Worlds within worlds:

evolution of
the vertebrate gut
microbiota
Ruth E. Ley, Catherine A. Lozupone, Micah
Hamady||, Rob Knight and
Jeffrey I. Gordon

presented by Yahong Wen

Department of Molecular and Cellular Biochemistry
 you are what you eat-diet and human
evolution
Homo
Australopithecus erectus
feed on Bulbs and
seeds and roots
soft fruits
~2 Mya and
~4.4 Mya persisted for
(million years ~1 Myr.
ago) until ~2.5
Mya

H. sapiens
meat

Pleistocene

Pictures adapted from google

you are what you eat
-Diet and Human evolution
Diet not only affect human structure, but
also genes:

Human have roughly three times of Amylase

gene than chimpanzee: intensive starch diet

Genetically regulated lactose tolerance is in

association with cattle milk consumption
Does diet shape the microbiota in our gut ?

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

Recall what is UniFrac:
Distance Measure
Measures the evolutionary distance between
microbial communities

Information adapted from

dparks.wdfiles.com/local--
files/exploringmicrobial.../UniFrac.ppt
What is OTU

Operational taxonomic Unit (OTU): definition of a

taxonomic unit based on sequence divergence

species 97% sequence homology

genus 90% sequence homology
family 80% sequence homology
Primary study

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 genus-

level OTUs than samples from other species
Different species have different diet!

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 www.stanceequine.com/horsecondition.p

Diet and gut morphology shape
mammalian gut microbiota
Principal Coordinates
analysis(PCoA)
B 4
C 3 6
D 4 3 3
A B C
PC2

B C

PC1
Bacteria community composition between gut
associated and free-living communities
(PCoA of unweighted UniFrac values)
Firmicutes and Bacteroidetes are most
ubiquitous among vertebrate gut samples
Similar pattern observed in
individual bacterial phyla
(PCoA of unweighted UniFrac values)
Second approach: network analysis

schematic key of network

analysis1
Network analysis of bacterial communities from
animal associated and free-living communities
Network analysis of bacterial communities from
animal associated and free-living communitiesi
Schematic key of network analysis2
What are the phyla of
microorganisms within each habitat
Vertebrate gut/freeliving microorganism
community dichotomy
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
What are the selection forces?
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
Vertebrates Adaptive immune system
decides what microorganism can co-exist

dev.nsta.org/evwebs
Microorganisms selection
pressure on the host
Not Healthy Healthy

darmano.typepad.com/.../07/human_hierarchy
The unique biochemical environment helps
shape the microbiota within vertebrate gut

Stable Temperature
Nutrient rich
Anaerobic
Oxidized environment
Summary
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