对完整人体进行测量和干预

Shanghai Jiao Tong UniversityTCM-Assess and intervene at whole body level The Power of Top-down Thinking and Top-downThe Shanghai Version of Systemsvs. Bottom-upBiology The four diagnostic techniques “四诊” • 望、闻、问、切 Gut Microbiota and Whole-body The eight guiding principles for Systems Biology differentiation of syndromes “八纲辨证” 肠道菌群与人体系统生物学 • 表里 • 寒热 • 虚实 Liping Zhao • 阴阳 Shanghai Center for Systems Biomedicine Room 3-517, Biology Building, Shanghai Jiao Tong 感官测量 经验判断 University, Shanghai 200240, China 中国上海市东川路800号上海交通大学生物楼3－517 赵立平 “模糊的”整体 Holistic but empirical

从基因的角度解释和防治疾病的分子医学 Shanghai Jiao Tong University Shanghai Jiao Tong University DNA vs. QI “氣” Gene-centric，molecular medicine

TCM vs. Western Medicine 基因序列多样性与疾病易 • Diseased man vs. man’s disease 感性的关系 • 病的人与人的病 基因序列多样性与药物敏 • Stratification of patients vs. 感性的关系 classification of diseases 基因表达特性与药物代谢 • 病人分类与疾病分型 • Top-down vs. bottom-up 机理 • 自上而下与自下而上 基因表达特性与疾病发展 • Global vs. local 过程 • 整体到局部与局部到整体 ……….. • Intact person vs. Genes • 完整的人体与基因 定量测定 模式识别 精细的局部 Molecular detail at cellular level Molecular yet local but fragmentary at whole body level Complex systems share the same nature Complex systems share the same nature

Shanghai Jiao Tong University 复杂系统在本质上都是相似的 Shanghai Jiao Tong University 复杂系统在本质上都是相似的

1，鲁棒性 Robustness“To understand or Homeostasis the whole, 2，功能冗余 FunctionalOne must redundancy study the whole” 3，整体调控要理解整体就必须研究整体 Global regulation 4，涌现特性 Emergent properties

Engineering paradigm and TCM Engineering paradigm and TCM 工程学思维模式与中医理论 工程学思维模式与中医理论 Tools for understanding complex engineering systems can be applied in biomedicine Tools for understanding complex engineering systems can be applied in biomedicine

Complex systems share the same nature 涌现特性测量与复杂系统分类和监测 Shanghai Jiao Tong University 复杂系统在本质上都是相似的 UnderstandingClassification and the monitoring behavior ofof complexcomplex systems systems based on measurements of emergent functions 1，鲁棒性 Robustness“To understand or Homeostasis the whole, Systems states and 2，功能冗余 FunctionalOne must redundancy study the whole” state space models 3，整体调控要理解整体就必须研究整体 • Structural state 结构状态 Functional state State space model Global regulation • 功能状态 状态空间模型 4，涌现特性 System trajectory Emergent properties analysis • Attractors 吸引子 Engineering paradigm and TCM Initial conditions 工程学思维模式与中医理论 • 起始条件 Tools for understanding complex engineering systems can be applied in biomedicine • Disturbances 扰动 System trajectory analysis 系统轨迹分析 Changes in vibration, noise and exhaust gas for Shanghai Jiao Tong University engine health monitoring

结构健康监测 Structural Health Monitoring

振动、噪声和尾气的模式变化与发动机健康监测

Emergent functions of the cell

Shanghai Jiao Tong University 细胞的涌现特性 Classification and identification of complex systems based on the measurement of their emergent functions 基于涌现特性测量的复杂系统的 精细分类与鉴定

Secretome-extracellular proteins Vibration 振动 Classification in an unsupervised learning mode 分泌组－胞外蛋白质全谱 Noise 噪声 with no prior knowledge required Metabonome-extracellular metabolites 无监督的学习分类模式 代谢组－胞外代谢物全谱 Exhaust Gas 尾气 Nicholson 2004 Emergent functions of the human body 人体系统生物学与健康测量 Shanghai Jiao Tong University Shanghai Jiao Tong University 人体的涌现特性 (Whole-body systems biology and health assessment)

