gut microbiota and whole-body systems biology

1
Room 3-517, Biology Building, Shanghai Jiao Tong University, Shanghai 200240, China
8003517
The Power of Top-down Thinking and The Shanghai Version of Systems BiologyTop-down vs. Bottom-up
Shanghai Jiao Tong University
Tools for understanding complex engineering systems can be applied in biomedicine
Engineering paradigm and TCM
1 Robustness or Homeostasis 2 Functional redundancy 3 Global regulation 4 Emergent properties
“To understand the whole, One must study the whole”

the measurement of their emergent functions

Classification in an unsupervised learning mode with no prior knowledge required

System trajectory analysis
State space model
System trajectory analysis
Classification and monitoring of complex systems based on measurements of emergent functions
Structural Health Monitoring
Changes in vibration, noise and exhaust gas for engine health monitoring

Secretome-extracellular proteins Metabonome-extracellular metabolites
Vibration Noise Exhaust Gas
Nicholson 2004
Vibration Noise Exhaust Gas
Emergent functions of the human body
(Whole-body systems biology and health assessment) Health assessment and monitoring based on measurements of results of gene-environment interactions at the whole-body level Essential criteria
• • Non-invasive • • Global • • Dynamic, low-cost, high throughput • • Molecular-based • “”“” • Non-targeted • • Digital, quantitative, highly reproducible
Molecular assessment of human health at the whole-body level
——
Systems approaches for quantitative assessment and monitoring of human health

Cell composition of human body
• 10 human cells • 90 bacterial cells
Gene composition of human body
• Human genome (25,000 genes)
metabolism

Cell composition of human body
• 10 human cells • 90 bacterial cells
Gene composition of human body
• Human genome (25,000 genes)
metabolism
Include our microbiome
Nicholson JK, Nat Rev Microbiol,2005

Partner for health or Pathogen for diseases?
Foods
Health
Genome
Microbiome
Foods
Diseases
Genome
Microbiome
——
-Co-variation analysis between host global metabolism and gut microbiota
Li et al. , PNAS
Bifidobacterium pseudocatenula D86187, 100%
Ruminococcus bromii X85099, 100%
Pseudobutyrivibrio ruminis X95893, 100%
Bacteroides coprocola AB200225, 100%
Bacteroides uniformis AB215084, 100%
Bacteroides thetaiotaomicron AY895191, 100%
V3-b52 var211
CL-b14 var110
V3-b34 var134
CL-b16 var128
CL-b8 var77
CL-b11 var89
V3-b24 var88
V3-b6 var25
BAC-b31 var176
BAC-b16 var97
B acteroidetes
C lostridia
A ctinobacteria
molecular mechanistic studies
Liping Zhao Shanghai Center for Systems Biomedicine
USA Adult Obesity Trends* 1991, 1996, 2004
19961991 (*BMI ≥30, or about 30 lbs overweight for 5’4” person)
No Data <10% 10%–14% 15%–19% 20%–24% ≥25%
2004
Urban
Rural
60
12
28
52
13
35
0
20
40
60
80
pr ev
al en
Xu LIN
Prevalence of Type 2 Diabetes in Different Countries
0
2
4
6
8
10
12
14
ChinaUSA
Yoon et al., Lancet, 2006
Prevalence of Type 2 Diabetes in Different Countries
Xu LIN
monitoring
ZHAO lab, JIA lab
Week***
HFD 187±2 225±12 315±17 368±20 399±21 437±24 485±31 502±32
CD 185±3 212±7 299±21 344±30 365±38 386±41 416±47 424±48
week

M H1 H2 H3 H4 H5 H6 H7 M C1 C2 C3 C4 C5 C6 M
HFD CD
A 2nd week
M H2 H3 H4 H5 H6 H7 M C1 C3 C4 C5 C6 M
HFD CD
B 5th week M H1 H2 H3 H4 H5 H6 H7 C1 C2 C3 C4 C5 C6 M
HFD CD
C 8th week
M H1 H2 H3 H4 H5 H6 H7 M C1 C2 C3 C4 C5 C6 M HFD CD
D 9th week

