Piotr Nowak
Gut microbiota diversity predicts immune status in HIV-1
infection
Piotr Nowak MD, PhD. Karolinska Institutet, Stockholm
Hypothesis
The gut microbiota is changed in HIV infection which influences disease progression.
Antiretroviral therapy restores the composition of the gut microbiota.
Piotr Nowak
Study design – prospective observational
Patients (n=80) Inclusion criteria:
i) age >18 years ii) chronic HIV-1 infection iii) no antibiotics and probiotics <2 months iv) no diarrhea
Viremic untreated patients, n=28 n=19 followed longitudinally (median 10 months)
Elite controllers, n=3
HIV-negative controls, n=9
Piotr Nowak
HIV-1 infected subjects
Healthy Controls
Number of subjects 31 9
Age (years) 40.5 (19-67) 44.0 (28-62)
Male/female ratio 16/15 5/4
Ethnicity: Caucasian / African / Oriental
17/12/2 7/2/0
Mode of transmission: *MSM /IVDU /MSW
7/6/18
N/A
Years since diagnosis 3 (1-26) N/A
CD4 T cell count (cells/ul) 355 (120-2470) N/A
CD8 T cell count (cells/ul) 970 (380-2390) N/A
HIV-RNA (copies /ml) 48800 (<20**-990000) N/A
BMI 24 (18-36) N/A
** Three Elite controllers had undetectable HIV-1 RNA at baseline.
Patient characteristics
Piotr Nowak
Study design – prospective observational
Material and methods:
Blood and stool samples collected at baseline and at follow up.
16s rRNA from stool samples analysed by deep sequencing with Illumina platform (300 bp).
Plasma markers of microbial translocation /inflammation were analysed by ELISA or LAL assay.
Piotr Nowak
Results : number of observed taxa
Piotr Nowak
Results: alpha diversity
Piotr Nowak
Low diversity in HIV-1: low CD4-count
p=0.021
Piotr Nowak
Marker No of observed species Diversity (Shannon)
(r, p-value) (r, p-value)
CD4 T-cell count 0.59, p=0.009 0.40, p=0.02
CD4% 0.54, p=0.02 0.47, p=0.01
CD4/CD8 0.53, p=0.003 0.48, p=0.01
sCD14 -0.42, p=0.02 -0.41, p=0.02
LPS -0.51, p=0.007 -0.35, p=0.07
LBP -0.45, p=0.01 -0.32, p=0.09
sCD163 -0.48, p=0.02 -0.25, p=0.27
Diversity correlates with inflammation/microbial translocation
Piotr Nowak
Predictor Observed species
Covariates Beta-coefficient
(95% CI) p-value
Age, gender 0.88
(0.35-1.41) 0.002
Age, gender,
viral load
0.84
(0.28-1.40) 0.005
Age, gender,
BMI
1.02
(0.42-1.61) 0.002
Age, gender,
LPS
0.74
(0.23-1.26) 0.007
Age, gender,
sCD14
0.73
(0.17-1.28) 0.013
Piotr Nowak
No of bacterial species as independent predictors of CD4+ T cells in viremic patients (n=28)
Wei
ghte
d Un
ifrac
dive
rsity
inde
x
VP (n=2
8)
EC ( n=3
)
CTR (n=9
)0.2
0.3
0.4
0.5
0.6p<0.001
Interpatients (beta) diversity at baseline
Rela
tive
abun
danc
e(%
of to
tal b
acte
ria)
VP (n=28
)
EC (n=3)
CTR (n=9)
p__Actinobacteriap__Bacteroidetes
p__Firmicutesp__Proteobacteriap__Tenericutes
100%
50%
20%
Baseline composition of microbiota at phylum level in viremic patients, elite controlers and healthy controls
Five most abundant phyli are presented
Piotr Nowak
num
ber
of o
bser
ved
spec
ies
BL (n=16
)
FU (n=16
)0
100
200
300
400
500
p=0.001
Shan
non
dive
rsity
inde
x
BL (n=16
)
FU (n=16
)0
2
4
6
8p=0.006
a) b)
c)
Changes after ART: a) observed species b) intra- c) inter-patients diversity
Piotr Nowak
Conclusions
There are profound alterations both in diversity and composition of gut microbiota in HIV-1 infected patients.
Alpha diversity correlates positively with CD4 T cell counts inversely with sCD14, LPS, LBP and sCD163.
Short time ART does not restore gut microbiota.
Piotr Nowak
Acknowlodegments
Karolinska Institutet B. Barqasho U. Neogi A. Sönnerborg
Oslo University M. Troseid J. R. Hov E. Avershina K. Rudi
Piotr Nowak