Download Worlds within worlds: evolution of the vertebrate gut microbiota Ruth

“you are what you eat”-diet and human
evolution
Australopithecus
feed on
seeds and
soft fruits
Homo
erectus
Bulbs and
roots
~2 Mya and
persisted for
~1 Myr.
~4.4 Mya
(million years
ago) until ~2.5
Mya
H. sapiens
meat
Pleistocene
Pictures adapted from google
Diet not only affect human structure, but also
genes:
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Human have roughly three times of Amylase gene
than chimpanzee: intensive starch diet
Genetically regulated lactose tolerance is in
association with cattle milk consumption
Object: 16s rRNA gene sequence of gut
microorganism from human, non-human primates,
other mammal species, non-vertebrate and free
living microorganisms.
Two approaches applied:
 1. UniFrac distance
 2. Operational taxonomy unit(OTU) based analysis:
single level of phylogenetic resolution
Measures the evolutionary distance between
microbial communities
Similar Communities
Maximally Different Communities
UniFrac Distance Measure = (------) / (------ + ------)
Information adapted from
dparks.wdfiles.com/local-files/exploringmicrobial.../UniFrac.ppt
Operational taxonomic Unit (OTU): definition of a
taxonomic unit based on sequence divergence

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“species” 97% sequence homology
“genus” 90% sequence homology
“family” 80% sequence homology
1. UniFrac distances between samples from same
species were significantly smaller than distances
between samples from different species
2. samples from same species share more genuslevel OTUs than samples from other species
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Herbivore : animals which only eat plant material ,
foregut fermenter vs hindgut fermenter
Ominivore: animals which eat both plants and meat
Carnivore: animals which eat meat, have simple gut
Image adapted from
B
C
D
4
3
4
A
6
3
B
3
C
PC2
A
B
C
PC1
schematic key of network
analysis1
1. Principal coordinate analysis(PCoA) and network
diagram clearly separates bacterial communities
obtained from the
vertebrate gut from freeliving communities
2. Obvious dichotomy is observed across bacterial
tree and within phyla


Random immigration, birth events and death
events (Neutral model) : tree holes, human lungs
and lakes
Adaptive immune system, selection pressure on the
host, nutrient-redox potential dichotomy
:vertebrate gut
dev.nsta.org/evwebs/1887/present_technolo
Not Healthy
Healthy
darmano.typepad.com/.../07/human_hierarchy
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Stable Temperature
Nutrient rich
Anaerobic
Oxidized environment
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Mammalian gut microbiota is related to diet and
gut morphology : mammalian gut bacterial
community type can be roughly categorized into
herbivore, omniviore and carnivore
Overal, gut microbiota among vertebrates are
closer related to each other than to other
communities, as demonstrated by PCoA and
network analysis
Selection pressure on vertebrate gut microbiota:
Adaptive immune system, selection pressure on the
host, nutrient-redox potential dichotomy