultivation Practice Resul
The rice fields that we
practices, organic farm
tion called ecofarmin
farming in that chemica
are all permitted but
harvest fumigants are n
itself does significantly
partments overall (P =
a significant interaction
the rhizocompartment
indicating that the α-d
affected differentially b
the rhizosphere comp
practice, with the mean
zospheres than organi
Dataset S14), whereas
crobial communities (
tests; Dataset S14). U
practices are separable
the WUF metric (Fig
Fig. 4. Root-associated microbiomes from field-grown plants are separable
Edwards et al. 2015. Structure,
variation, and assembly of the
root-associated microbiomes of
rice. PNAS 24;112(8):E911-20.
doi: 10.1073/pnas.1414592112

Rice: Functional Enrichment x Genotype
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.

Rice Developmental Time Series
of magnitude greater than in any single pla
Under controlled greenhouse conditions, the
described the largest source of variation in
munities sampled (Dataset S5A). The patter
tween the microbial communities in eac
consistent with a spatial gradient from the
rhizosphere and rhizoplane into the end
Similarly, microbial diversity patterns withi
same pattern where there is a gradient in α
rhizosphere to the endosphere (Fig. 1B). E
pletion of certain microbes across the rhizo
cates that microbial colonization of rice ro
process and that plants have the ability to se
crobial consortia or that some microbes are
root colonizing niche. Similar to studies in Ar
that the relative abundance of Proteobacteri
endosphere compared with soil, and that the
of Acidobacteria and Gemmatimonadetes de
to the endosphere (9–11), suggesting that
different bacterial phyla inside the roots mig
land plants (Fig. 1D and Dataset S6). Unde
house conditions, soil type described the se
of variation within the microbial communit
However, the soil source did not affect the p
between the rhizospheric compartments, s
rhizocompartments exert a recruitment effec
sortia independent of the microbiome source
By using differential OTU abundance an
partments, we observed that the rhizospher
ment role for a subset of microbial OTUs
(Fig. 2). Further, the majority of the OTU
rhizosphere are simultaneously enriched in th
endosphere of rice roots (Fig. 2B and SI Ap
consistent with a recruitment model in which
the root attract taxa that can colonize the end
that the rhizoplane, although enriched for O
enriched in the endosphere, is also uniquely e
of OTUs, suggesting that the rhizoplane ser
Edwards et al. 2015. Structure,
variation, and assembly of the
root-associated microbiomes of
rice. PNAS 24;112(8):E911-20.
doi: 10.1073/pnas.1414592112

Dealing with Complexity 2: 
 
Metagenomics

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

Metagenomics
metagenomics
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG

Metagenomics
metagenomics
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG

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

Culture Independent “Metagenomics”
DNA DNADNA
Taxa Characters
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

inputs of fixed carbon or nitrogen from external sources. As with
Leptospirillum group I, both Leptospirillum group II and III have the
genes needed to fix carbon by means of the Calvin–Benson–
Bassham cycle (using type II ribulose 1,5-bisphosphate carboxy-
lase–oxygenase). All genomes recovered from the AMD system
contain formate hydrogenlyase complexes. These, in combination
with carbon monoxide dehydrogenase, may be used for carbon
fixation via the reductive acetyl coenzyme A (acetyl-CoA) pathway
by some, or all, organisms. Given the large number of ABC-type
sugar and amino acid transporters encoded in the Ferroplasma type
Figure 4 Cell metabolic cartoons constructed from the annotation of 2,180 ORFs
identified in the Leptospirillum group II genome (63% with putative assigned function) and
1,931 ORFs in the Ferroplasma type II genome (58% with assigned function). The cell
cartoons are shown within a biofilm that is attached to the surface of an acid mine
drainage stream (viewed in cross-section). Tight coupling between ferrous iron oxidation,
pyrite dissolution and acid generation is indicated. Rubisco, ribulose 1,5-bisphosphate
carboxylase–oxygenase. THF, tetrahydrofolate.
articles
NATURE | doi:10.1038/nature02340 | www.nature.com/nature 5©2004 NaturePublishing Group
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

