Jeremy Glasner, Ph.D.
December 1, 2015

Microbes have been evolving for a long time and are extremely diverse

Provide good evidence for natural selection on genome scale

Microbiome data provides evidence of diversity of microbial populations
in varying environments

Symbioses between bacteria and hosts evolve commonly

Many modalities exist for transmission of bacterial traits such as
pathogenesis and drug resistance
KEY LESSONS FROM MICROBIAL
EVOLUTION
Bacteria are the dominant form of life on the planet
https://en.wikipedia.org/wiki/Biomass_(ecology)
The appearance of Life
•The timetable
• 3.6-3.7 billion years ago: appearance of life
• 2.5 billion years ago oxygen-forming photosynthesis
• ~2.2 billion years ago: aerobic respiration
• ~1.5 billion years ago: first evidence of fossil eukaryotes
Fossil evidence of ancient microbes is scant,
but suggests very ancient origin, likely ~3.5
billion years ago
Bacteria now
commonly
studied by
genome
sequencing and
tend to have
small genomes
~1-10 Mb
Genome Sizes" by Abizar at English Wikipedia. Licensed under CC BY-SA 3.0 via Wikimedia Commons http://commons.wikimedia.org/wiki/File:Genome_Sizes.png#mediaviewer/File:Genome_Sizes.png
Variation in
Number of
Genes Across
Tree of Life
Genome Sizes" by Abizar at English Wikipedia. Licensed under CC BY-SA 3.0 via Wikimedia Commons http://commons.wikimedia.org/wiki/File:Genome_Sizes.png#mediaviewer/File:Genome_Sizes.png
Number of
genes as a
function of
Genome Size
Genome Sizes" by Abizar at English Wikipedia. Licensed under CC BY-SA 3.0 via Wikimedia Commons http://commons.wikimedia.org/wiki/File:Genome_Sizes.png#mediaviewer/File:Genome_Sizes.png
 Genome
WHAT IS AN
OME?
 Transcriptome
 Exome
 Methylome
 Phenome
Genome-Scale datasets
are becoming routinely
available from many
organisms and even
populations and
provide incredible
insight into the
evolution of organisms
OUR LITTLE ENDOSYMBIONT GENOME
MCKINNEY, Emily A. and OLIVEIRA, Marcos T.. Replicating animal mitochondrial DNA. Genet. Mol. Biol. [online]. 2013, vol.36, n.3, pp. 308-315. ISSN 1415-4757.
nuclear
genome
mitochondrial
genome
microbiome
OUR GENOME(S)
Most microbes are unculturable
New DNA sequencing-based methods allow
us to observe all of the genomes present in a
sample without needing to grow a culture
Metagenomics is the popular term for
sequencing the genomes from a sample
Often sequence 16S ribosomal RNA genes
(highly conserved)
http://www.wagsrevue.com/thewag/?q=content/graphic-science-1
http://www.wagsrevue.com/thewag/?q=content/graphic-science-1
http://www.wagsrevue.com/thewag/?q=content/graphic-science-1
http://www.wagsrevue.com/thewag/?q=content/graphic-science-1
http://www.wagsrevue.com/thewag/?q=content/graphic-science-1
Key findings from the human microbiome project
Carriage of microbial taxa varies while metabolic pathways
remain stable within a healthy population.
C Huttenhower et al. Nature 486, 207-214 (2012) doi:10.1038/nature11234
Yes, the
microbiome
can affect
behavior
http://phylogenomics.blogspot.com/
Diminished
diversity in the
human gut
microbiome
compared to apes
http://u.osu.edu/sabreelab/author/sabree8/
Symbiosis is an “intimate”, “long-term” (evolutionary-relevant time?)
interaction between (different types of) organisms encompassing
the range from mutualism to parasitism
SYMBIOSIS- MAIN VARIABLES
 Route
of infection (maternal, horizontal, mixture)
 Mechanisms
 Location