Anaerovibrio Anaerovibrio
Gram-positive
Interactions between gut microbiota, diet and host genotype for host health

Apoa-1gene Knockout Mice Apoa-1
Reduced HDL-cholesterol levels Susceptibility to high-fat dietary-induced atherosis Insulin resistance and early symptoms of diabetes
Shanghai Jiao Tong UniversityApolipoprotein A-and 2 type Diabetes
Chen lab, 2007
APOA-could activate AMPK and affect the energy and glucose metabolism of the cell.
Shanghai Jiao Tong University Animal trial scheme
High-fat diet group
5 mice (KF)
Normal diet group
5 mice (KN)
3 replicates from this step
PCR-DGGE Fingerprinting
M KF1 KF2 KF3 KF4 KF5 M KN1 KN2 KN3 KN4 KN5 M
M WF1 WF2 WF3 WF4 WF5 M WN1 WN2 WN3 WN4 WN5 M
HFD
CK
Wildtype mice
A
B
C
D
M 1 2 3 4 5 M 1 2 3 4 5 M M 1 2 3 4 5 M 1 2 3 4 5 M
ApoA- -/-/ HF ApoA- -/-/ CH Wt / HF Wt / CH
Shanghai Jiao Tong University TRFs of KF and KN groups
Alu Hae Hha Msp Csp6
Band Similarity (%)
8 100 Lactobacillus johnsonii (AB186343) Firmicutes, Bacilli, Lactobacillales, Lactobacillaceae, Lactobacillus
15 100 Helicobacter ganmani (T) (AF000221) Proteobacteria, Epsilonproteobacteria, Campylobacterales, Helicobacteraceae, Helicobacter
98 uncultured bacterium (DQ815337) Bacteroidetes,Bacteroidetes,Bacteroidales, Porphyromonadaceae, Tannerella
80 Porphyromonas gulae (ATCC51700) Bacteroidetes,Bacteroidetes,Bacteroidales, Porphyromonadaceae, Porphyromonas
99 uncultured bacterium (DQ815337) Bacteroidetes,Bacteroidetes,Bacteroidales, Porphyromonadaceae, Tannerella
81 Porphyromonas circumdentaria Bacteroidetes,Bacteroidetes,Bacteroidales, Porphyromonadaceae, Porphyromonas
Actinobacteria, Actinobacteridae, Bifidobacteriales, Bifidobacteriaceae, Bifidobacterium
98 Bifidobacterium animalis subsp. Animalis (AB186294)
Actinobacteria, Actinobacteridae, Bifidobacteriales, Bifidobacteriaceae, Bifidobacterium
93 Bryantella formatexigens (T) (AJ318527) Firmicutes, Clostridia, Clostridiales, Clostridiaceae, Bryantella
99 uncultured bacterium (EF099100) Firmicutes, Mollicutes, Incertae sedis 8, Erysipelotrichaceae
86 Eubacterium cylindroides (L34617) Firmicutes, Clostridia, Clostridiales, Eubacteriaceae, Eubacterium
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16
7
6
Normal ch
4
3
2
1
5
4
3
2
1
5
4
3
2
1
5
4
3
2
1
Wt
Gram-positive Gram-negative
Band10 and Band 11 were Bifidobacterium spp.
M 1 2 3 4 5 M 1 2 3 4 5 M M 1 2 3 4 5 M 1 2 3 4 5 M
ApoA- -/-/ HF ApoA- -/-/ CH Wt / HF Wt / CH
10
11
10
11
0
0.5
1
1.5
2
2.5
3
3.5
4
KN1 KN2 KN3 KN4 KN5 WN1 WN2 WN3 WN4 WN5 KF1 KF2 KF3 KF4 KF5 WF1 WF2 WF3 WF4 WF5
A bu
nd an
ce o
fb ifi
do ba
ct er
iu m
sp p.
(C op
y N
um be
r / n
g to
ta l
fe ca
A )
1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5
ApoA -/- / HFApoA -/- / CH Wt / HFWt / CH
×105
0
5
10
15
20
25
30
35
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35
Bifidobacteriales
% o
al S
eq ue
nc es
1 2 2 2 3 4 5 5 5 1 1 1 2 3 4 4 4 5 1 2 3 3 3 4 5 5 5 1 1 1 2 3 4 5 5 5
ApoA- -/-
Shanghai Jiao Tong University Proteobacteria
0
1
2
3
4
5
6
7
8
9
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 1 2 2 2 3 4 5 5 5 1 1 1 2 3 4 4 4 5 1 2 3 3 3 4 5 5 5 1 1 1 2 3 4 5 5 5
ApoA- -/-
ApoA- -/- normal chow Wild-type normal chow
1 2 2 2 3 4 5 5 5 1 1 1 2 3 4 4 4 5 1 3 3 3 4 5 5 5 1 1 1 2 3 4 5 5 5
Wild-type high fat dietApoA- -/- high fat diet
Bifidobacteriales vs.Desulfovibrionales
ApoA- -/- normal chow Wild-type high fat diet Wild-type normal chow
% o
al S
eq ue
nc es
1 2 2 2 3 4 5 5 5 1 1 1 2 3 4 4 4 5 1 2 3 3 3 4 5 5 5 1 1 1 2 3 4 5 5 5 ApoA- -/- high fat diet
1 2 2 2 3 4 5 5 5 1 1 1 2 3 4 4 4 5 1 2 3 3 3 4 5 5 5 1 1 1 2 3 4 5 5 5 ApoA- -/- high fat diet ApoA- -/- normal chow Wild-type high fat diet Wild-type normal chow
Clostridiales Erysipelotrichales
Cani, P.D 2007
——