 
Sequencing Isn’t Everything

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
Lizzy Wilbanks
@lizzywilbanks

 
Reference Data Very Limited

2007-2014: GEBA
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree

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

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.
Tanja 
Woyke

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

 
Need to Understand Whole Systems

Mom
Coming Next … Whole Systems

Mom Other People

Mom The Microbes We EatOther People

Mom The Microbes We Eat
Built
Environment
Other People

PetsBuilt
Environment
Other People

PetsBuilt
Environment
Other People
Many Taxa

Public Understanding: 
 
Outreach and Community Engagement At
Every Level is Critical

Education Outreach
http://microBE.net
http://gut-check.net

The Rise of Citizen Microbiology
Darlene Cavalier

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

Glyphosate And Autism / Alzheimers
The key pathological biological effects of glyphosate — disruption of
the gut bacteria, impairment of sulfate transport, and interference
with CYP enzyme activity—can easily explain the features that are
characteristic of autism

Abstract
Glyphosate, the active ingredient in Roundup®, is the most popular
herbicide used worldwide. The industry asserts it is minimally toxic to
humans, but here we argue otherwise. Residues are found in the main
foods of the Western diet, comprised primarily of sugar, corn, soy and
wheat. Glyphosate's inhibition of cytochrome P450 (CYP) enzymes is an
overlooked component of its toxicity to mammals. CYP enzymes play
crucial roles in biology, one of which is to detoxify xenobiotics. Thus,
glyphosate enhances the damaging effects of other food borne chemical
residues and environmental toxins. Negative impact on the body is
insidious and manifests slowly over time as inflammation damages cellular
systems throughout the body. Here, we show how interference with CYP
enzymes acts synergistically with disruption of the biosynthesis of
aromatic amino acids by gut bacteria, as well as impairment in serum
sulfate transport. Consequences are most of the diseases and conditions
associated with a Western diet, which include gastrointestinal disorders,
obesity, diabetes, heart disease, depression, autism, infertility, cancer and
Alzheimer’s disease. We explain the documented effects of glyphosate and
its ability to induce disease, and we show that glyphosate is the “textbook
example” of exogenous semiotic entropy: the disruption of homeostasis by
environmental toxins.

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
Weeds Die

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
Harvest

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
G
G
G
G
G
Harvest

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
G
G
G
G
G
Glyphosate
consumed
Harvest

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
G
G
G
G
G
Glyphosate
consumed
Harvest
G
G
G
G
G

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
G
G
G
G
G
Glyphosate
consumed
Gut
Microbiome
Altered
Harvest
G
G
G
G
G

Implied Model
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
G
G
G
G
G
Glyphosate
consumed
Gut
Microbiome
Altered
Health
Problems
Harvest
G
G
G
G
G

Evidence Lacking
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
G
G
G
G
G
Glyphosate
consumed
Gut
Microbiome
Altered
Health
Problems
Harvest
G
G
G
G
G
Evidence??

Glyphosate and the Microbiome
• Case study for public understanding of
the microbiome
• Started to build collection of papers to
share with the public to enable open
conversation
• See https://www.zotero.org/groups/
glyphoate_microbiota_and_microbiomes
• Zotero is an open source, open social
reference sharing tool

Summary from Literature
• No evidence of a direct effect of
glyphosate on the human microbiome
• Some culture based experiments show
effects on various human associated
microbes
• Glyphosate can effect plant and soil
microbiomes but inconsistent results in
the literature

Some Thoughts
• Most studies are very indirect
• Dosage and exposure levels need to be
better taken into account
• Need studies of communities not cultures
• EVERYTHING affects the microbiome -
key is whether an effect has significant
consequences

Alternative Possibility
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
Altered  
Microbiome
consumed
Gut
Microbiome
Altered
Health
Problems
Harvest
Plant
Microbiome
Changes?

