Esa presentation lorenzi

1. Effect of space travel on the
astronauts’ microbiome and
health.
Hernán A. Lorenzi
Assistant Professor
J. Craig Venter Institute
ESA
October 2020

2. 2
The human microbiome in health and disease
Hernan Lorenzi, JCVI
• Cosmic radiation
• Microgravity
• Stress
• Diet
• Immune dysregulation
• Sleep deprivation
• Increased oxidative stress
• Altered light/dark cycles
• Isolation and low environmental
biodiversity
Anti-inflammatory activity
from fiber intake
Stimulation of
the Immune System
Protection against
microbial infections
Synthesis of essential
compounds
and detoxification
Chronic diseases
(obesity, diabetes
allergy, IBD, etc.)Cancer
(colon, liver, etc.)
Microbial
Infections
human
microbiome
Healthy Microbiome
Altered Microbiome
Mental disorders
(anxiety, depression)
Microbialdysbiosis
Reducedmicrobialdiversity
Endocrine
regulation
Diarrhea

3. 3
Project Aims
Hypothesis: Long-term exposure to stressors associated with spaceflight affects the
composition of the astronauts’ microbiome.
§ Aim 1: To characterize changes occurring in the gut, oral, skin and nose microbiomes of
astronauts during a six-month/one-year space mission to the International Space Station.
§ Aim 2: To assess astronauts’ immune function and stress levels and their association with
changes in the crew microbiome.
§ Aim 3: To investigate the interaction between the astronauts’ microbiome and the
microbes that inhabit the International Space Station (ISS).
3

4. 4
Body x 4
fecal
saliva
blood
water
ISS surface
EHH survey
Experimental design
Longitudinal study; N=9 astronauts that stay 6 months (N=8) or 1 year (N = 1) in the ISS
4
L-240 L-150 L-90 L-60 FD7 FD90 FD180 R-1 R+0/1 R+30 R+60 R+180
Time (days)
Preflight Postflight
astronauts’
microbiome
stress immune
system
environmental
microbiome
EHH
survey
Data
types
-16S v4
-metagenomic
sequencing
cortisol
HSV/VZV/EBV
virus
reactivation
cytokines 16S v4 -Metadata:
diet
health status
Temp
Humidity
Aim 1
Aim 2
Aim 3

5. 5
Astronauts’ microbiome (alpha and beta diversity)
Alpha diversity and richness Beta diversity
Pre-In(between)
Pre-In(within)
Pre
In
Post
Pre
In
Post
Pre
In
Post
Pre
In
Post
Pre
In
Post
Pre-Post(between)
Pre-Post(within)
Pre-In(between)
Pre-In(within)
Pre-In(between)
Pre-In(within)
Pre-In(between)
Pre-In(within)
Pre-In(between)
Pre-In(within)
Pre-Post(between)
Pre-Post(within)
Pre-Post(between)
Pre-Post(within)
Pre-Post(between)
Pre-Post(within)
Pre-Post(between)
Pre-Post(within)

6. 6 Hotz Vitaternam et al., Microbiome (2019)
The gut microbiome of mice experience changes in space similar to
astronauts (Hotz Vitaternam et al., Microbiome (2019))