AIMS TO MODEL HUMAN GLOBAL METABOLIC REGULATION -THE BASIC HOLISTIC PHILOSOPHY IS IN HARMONY WITH THEORY OF TRADITIONAL CHINESE MEDICINES

GLOBAL SYSTEMS BIOLOGY IS THE TOP-DOWN INTEGRATION OF MULTI-OMICS DATA TO DECIPHER GENE-ENVIRONMENT INTERACTIONS IN RELATION TO DISEASE DEVELOPMENT.

:
Nicholson
“Normal”
cystine
Alcohol
Analgesics
——
Shanghai Jiao Tong University Our mission
“Systems approaches for assessing human health precisely and non-invasively—with high-throughput and low-cost molecular profiling of biological information in the extracellular spaces of human bodies (e.g. blood proteins, urine metabolites, and gut bacteria)—can enable us to conduct large scale cohort studies to discover pre-disease biomarkers associated with the transition from health to disease. Models based on these pre-disease biomarkers can help us monitor human health with predictive power for effective preventive management of public health. This strategy will eventually lead to modernization of the Traditional Chinese Medicine practice of treating diseases before they occur.”
Nutritional Nutritional interventionintervention
Preventive Management of Metabolic Diseases via Nutritional Modulation
Nutrition, gut microbiota, host immunity and metabolism, and their interactions in the development of obesity and related metabolic diseases
Opening novel avenues to combat these conditions in a predictive, preventive and personalized manner
Study design: 500 pairs of age, sex and lifestyle matched overweight/obese and non-obese individuals
• Case BMI ≥ 26 kg/m2
• Control18 ≤ BMI ≤ 23kg/m2
Inclusion criteria:
• Urban residents in Shanghai • Residence ≥ 10 yrs • Age: 35-54, male > 40% • Without currently participating other study • Without physical disabilities and mental disorder
Population-based Case-Control Study
Lifestyle & Health Status
CES-D questionnaireMental Health Height, Weight, Blood pressure, Waist circumferences, Hip circumferences DEXA: Fat, lean mass and bone density, % body fat, % trunk fat
Anthropometrics Body Composition
Demographic Information
HNF4A, PPARG, PCK1, G6PC, PPARGC1A, NR3C1, ESRRA, ADIPOQ, RBP4, ENPP1,etc.
Gene variants
BiomarkerCategory
Pattern recognition
Urine
Fecal matters
Genetic mutation Fat metabolism PPARA PPARD PPARGC1B Energy metabolism ADIPOQ INSIG2,
ADIPOR1/2
• Lipid level TchLDL HDLTG
• Inflammatory factorsCRP IL6TNFR1/R2, RBP4
• Adipocytokines: Adiponectin, Resistin, PAI RBP4
• Structural differences of gut flora
• Functional bacteria associated with obesity
• Major diet/nutrients associated with obesity
• Genetic susceptibility and obesity-associated gut microbiota
• Mechanisms of obesity-associated gut microbiota affecting metabolism
Obese ones (500)
Normal ones (500)
• Gut microbiota structure
interactions
• Databases and kits • Diet-based prevention of metabolic diseases
• The beverage or additive that works just for you
Specific Aims
the measurement of their emergent functions