of benefiting or exploiting hosts
of symbionts in host body:
intracellular, between cells, in specialized organ or in other tissues, within
gut lumen, etc.
 Molecular
mechanisms of invading host tissues or cells:
similarities and differences between symbionts and pathogens
Plants
Mixed
Animals
Escherichia,
Salmonella, etc.
Xenorhabdus,
Photorhabdus,
Proteus
Soft rotters
Edwardsiella,
Hafnia
Yersinia, Serratia,
Ewingella
Specialization in plants
Animals
Animals
Animals
Specialization in animals
Enterobacteria contain many
pathogens, as well as many
commensals of plants and
animals
Mechanisms of bacterial pathogenesis
EVOLUTION OF
PATHOGENESIS
THROUGH HORIZONTAL
GENE TRANSFER
Can transfer DNA from donor cell to recipient cell
e.g. in E. coli a plasmid called “F” for fertility
contains genes encoding a structure called a pilus
that can transfer the plasmid, and occasionally large
pieces of the E. coli chromosome to cells that lack
the F plasmid. The transferred DNA can sometimes
recombine into the recipient’s genome
Bacterial Conjugation
So even traditionally “asexually”
reproducing organisms do exchange
genetic material and undergo
recombination, “sex”, but it is often called
“lateral gene transfer since it
mechanistically somewhat different from
sex in most eukaryotes that involves
meiosis and recombination
http://okanogan1.com/wp/wp-content/uploads/2011/02/brinton_conjugation_small.gif
Horizontal Gene Transfer (= Lateral Gene
Transfer): Transfer of genetic material (DNA) to another
organism that is not its offspring.
• Transformation
• Transduction
• Conjugation
Horizontal gene transfer between
bacteria was first described in
Japan in a 1959 publication that
demonstrated the transfer of
antibiotic resistance between
different species of bacteria
Horizontal Gene Transfer
Consequences:
• Phylogenetic relationships are sometimes difficult to
discern (as genetic material is being swapped around)
• Rapid transfer of functional genes: pathogenicity
genes, rapid evolution of drug resistance
• Bacteria effectively have a HUGE genome size (PanGenome), a large genome to draw from, as individual
cells can share genes with other individuals
Blattner et al. 1997

Two E. coli
genomes
(Perna et al., 2001)

Three E. coli
genomes
(Welch et al., 2002)
Lineage-specific
“islands” can be a
significant fraction
(up to 30%) of the
genome
Pan-Genome
Genome of any one organism
Genome of the “species”
Core
Core
Variable
The Pan Genome (yellow +
blue) of a prokaryotic
“species” is much larger
than the genome of any one
bacterial organism or of the
core genome (blue) of the
species
Variable
Touchon M, Hoede C, Tenaillon O, Barbe V, et al. (2009) Organised Genome Dynamics in the Escherichia coli Species Results in
Highly Diverse Adaptive Paths. PLoS Genet 5(1): e1000344. doi:10.1371/journal.pgen.1000344
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344
Evolution of new symbiotic relationships in bacteria can occur by gene acquisition
e.g. the evolution of different pathogenic types of E. coli is thought to occur by horizontal
(lateral) gene transfer of pathogenicity genes/islands of genes
Example of acquisition of genes encoding
type III secretion systems in pathogenic E.
coli that can deliver pathogenicity
determinants directly into eukaryotic host
cells
…it can be hard to determine the environment that matters
most in the context of many co-evolutionary events…
commensal in one species, pathogenic in another…
http://www.compoundchem.com/wp-content/uploads/2014/09/A-Guide-to-Different-Classes-of-Antibiotics.png
Antibiotics target highly conserved aspects of bacterial growth and metabolism
Antibiotics are often useful for only a subset of bacteria –
e.g. evolutionarily/phenotypically related groups
Evolution of Antibiotics and Antibiotic Resistance
Why do antibiotics kill bacterial cells but not human cells?
Because they target bacterial specific metabolic processes or very
specific differences between processes conserved between humans
and bacteria
note: chemotherapeutic drugs are hard to develop because…
Antibiotics kill! They are lethal! That is extremely strong selection!
If there are antibiotic resistant variants in the population they will quickly
rise to fixation!
Hospitals are evolutionary breeding grounds for selecting for multipledrug resistant antibiotic strains of bacteria.
Indiscriminant use of antibiotics reduces their long-term utility –e.g.
animal agriculture
The evolutionary arms race
between antibiotics and
antibiotic resistance
For every mechanism of
offense there seems to be a
good defense…
http://www.cmaj.ca/content/180/4/408.figures-only
Antibiotic resistance genes
spread among bacteria because
they have multiple mechanisms
for exchanging DNA (aka
Lateral/Horizontal Gene
Transfer)
(Phylogenetic evidence for gene transfer from organelles)
Cyanobacteria
Cyanobacteria
Eukaryote- Plant
Cyanobacteria
Bacteria
Bacteria
Bacteria
Bacteria
Eukaryote-protozoan
Eukaryote-protozoan
Eukaryote-animal
Eukaryote-fungal
e.g. Arabidopsis genome has >1000 genes from cyanobacteria
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”
Beneficial microbes in animal hosts-examples
1
Insect-nutritional mutualists (aphids & Buchnera)
Many invertebrates have specialized intracellular
associations with bacteria that make nutrients
Examples: marine bivalves, leeches, many insects
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”
Metazoa: ancestral loss of
many genes underlying
biosynthesis of compounds
essential for metabolism,
including many amino acids
and many cofactors.
-->dietary requirements.
Little or no gene uptake
Adapted from slide from Nancy Moran’s Oct 3,
2006 lecture “Symbiotic Bacteria in Animals”
Tree of Life, N. Pace
Routes of transmission
 Vertical
(parent to offspring)
 Horizontal