人体系统生物学通过在人体水平测定基因与环境互作的结果来准确评估 Metabonome 和监测人体的健康 Health assessment and monitoring based on measurements of results 代谢组 of gene-environment interactions at the whole-body level Metagenome 具有下列特征Essential criteria： • 非破坏性测量，可直接用于人体 元基因组 • Non-invasive • 整体测量，反映全身的健康状况 Secretome • Global • 高通量、低成本可实现大样本人群的动态监控 分泌组 • Dynamic, low-cost, high throughput • 以核酸、蛋白和代谢物等生物分子为测定对象 Urine-metabolites Vibration 振动 • Molecular-based 尿液代谢物谱 • 非靶向测定，通过“全谱扫描”和“盲分类”可以监测任何类型的健康变化 Feces- Noise 噪声 • Non-targeted 粪便细菌谱 • 数字化测量，可实现高度信息化 Blood-proteins Exhaust Gas 尾气 • Digital, quantitative, highly reproducible 血液蛋白质谱

人体健康的分子测量 MolecularShanghai Jiao Tong assessment University of human health at the whole-body level ——人体健康状况的多参数、多指标评估

分泌蛋白质组学 Systems approaches for Protein secretome quantitative assessment and 元基因组学 monitoring of human health Metagenome 代谢组学 用系统定量的方法进行 Metabonome

on 人体健康状况的评价与监测 Primary Molecules ti a tr Secondary Molecules il n F io lut Di C R on e c s en o tr r atio Molecular Profiling and Covariation Analysis p n TMAO creatinine ti hippurate o allantoincreatininetaurine citrate n 全谱分子扫描技术与模式识别 hippurate urea water 2-oxoglutarate fumarate succinate 振动、噪声、尾气 ppm 7 6 5 4 3 2 1 与发动机健康监测 New view on human body Shanghai Jiao Tong University The Superorganism Concept * Cell composition of human *Joshua Lederberg body • 10％ human cells • 90％ bacterial cells Genome Gene composition of 基因组 Gut Microbiota and Whole- human body Foods • Human genome (25,000 食物 Health genes) body Systems Biology Drugs 健康 •Karyome 药物 • Mitochondrome • Microbiome Microbiome • 1000 species Liping Zhao 微生物组 • 1 million genes Shanghai Center for Systems Biomedicine • Diverse and active School of Life Science and Biotechnology metabolism Human microbiome- Shanghai Jiao Tong University the second genome acquired after birth 微生物组－人后天获得的第二个基因组

New view on human body Modulation of the second Shanghai Jiao Tong University The Superorganism Concept * Shanghai Jiao Tong University genome in the Superorganism Cell composition of human *Joshua Lederberg body • 10％ human cells • 90％ bacterial cells Genome Genome Genome 基因组 基因组 Gene composition of 基因组 human body Foods Health Foods Diseases 全基因组关联分析要包括肠道菌群的基因Foods 食物 健康 食物 疾病 • Human genome (25,000 食物 Health Whole-genomegenes) association studies should Drugs 健康 •Karyome 药物 • MitochondromeInclude our microbiome Microbiome Microbiome 微生物组 微生物组 • Microbiome Microbiome • 1000 species 微生物组 • 1 million genes • Diverse and active metabolism Human microbiome- Partner for health or Pathogen for diseases? the second genome acquired after birth 微生物组－人后天获得的第二个基因组 TCM works primarily via modulation of gut microbiota 肠道菌群其实一直就是中医药的主要作用靶点Shanghai Jiao Tong University

Functional analysis of gut microbiota -Co-variation analysis between host global metabolism and gut microbiota