Classification in an unsupervised learning mode with no prior knowledge required

——
drugdrug
Healthy spaceHealthy space
for preventive management of public health for discovery of pre-disease biomarkers with predictive power
The four diagnostic techniques “”
• The eight guiding principles for differentiation of syndromes “”
• • • •
Gene-centricmolecular medicine
………..
but fragmentary at whole body level
Shanghai Jiao Tong University DNA vs. QI “”
TCM vs. Western Medicine • Diseased man vs. man’s disease • • Stratification of patients vs.
classification of diseases • • Top-down vs. bottom-up • • Global vs. local • • Intact person vs. Genes •
Four diagnostic techniques Wang, Wen, Wen, Qie “ ”
Eight guiding principles Yin, Yang, Han, Re Biao, Li, Xu, Shi
“ ”
“ZHENG ” differentiation for patient stratification
Diagnosis and Prognosis, Efficacy and Safety Evaluation,
Drug Discovery
Understanding how TCM works
Shanghai Jiao Tong University Trajectory plot of OSC-PLS model for individual subject pre and post exposure to
chamomile tea
Nicholson
Subject does not return to pre-dose space after 2 weeks- changes are in the gut microbiota
0
10
20
30
40
50
Wu group, Jia group, Zhao group
Reduction of ACF formation by TCM herbal extracts
Shanghai Jiao Tong UniversityCoptidis rhizoma, Evodia rutaecarpa herbal pair
Coptidis Rhizoma Evodiae Fructus
Major component: evodiamine rutaecarpinehydroxy- evodiamine limoninsynephrineevodente
-5
0
5
10
15
control 9th model 9th herb pair 9th
PCA scores plot of the 16S rRNA gene V3 region DGGE profiles of different groups
Shanghai Jiao Tong UniversityA 3DA 3D--PCA sores plot of GC/MS PCA sores plot of GC/MS spectral data from the three group spectral data from the three group rats at the 9rats at the 9thth week (n=8 per week (n=8 per group; DMHgroup; DMH--induced, red dots; induced, red dots; healthy, blue dots; herb treated, healthy, blue dots; herb treated, black dots; each dot denotes an black dots; each dot denotes an individual ratindividual rat
TimeTime--dependent mean fold changesdependent mean fold changes of those differential metabolites of of those differential metabolites of
healthy group, DMHhealthy group, DMH--induced group induced group and herb treated group at 3rd, 5th, and herb treated group at 3rd, 5th, 7th, and 9th week7th, and 9th week ..
Jia group
Traditional medicine Western medicine New medicine
drugdrug
Healthy spaceHealthy space
for preventive management of public health for discovery of pre-disease biomarkers with predictive power
What is a microbial community?
Cytoplasm Nucleoid
“The Whole is bigger than the sum of the parts”
• The whole has some new properties that the parts have not
Community structure (population composition) determines ecological function (the function that can be realized only when the members work together)
Emergent properties – Functions of the community
Shanghai Jiao Tong UniversityContinuous culture-the chemostat
In such a device, the population density is controlled by the concentration of limiting nutrient in the reservoir, and the growth rate is controlled by the flow rate. Both parameters can be set by the experimenter
Composition of the community
Determination of 16S rRNA gene sequences • MT1 Pseudomonas sp. • MT4 Pseudomonas sp. • MT3 Alcaligenes sp. • MT2 Empedobacter sp.
The relative abundances • Polyclonal rabbit antisera specific for each of the
members • MT1 84±3% • MT3 and MT4 8±4% • MT2 1%
Shanghai Jiao Tong University Interdependence
“The community seems to be so stable because each member plays a crucial role, either in providing carbon skeletons for the others (MT1) or in scavenging toxic metabolites that inhibit the primary degrader if they accumulate.”
Structural shifts of gut microbiota induced by carcinogen during
precancerous lesion development
Shanghai Jiao Tong University Development of Colorectal cancer
DysplasiaACF under a light microscopy×40
polypous adenoma adenocarcinoma
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10
20
30
40
50
Wu group, Jia group, Zhao group
Reduction of ACF formation by TCM herbal extracts
The third week
control modelMr Mr
The ninth week
control modelMr Mr
DNA fingerprinting of gut microbiota GC/MS profiling of host metabolism
Concomitant shifts of gut microbiota and host global metabolism
away from healthy control during precancerous lesion formation in DMH treated group
Gut microbiota structure
Key metabolites for differentiation between healthy and precancerous animals
Increased urinary excretion • citrate, • 4-hydroxy-benzeneacetic acid, • 4-hydroxyphenyl-propionic acid,
Decreased endogenous metabolites • butanedioic acid, • benzeneacetic acid, • glycine, • 4-methyl-phenol, • hippuric acid, • phenylacetyl-glycine.
19 98 Ruminococcus obeum (AY169419) Firmicutes;Clostridia;Lachnospiraceae
25 95 Allobaculum stercoricanis(AJ417075) Firmicutes; Mollicutes; Allobaculum.
97 uncultured bacterium(AY986052) Bacteroidetes;Porphyromonadaceae
Key gut bacteria for differentiation between healthy and precancerous animals