May live in the environment (outside hosts), or
not
 Mixture

of vertical and horizontal
Eg acquire from other individuals in the same
family or colony (termites, humans… )
Termite with gut removed
Diverse microbes in termite gut
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”
late embryos
maternal bacteriocytes
containing symbionts
early embryos with
symbionts visible
1 mm
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”
J. Sandström
Buchnera aphidicola within pea aphid bacteriocyte
1mm
J. White
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”
Aphid eggs containing
Buchnera from mother
0.5 mm
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”
A. Mira
The Buchnera gene set (570 genes) is a subset of that of E. coli (~4500 genes)
Shigenobu et al 2000 Nature
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”
Essential amino acid biosynthetic pathways
argA argB argC argD argE
carAB argF argG argH
Glutamate---> ---> ---> ---> ---> Ornithine ---> ---> ---> ---> ARG
ilvHI ilvC ilvD ilvE
tyrA tyrA hisC
Chorisimate ---> ---> ---> TYR
proB proA proC
Pyruvate ---> ---> ---> ---> VAL
ilvA
Nonessential amino acid biosynthetic pathways
Glutamate ---> ---> ---> PRO
serA serC serB
ilvHI ilvC ilvD ilvE
3-Phosphoglycerate ---> ---> ---> SER
Threonine ---> a-Ketobutyrate ---> ---> ---> ---> ILE
+ Pyruvate
glyA
Serine ---> GLY
ilvHI ilvC ilvD leuA leuCD leuB ilvE
Pyruvate ---> ---> ---> ---> ---> ---> ---> LEU
cysE cysK
aroH aroB aroD aroE aroK aroA aroC
PEP+Erythrose ---> ---> ---> ---> ---> ---> ---> Chorismate
4-Phosphate
Serine ---> ---> CYS
gtBD/gdhA
2-oxoglutarate ---> GLU
pheA pheA hisC
Chorismate ---> ---> ---> PHE
glnA
Glutamate ---> GLN
trpEG trpD trpC trpC trpAB
Chorismate ---> ---> ---> ---> --->
aspC+tyrB
TRP
Oxaloacetate --->
thrA asd thrA
thrB thrC
asnB/asnA
Aspartate ---> ---> ---> Homoserine ---> ---> THR
Aspartate --->
metB metC metE
Homoserine ---> ---> --->
ASP
MET
thrA asd dapA dapB dapD dapC dapE dapF lysA
ASN
alaB/avtA
Pyruvate ---> ALA
Aspartate ---> ---> ---> ---> ---> ---> ---> ---> ---> LYS
hisG hisI hisA hisHF hisB hisC hisB hisD
PRPP + ATP ---> ---> ---> ---> ---> ---> ---> ---> HIS
Adapted from slide from Nancy Moran’s Oct 3, 2006
lecture “Symbiotic Bacteria in Animals”
GENE / product present in Buchnera
GENE / product absent in Buchnera
(based on Shigenobu et al 2000)
Tiniest Tiny Genomes
Moran NA, Bennett GM. The tiniest tiny genomes. Annu Rev Microbiol. 2014;68:195-215. doi: 10.1146/annurev-micro-091213-112901. Epub 2014 Jun 2. PubMed PMID: 24995872.
“The extreme case, to date, is the
genome of “Candidatus Nasuia
deltocephalinicola,” one of two
obligate symbionts of the
leafhopper Macrosteles
quadrilineatus; this Nasuia strain
possesses a mere 137 proteincoding genes and a genome of only
112 kb”
evolutionary innovations
through symbiosis: examples
• Eukaryotic cell (mitochondria)
• Photosynthesis in eukaryotes (plastids)
• Colonization of land by plants
(mycorrhizae)
• Nitrogen fixation by plants (rhizobia)
• Animal life at deep sea vents
(chemoautotrophic life systems)
• Use of many nutrient-limited niches by
animal lineages
Adapted from slide from Nancy Moran’s Oct 3, 2006 lecture “Symbiotic Bacteria in Animals”