Evidence??
Alternative Possibility
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
Altered  
Microbiome
consumed
Gut
Microbiome
Altered
Health
Problems
Harvest
Plant
Microbiome
Changes?

Alternative Possibility 2
Add
Glyphosate G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Weeds Die
Soil
Microbiome
Changes?

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

Implied Model for BVTs
1
2
3-6
Inverts Vertebrates Protists Bacteria

Letter to Eric Lander
Dear Eric, 
 
The genome paper is terrific, with lots of beautiful discoveries and 
exciting results. However, we'd like to draw your attention to one 
rather problematic conclusion, which seems to be getting the press's 
attention as well. 
 
The claim that 223 genes were laterally transferred from bacteria into 
human is not supported by generally accepted computational or 
statistical methods. Most researchers in the field of molecular 
evolution would view this claim with extreme skepticism.  
 
Your claim relies on an analysis that uses a method that Koonin and 
his group have used repeatedly, which works like this: compare all the 
human genes to all other genes. See which ones hit bacteria and don't 
hit invertebrates. Then report that those genes have been laterally 
transferred into vertebrates. I think you will see pretty quickly 
that, given the large number of bacterial genomes (30+) and the very 
small number of invertebrates (4), this idea simply doesn't work 
statistically. Another way to look at it is as follows: first compare 
human to all bacteria. Collect 1000s of genes shared by both. Then 
filter this human-bacteria set by comparing it to C. elegans. 
Remove anything you find. Filter again using Drosophila, Arabidopsis, 
and yeast. In your group's analysis, 223 genes remained at the end. 
It seems likely that with the addition of more invertebrate genomes, 
this number would drop further. Even if it didn't, absence of genes 
can be explained easily by gene loss, a well-known and well-documented 
phenomenon (which is dismissed in your paper as less parsimonious). 
While there is substantial evidence for some cases of lateral gene 
transfer, there are a variety of other reasons why these 223 genes are 
unlikely to have been transferred from bacteria to vertebrates, which 
we'd be happy to discuss with you at more length if you're interested. 
 
We realize that in the rush to put together a manuscript of this scale 
and scope, you might not have been able to scrutinize some sections as 
closely as others. We hope you will take a closer look and perhaps 
steer reporters away from the claims about horizontal transfer. We've 
already read statements in The Washington Post to the effect that 
bacteria could infect humans and get into our genome. Such a 
startling claim needs much stronger evidence than anyone has today. 
 
Steven Salzberg and Jonathan Eisen 
The Institute for Genomic Research  
9712 Medical Center Drive, Rockville, MD 20850 
We’ve already read statements in
The Washington Post to the effect
that bacteria could infect humans
and get into our genome. Such a
startling claim needs much
stronger evidence than anyone
has today.

Alternative explanations
• Gene loss from non-vertebrate
eukaryotes
• Rapid divergence in non-vertebrate
eukaryotes
• Incomplete genomes (e.g., D. melanogaster)
• Bad annotation/gene finding
• Contamination

Skepticism Needed
I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is
up to them to exclude other MORE plausible alternatives and I just do not think
they have done that.

Lateral Gene Transfer 101
• DNA does not stay confined within single
lines of descent
• Recombination within species (e.g., via sex)
• Hybridization between species
• Lateral gene transfer (LGT) between even
distantly related species
• LGT much more common than once
appreciated

LGT Features
• Major impact on evolution, ecology,
function of species
• Many mechanisms
• Frequency?
• Reasonably common in microbes
• Less common in multicellular organisms
especially when germ line isolated
• Many constraints limit frequency
• Most common when driven by selfish elements,
population structure or selection

Jonathan Eisen talk at #UCDavis 10/19/15 on "Microbiomes in Food and Agriculture"

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Jonathan Eisen talk at #UCDavis 10/19/15 on "Microbiomes in Food and Agriculture"