AIMS TO MODEL HUMAN GLOBAL METABOLIC REGULATION -THE BASIC HOLISTIC PHILOSOPHY IS IN HARMONY WITH THEORY OF TRADITIONAL CHINESE MEDICINES

GLOBAL SYSTEMS BIOLOGY IS THE TOP-DOWN INTEGRATION OF MULTI-OMICS DATA TO DECIPHER GENE-ENVIRONMENT INTERACTIONS IN RELATION TO DISEASE DEVELOPMENT.

:
Nicholson
“Normal”
cystine
Alcohol
Analgesics
JAPANESE
AMERICAN
Nicholson
Chinese Populations.
Gut Microbiota and Whole-body Systems Biology
Classification and identification of complex systems based on the measurement of their emergent functions
Structural Health Monitoring
(Whole-body systems biology and health assessment)
Molecular assessment of human health at the whole-body level——
Systems approaches for quantitative assessment and monitoring of human health
New view on human bodyThe Superorganism Concept *
New view on human bodyThe Superorganism Concept *
Co-metabolism of host and gut bacteria
Modulation of the second genome in the Superorganism
Functional analysis of gut microbiota-Co-variation analysis between host global metabolism and gut microbiota
Gut Microbiota and Diet-induced Metabolic Syndrome
Prevalence of Obesity
“”Structural segregation analysis of gut microbiota and host health monitoring
Interactions between gut microbiota, diet and host genotype for host health
Apoa-1gene Knockout MiceApoa-1
Animal trial scheme
RT-PCR of Bifidobacterium spp.
Metabolic Endotoxemia Initiates Obesity and Insulin Resistance
Our mission
Population-based Case-Control Study
Classification and identification of complex systems based on the measurement of their emergent functions
TCM-Assess and intervene at whole body level
Trajectory plot of OSC-PLS model for individual subject pre and post exposure to chamomile tea
Precancerous lesion of colon cancer
Coptidis rhizoma, Evodia rutaecarpa herbal pair
16S rRNA gene V3 fragment DGGE profiles
PCA scores plot of the 16S rRNA gene V3 region DGGE profiles of different groups
Emerging of New Medicine
What is a microbial community?
Structure of a bacterial cell
From individual cell to population
Emergent properties – Functions of the community
Why communities?
Structural shifts of gut microbiota induced by carcinogen during precancerous lesion development
Precancerous lesion of colon cancer
Monitoring of host metabolism and gut microbiota

FUNDAMENTAL METABOTYPE DIFFERENCESPCA-DA of population data (disease outliers removed)
Prediction of individualized drug response

gut microbiota and whole-body systems biology

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