7. 7

8. 8
Cytokine
Cytokine vs GI
microbiota
correlation (D)
SE
Correlation
p-value
Inflight
cytokine
change
Bacteria Genus
Inflight OTU
change
CXCL8/IL-8 -0.581 0.144 5.43E-05 ⬆ Otu000010 Fusicatenibacter ⬇
-0.622 0.126 8.57E-07 Otu000010 Fusicatenibacter ⬇
-0.36 0.087 3.69E-05 Otu000011 Dorea ⬇
TNFa -0.467 0.099 2.32E-06 ⬆ Otu000010 Fusicatenibacter ⬇
IL-17 0.464 0.114 4.35E-05 ns Otu000054 Faecalibacterium ⬆⬆⬆
-0.5 0.12 3.09E-05 Otu000011 Dorea ⬇
-0.5 0.102 8.89E-07 Otu000028 Ruminococcus_2 ⬇⬇⬇
0.618 0.12 2.85E-07 ns Otu000038 Akkermansia ⬇⬇
-0.611 0.06 4.33E-24 ns Otu000165 Lachnospiraceae (uncl.) ⬆
IL-2 ⬆
IL-4 -0.622 0.155 5.87E-05 ns Otu000010 Fusicatenibacter ⬇
IL-10 -0.379 0.103 2.46E-04 ns Otu001908 Roseburia ⬇⬇
G-CSF -0.364 0.08 5.67E-06 ns Otu000016 Blautia ⬆⬆
FGF basic 0.357 0.098 2.85E-04 ns Otu000054 Faecalibacterium ⬆⬆⬆
Tpo 0.352 0.099 3.71E-04 ns Otu000071 Lachnospiraceae (uncl.) ⬇⬇
-0.556 0.087 1.72E-10 Otu000010 Fusicatenibacter ⬇
-0.42 0.106 7.08E-05 Otu000011 Dorea ⬇
CCL2/MCP-1 ⬆
CCL4/MIP-1B -0.38 0.1 1.49E-04 ⬆ Otu000011 Dorea ⬇
CCL5/RANTES 0.521 0.138 1.55E-04 ns Otu000060 Lachnoclostridium ⬆
VEGF ns
IL-1B ⬆
IFNg
IL-1ra ⬆
1.9
2
2.1
2.2
2.3
2.4
2.5
2.6
L-180 FD10 FD180 R+0 R+180
CCL2/MCP-1
1
1.2
1.4
1.6
1.8
2
2.2
2.4
2.6
L-180 FD10 FD180 R+0 R+180
CCL4/MIP-1B
0
0.5
1
1.5
2
2.5
3
3.5
L-180 FD10 FD180 R+0 R+180
CXCL8/IL-8
0.5
0.6
0.7
0.8
0.9
1
1.1
1.2
1.3
1.4
L-180 FD10 FD180 R+0 R+180
G-CSF
0
0.2
0.4
0.6
0.8
1
1.2
1.4
L-180 FD10 FD180 R+0 R+180
IL-1B
1.5
2
2.5
3
3.5
4
L-180 FD10 FD180 R+0 R+180
IL-1ra
1.4
1.45
1.5
1.55
1.6
1.65
1.7
1.75
L-180 FD10 FD180 R+0 R+180
IL-2
1.15
1.2
1.25
1.3
1.35
1.4
1.45
1.5
1.55
1.6
L-180 FD10 FD180 R+0 R+180
TNFa
*** *** **
*** *
**
o
** o
**
***
o
Association between changes in cytokine profiles and bacterial
composition of the GI microbiome.
Cytokine changes in plasma
Correlation between plasmidic cytokines and GI microbiome
Postitive cytokine-OTU correlation
Negative cytokine-OTU correlation
o, p-value < 0.1; *, p-value < 0.05;
**, p-value < 0.01; ***, p-value < 0.01

9. 9
Changes in the Astronauts’ microbiome are already evident
within the first two weeks of the space mission
More similar in ISS
Less similar in ISS
A
B C
D

10. 10
Interaction between the Astronauts’ skin microbiome and
microbial communities from the ISS
Alpha diversity
Beta diversity
D
A
B
C

11. 11
ECNumber Description logFC logCPM F PValue FDR
3.2.1.14 chitinase 1.921 4.698 30.812 0.000 0.001
3.2.1.46 galactosylceramidase 1.542 5.267 23.430 0.000 0.004
1.1.1.20 glucuronolactonereductase -0.250 10.566 16.425 0.000 0.021
1.1.1.205 inosine-5'-phosphatedehydrogenase -0.250 10.566 16.425 0.000 0.021
4.4.1.11 methioninegamma-lyase 0.885 4.946 16.410 0.000 0.021
4.4.1.2 homocysteinedesulfhydrase 0.885 4.946 16.410 0.000 0.021
4.7.1.1 alpha-D-ribose1-methylphosphonate5-phosphateC-P-lyase -1.012 5.136 15.675 0.000 0.025
4.2.2.6 oligogalacturonidelyase 1.057 4.279 24.131 0.000 0.030
1.14.14.17 squalenemonooxygenase 1.044 4.152 14.512 0.000 0.031
1.8.1.7 glutathione-disulfidereductase -1.641 4.696 13.231 0.001 0.049
●
●
●
● ●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ●
●
●● ●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ●●
●●
−0.3 −0.2 −0.1 0.0 0.1 0.2 0.3
−0.2−0.10.00.10.20.3
MDS1
MDS2
AstB
AstC
AstD
AstF
AstG
AstJ
●
●
●
In
Post
Pre
p (pre vs in) = 0.028
p (pre vs post) = 0.534 ECNumber Description logFC logCPM F PValue FDR
3.7.1.3 kynureninase 0.961 4.20547824 22.382708 2.73E-05 0.02233987
Preflight vs Inflight
Preflight vs Postflight
Up inflight/postflight Down preflight
Changes in metabolic capacity of the GI microbiome