Li et al. , PNAS

Shanghai Jiao Tong University Shanghai Jiao Tong University Phylogenetic DGGE Band and Nearest Neighbour Correlation Metabolite linkage grouping Variable Shanghai Jiao Tong University http://www.upi.com/NewsTrack/Science/2008/02/06/study_maps_gut_microflora/6812/ 4-deoxyerythronate BAC-b16 Bacteroides thetaiotaomicron ------var97 AY895191, 100% citrate Study maps gut microflora 2,3-dihydroxybutyrate BAC-b31 Bacteroides uniformis var176 AB215084, 100% hippurate Published: Feb. 6, 2008 at 10:24 AM creatinine LONDON, Feb. 6 (UPI) -- A British-Chinese study has mapped the bacteria living in seven members of Bacteroides coprocola V3-b6 a Chinese family to determine the role of gut microbes in bodily processes. var25 AB200225, 100% dihydrothymine

4-hydroxyphenylacetylglycine V3-b24 Pseudobutyrivibrio ruminis The researchers from Imperial College London and China's Jiao Tong University said the makeup of var88 X95893, 100% 3-aminoisobutyrate each person's gut microflora influences their health, with abnormalities in gut microbes linked to taurine Clostridia CL-b11 bacterium mpn-isolate group25 diseases such as diabetes and obesity. var89 AF357573, 99% 3,5-hydroxybenzoate However, the relationship between different species of bacteria and different processes has previously dimethylamine CL-b8 Ruminococcus bromii been defined only at a broad level, the scientists said, noting that prior to their study, only five people var77 X85099, 100% lactate had had their gut microflora profiled in depth, with that data being published. CL-b16 Faecalibacterium prausnitzii ATCC27768, 2-hydroxyisobutyrate var128 AJ413954, 97% glycine "Now we have developed a new way of exploring the connections between bugs and man we can hope

V3-b34 glycolate to find a 'Rosetta Stone' to translate the functional properties of the bugs and so improve therapies to

Actinobacteria Faecalibacterium prausnitzii 1-88 var134 treat disorders of the gut and related conditions," said Imperial College London Professor Jeremy AY169430, 99% 4-hydroxyphenylacetate Nicholson, lead author of the study. CL-b14 Subdoligranulum variable BI-114 2-amino-3-hydroxyl-3-methylbutyrate var110 AJ518869, 97% 4-cresol sulfate The research, led by Professor Liping Zhao of Jiao Tong University in Shanghai, appears in the V3-b52 Bifidobacterium pseudocatenula guanodinoacetate Proceedings of the National Academy of Science. var211 D86187, 100% phenylacetylglutamine © 2008 United Press International. All Rights Reserved. This material may not be reproduced, redistributed, or manipulated in any form.

Please click on the link below to view the entire article. http://www.upi.com/NewsTrack/Science/2008/02/06/study_maps_gut_microflora/6812/

Shanghai Jiao Tong UniversityHighlighted by Nature Review Microbiology Shanghai Jiao Tong UniversityHighlighted by Nature Review Microbiology http://www.upi.com/NewsTrack/Science/2008/02/06/study_maps_gut_microflora/6812/ http://www.upi.com/NewsTrack/Science/2008/02/06/study_maps_gut_microflora/6812/ ------Study maps gut microflora Study maps gut microflora

Published: Feb. 6, 2008 at 10:24 AM Published: Feb. 6, 2008 at 10:24 AM LONDON, Feb. 6 (UPI) -- A British-Chinese study has mapped the bacteria living in seven members of LONDON, Feb. 6 (UPI) -- A British-Chinese study has mapped the bacteria living in seven members of a Chinese family to determine the role of gut microbes in bodily processes. a Chinese family to determine the role of gut microbes in bodily processes.

The researchers from Imperial College London and China's Jiao Tong University said the makeup of The researchers from Imperial College London and China's Jiao Tong University said the makeup of each person's gut microflora influences their health, with abnormalities in gut microbes linked to each person's gut microflora influences their health, with abnormalities in gut microbes linked to diseases such as diabetes and obesity. diseases such as diabetes and obesity.

