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HCV patients' gut microbiome

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Abd Elrahman Mahmoud

on 19 March 2016

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Transcript of HCV patients' gut microbiome

H
C
V

P
atients'

Gut
M
icro
b
iome

A
ccording
t
o
W
H
O
EGYPT

Highest
prevalence on the world
Approximately
20% of Egyptian blood donors
are anti-HCV positive
14.7%
of the population- about
13 millions
are infected.
C
ausality
MOST of current research study
Virus

C
OTHER CAUSES
A
ccelerate
L
iver
D
egeneration
70% OF BLOOD SUPPLY TO THE LIVER
N
EW
Q
UESTIONS
1- What is the structure of HCV patients gut microbiome? is there difference than healthy ?

2- Is there a specific species that might affect the liver state? (Beneficial or not)?
H
OW
T
O
A
NSWER
COLLECTING
S
tool
s
amples:
From
healthy
&
HCV
patients
D
NA
e
xtraction
s
tep
Sequencing step (NGS)
D
ata
a
nalysis &
i
nterpretation
T
H
A
N
K
S
Abdelrahman Mahmoud

BY
Data Output = 15 million sequence
QIIME
Phyloseq
- Faculty of Pharmacy
- BSU (Graduated 2013)

- Biotechnology master

Faculty of postgraduate studies of advanced sciences - BSU
A
bdelrahman
M
ahmoud
A
stonishing
S
cientific
H
istory
Book:
What Is Life?
Erwin Schrödinger
1944
Structure
DNA
Central Dogma

S
EQUENCED
G
ENOME
THE FIRST
-Bacteriophage Fx174
a viral genome with only
5,368
base pairs.
- 4 years.
- Noble prize
- Human genome sequencing
2.5 million years
Biologist Dream

S
EQUENCING
H
UMAN
G
ENOME
Human Genome Project
Total cost:
3$ BILLIONS
The project got underway in

2001
HUMAN GENOME PROJECT
BEFORE
AFTER
100.000 GENES
20.000 GENES
FRUIT FLY
H
uman
M
icrobiome
P
roject
N
EW
D
ISCOVERIES
M
Y
H
YPO
TH
ESIS
T
HE
G
UT
M
ICROBIOME
1 :10
Human : Microbial
cells
of known bacteria
at least
1000
different species
More than
3 million genes
(150 times more than human genes).
1.5 KG =
WEIGHT
Worsen LIVER STATE
THROUGH
S
PECIFIC
S
PECIES
70 % BLOOD SUPPLY
THROUGH PORTAL VIEN*
B
ACTERIAL
M
ETABOLOITIES
* Gut-liver axis: The impact of gut microbiota on non alcoholic fatty liver disease
Present part of our results at
13th Annual Rocky Mountain Bioinformatics Conference -
COLORADO - USA
3D
Frederick Sanger
1990
ENCODE
3.3 BILLIONS
META
GENOMICS
In Greek,
meta
means
“transcendent”

Transcending the
individual organism
to focus on the genes in the community and how genes might influence each other’s activities in serving collective function

In brief:
studying bacterial as

communities
not as
individuals
!

face Metagenomics studies !
In the pure-culture paradigm,
the presence of multiple species in the same culture medium means
“contamination,” !
Difficulties
it was difficult to study microbes in their own environments;
microbiologists studied

individual species
one by one
in the laboratory.
WHEN CULTURED ON PETRI DISH >>>
NOT GROW !!

SOLUTION
THE
N
EXT
G
ENERATION
S
EQUENCING (
NGS
)
TECHNOLO
GY
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