12. 12
Gene set enrichment analysis of metabolic pathways
More abundant inflight
Pathway stat.mean p.val q.val set.size
ko02040 Flagellar assembly 3.1237 4E-13 9E-11 35
ko02020 Two-component system 2.3464 5E-09 7E-07 274
ko02030 Bacterial chemotaxis 1.8097 9E-06 7E-04 24
ko00440 Phosphonate and phosphinate metabolism 1.3860 5E-04 3E-02 15
Pathway stat.mean p.val q.val set.size
ko00540 Lipopolysaccharide biosynthesis 1.795 0.0000 0.0043 35
AstB_Pre
AstC_Pre
AstD_Pre
AstF_Pre
AstG_Pre
AstJ_Pre
AstB_In
AstC_In
AstD_In
AstF_In
AstG_In
AstJ_In
K02844
K02850
K12981
K03275
K03280
K02840
K02560
K21345
K15669
K12975
K21344
K02843
K03276
K02841
K03269
K03274
K02535
K00979
K00912
K07031
K03273
K01627
K06041
K00748
K03271
K16363
K03272
K02527
K03270
K03278
K02847
K00677
K02517
K02536
K19353
−2 0 2
Value
Color Key
Preflight Inflight
K03280
K02840
K02560
K21345
K15669
K12975
K21344
K02843
K03276
K02841
K03269
K03274
K02535
K00979
K00912
K07031
K03273
K01627
K06041
K00748
K03271
K16363
K03272
K02527
K03270
K03278
K02847
K00677
K02517
K02536
K19353
−2 0 2
Value
Color Key
Two-way change
0
100
200
300
400
500
600
700
800
900
1000
Preflight Inflight Preflight Inflight
AstB AstD
Abundance
Genus
Syntrophobotulus
Thermosulfidibacter
Pelosinus
Sebaldella
Odoribacter
Clostridium
Megasphaera
Denitrovibrio
Butyrivibrio
Ruminiclostridium
Faecalibaculum
Faecalibacterium
Serratia
Marinitoga
Escherichia
Burkholderiales bacterium YL45
[Eubacterium] rectale
Muribaculum
Parabacteroides
Dialister
Acidaminococcus
Alistipes
Akkermansia
Prevotella
Bacteroides
Pathway: Lipopolysaccharide (LPS) biosynthesis:
AstB
AstC
AstD
AstF
AstG
AstJ
Up
Inflight
Up
Preflight

13. 13
Pathway: Butyrate and Proprionate Metabolism
Up
Inflight
Down
Inflight
Butyrate pathway Proprionate pathway
Butanoate
Propionate
AstB
AstC
AstD
AstF
AstG
AstJ

14. 14
Pathway: Vitamin Biosynthesis
Up
Inflight
Down
Inflight
Thiamine
Folate
Biotin
AstB
AstC
AstD
AstF
AstG
AstJ
Vitamin B6

15. 15
Conclusions
q Our study revealed that the skin, nose and GI microbiomes are altered during a mission to space.
q Reduction in skin Proteobacteria may be related with the high frequency of skin rushes and
hypersensitivity reactions experienced by astronauts in space.
q We found an association between compositional changes in the GI microbiome and changes in the
concentration of some plasma cytokines. Whether microbiome changes are causative of immune
dysregulation observed during spaceflight remains to be determined.
q There is a fluid interaction between the skin microbiome and the microbial communities of the ISS.
q Metagenomic analysis suggests that the metabolic capacity of the GI microbiome changes in space.
However, no major changes were detected in the genes encoding for SCFA and vitamins.

16. 16
Acknowledgments
Hernan Lorenzi
Manny Torralba
Kelvin Moncera
Yun Zhang
Karen Nelson
JCVI Sequencing
Core
Eduardo Zurek
C. Mark Ott
Duane Pierson
Satish Mehta
Brian Crucian
Cherie Oubre
Alan Feiveson
ISSMP experiment team
NASA Astronaut Corps
Funding provided by NASA’s
Human Research Program