However, the relationship between different species of bacteria and different processes has previously However, the relationship between different species of bacteria and different processes has previously been defined only at a broad level, the scientists said, noting that prior to their study, only five people been defined only at a broad level, the scientists said, noting that prior to their study, only five people had had their gut microflora profiled in depth, with that data being published. had had their gut microflora profiled in depth, with that data being published.

"Now we have developed a new way of exploring the connections between bugs and man we can hope "Now we have developed a new way of exploring the connections between bugs and man we can hope to find a 'Rosetta Stone' to translate the functional properties of the bugs and so improve therapies to to find a 'Rosetta Stone' to translate the functional properties of the bugs and so improve therapies to treat disorders of the gut and related conditions," said Imperial College London Professor Jeremy treat disorders of the gut and related conditions," said Imperial College London Professor Jeremy Nicholson, lead author of the study. Nicholson, lead author of the study.

The research, led by Professor Liping Zhao of Jiao Tong University in Shanghai, appears in the The research, led by Professor Liping Zhao of Jiao Tong University in Shanghai, appears in the Proceedings of the National Academy of Science. Proceedings of the National Academy of Science.

© 2008 United Press International. All Rights Reserved. © 2008 United Press International. All Rights Reserved. This material may not be reproduced, redistributed, or manipulated in any form. This material may not be reproduced, redistributed, or manipulated in any form.

Please click on the link below to view the entire article. Please click on the link below to view the entire article. http://www.upi.com/NewsTrack/Science/2008/02/06/study_maps_gut_microflora/6812/ http://www.upi.com/NewsTrack/Science/2008/02/06/study_maps_gut_microflora/6812/ 人源菌群微型猪模型可用于分子机理研究

Shanghai Jiao Tong University Human-flora associated pig model for molecular mechanistic studies

Gut Microbiota and Diet-induced HFA 37d Metabolic Syndrome HFA 25d

HFA 17d

HFA 12d Liping Zhao Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University 人体代谢空间 人源菌群猪代谢变化

赵立平组、华修国组

Nutritional Transition Prevalence of Obesity Shanghai Jiao Tong University Shanghai Jiao Tong University

Change of Energy Sources (1992 -2002) •Worldwide (WHO) Overweight : 1,200,000,000 Urban 80 Obese: 300,000,000 60 60 52 1992 35 2002 40 28 •China (National Nutrition Survey, 2002) Energy% 20 12 13

0 Chinese Adults (≥18 yrs ) carbohydrate protein fat 35 30 Rural 30 80 71 25 22.8 61 20.6 Overweight 60 1992 20 16.4 Obesity 2002 15 12.3 40 28 10 7.1 prevalence (%) prevalence

Energy% 19 6 20 10 11 5 3.6 0 0 carbohydrate protein fat 1992 2002 2002(Big city) 2002 (rural) National Nutrition Survey, 2002 Prevalence of Type 2 Diabetes 环境、菌群、遗传与健康的关系 Shanghai Jiao Tong University Environments, gut microbiota, genetics and health

Age Sexy Diet Diet USA China Yoon et al., Lancet, 2006 Disease & Genetics Drug Prevalence of Type 2 Diabetes in Different Countries Prevalence14 of Type 2 Diabetes in Different Countries 12 10 8 urban Gut SYMBIOTIC ASSOCIATION Host 6 rural Metabolism 4 Microbiome 2

Prevalence of diabetes (%) 0 Total Young Middle-aged Aged

Prevalence of Type 2 Diabetes in Chinese (≥18 yrs) China National Nutrition Survey, 2002

Apoa-1gene Knockout Mice Shanghai Jiao Tong University Apoa-1基因敲除小鼠

Apoa-1gene

knockout Interactions between gut microbiota, C57BL/6 mice Apoa-1-/- mice diet and host genotype for host health Reduced HDL-cholesterol levels 食物、基因型和菌群互作影响宿主的健康 Susceptibility to high-fat dietary-induced atherosis Insulin resistance and early symptoms of diabetes

赵立平组、陈雁组 ZHAO Lab, CHEN Lab Strategy for targeting the mouse Apoa-l gene. Apolipoprotein A-Ⅰ (Williamson, 1992, PNAS) ShanghaiApolipoprotein Jiao Tong University A-Ⅰand 2 type Diabetes ShanghaiApolipoprotein Jiao Tong University A-Ⅰand 2 type Diabetes

APOA-Ⅰcould activate AMPK and affect the energy and glucose metabolism of the cell.

Chen lab, 2007 Chen lab, 2007

Animal trial scheme Growth Curve Shanghai Jiao Tong University Shanghai Jiao Tong University

Food intake Apoa-1-/- Wild-type

C57BL/6 mice C57BL/6 mice

(male) (male)

Glucose Tolerance Test High-fat diet group Normal diet group High-fat diet group Normal diet group 5 mice (KF) 5 mice (KN) 5 mice (WF) 5 mice (WN) Shanghai Jiao Tong University Shanghai Jiao Tong UniversityPCR-DGGE Fingerprinting

M KF1 KF2 KF3 KF4 KF5 M KN1 KN2 KN3 KN4 KN5 M WF1 WF2 WF3 WF4 WF5 M WN1 WN2 WN3 WN4 WN5 M M HFD CK HFD CK 普通食物 a. AluⅠ 3 replicates from this step 高脂食物 普通食物 高脂食物 b. HaeⅢ c. HhaⅠ d. MspⅠ e. Csp6Ⅰ Restriction fragments separated on CEQ 8000

Apoa-I 基因敲除小鼠 野生型小鼠 Apoa-I gene knock-out mice Wildtype mice

肠道菌群结构可以反映高脂食物和宿主基因型作用下的健康特征 Gut microbiota structure reflecting host health status

A C 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

Shanghai Jiao Tong University Shanghai Jiao Tong University TRFs of KF and KN groups

B ApoA-Ⅰ -/-/ HF ApoA-Ⅰ -/-/ CH Wt / HF Wt / CH

D 50

1 1 1 1 0 3 3 2 5 3 2 2 5 5 2 4 5 1 1

PC3(12%) 5 2 3 5 4 4 -50 2 2 3 1 2 4 3 1 2 4 4 1 3 5 1 3 4 5 5 3 5 5 2 5 -100 2 3 2 -100 4 2 1 4 11 4 4 4 -50 3 3 PC2(17%) AluⅠ HaeⅢ HhaⅠ MspⅠ Csp6Ⅰ 0 -150 -100 -50 0 50 50 PC1(57%) 100 Gram-positive Gram-negative Normal chow / Information of Closed Relatives Normal ch Apoa-Ⅰ-/- / DGGE 5 NO.2 NO.3 Band Similarity Organism (Acession no.) Phylogenetic affiliation wt/ Shanghai Jiao Tong (%)University Shanghai Jiao Tong University NO.2 Wt 4 3 8 100 Lactobacillus johnsonii (AB186343) Firmicutes, Bacilli, Lactobacillales, Lactobacillaceae, high fat diet Lactobacillus 2

15 100 Helicobacter ganmani (T) (AF000221) Proteobacteria, Epsilonproteobacteria, Campylobacterales, 1 Helicobacteraceae, Helicobacter 5 98 uncultured bacterium (DQ815337) Bacteroidetes,Bacteroidetes,, 4 6 , Tannerella ApoA-Ⅰ -/-/ 3 high fat diet 80 gulae (ATCC51700) Bacteroidetes,Bacteroidetes,Bacteroidales, 2 Porphyromonadaceae, Porphyromonas 1 99 uncultured bacterium (DQ815337) Bacteroidetes,Bacteroidetes,Bacteroidales, 5 7 Porphyromonadaceae, Tannerella Ⅰ 4 81 Porphyromonas circumdentaria Bacteroidetes,Bacteroidetes,Bacteroidales, ApoA- -/-/ 3 Porphyromonadaceae, Porphyromonas normal diet 2 10 100 Bifidobacterium pseudolongum subsp. Actinobacteria, Actinobacteridae, Bifidobacteriales, Pseudolongum (AB186304) Bifidobacteriaceae, Bifidobacterium 1 5 100 uncultured bacterium (EU511073) 11 Wt 4 3 98 Bifidobacterium animalis subsp. Animalis Actinobacteria, Actinobacteridae, Bifidobacteriales, normal diet (AB186294) Bifidobacteriaceae, Bifidobacterium 2 1 99 uncultured bacterium (EF098678) Firmicutes C L B B E C C T H C E E E l a i i r T B L l r r r o c f f y lo lo a a a a e 16 o y y y st t id id si st st n n c w li st si si si ri o o o n n t s c 93 Bryantella formatexigens (T) (AJ318527) Firmicutes, Clostridia, Clostridiales, Clostridiaceae, Bryantella ri p p p b b b p ri ri e e e o o d e e e d a a a e d d r r ro n b l l l i c c lo i i e e i a iu o o o u i ct t t a a ll l id a c m tr tr tr m ll e e r le l a la a t i i i u ri ri ic s es l e c c c c b s u u h e r 99 uncultured bacterium (EF099100) Firmicutes, Mollicutes, Incertae sedis 8, Erysipelotrichaceae o h h h if j m a s g c a a a e o m ce a 12 l ce ce ce rm h p sp n ea a a a n s a m t e e e e so e . e a u n n u n 86 Eubacterium cylindroides (L34617) Firmicutes, Clostridia, Clostridiales, Eubacteriaceae, m ta i d i n i o Eubacterium s lo n g u m RT-PCR of Bifidobacterium spp.

Shanghai Jiao Tong University Shanghai Jiao Tong University 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

×105 4

3.5

spp. 3

2.5 10 10 2

11 bifidobacterium 1.5 11 1 Wt / CH ApoA-Ⅰ -/-/ HF ApoA-Ⅰ -/-/ CH Wt / HF 0.5 (Copy Number / ng total fecal DNA) Abundance of 0 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 KN1 KN2 KN3 KN4 KN5 WN1 WN2 WN3 WN4 WN5 KF1 KF2 KF3 KF4 KF5 WF1 WF2 WF3 WF4 WF5 Band10 and Band 11 were Bifidobacterium spp. ApoAⅠ -/- / CH Wt / CH ApoAⅠ -/- / HF Wt / HF Abundance distribution of Bifidobacteria Proteobacteria Shanghai Jiao Tong University Shanghai Jiao Tong University based on 454 sequencing

35

30

25 9 8 Bifidobacteriales 20 7

6 15 5

10 4 % of Total Sequences % of Total Sequences 3

2 5 1 0 0 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 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 1 2 3 4 5 6 7 8 9 101112131415161718192021222324252627282930313233343536 1 3 5 7 9 11131517192123252729313335 Animal ApoA-Ⅰ -/- ApoA-Ⅰ -/- Wild-type Wild-type Animal ApoA-Ⅰ -/- ApoA-Ⅰ -/- Wild-type Wild-type high fat diet normal chow high fat diet normal chow high fat diet normal chow high fat diet normal chow

Bifidobacteriales vs.Desulfovibrionales Shanghai Jiao Tong University 100% 80% 肠道菌群结构“分离分析”与 60% 宿主健康动态监测

40% Structural segregation analysis of

20% gut microbiota and host health

0% monitoring 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

ApoA-Ⅰ -/- high fat diet ApoA-Ⅰ -/- normal chow Wild-type high fat diet Wild-type normal chow 高脂食物、菌群变化与肥胖的发展 Bifidobacteriales -protecting gut barrier integrity High fat diet, gut microbiota and obesity Desulfovibrionales -producing endotoxin (LPS) ZHAO lab, JIA lab 赵立平组， 贾伟组 Progression of high fat diet induced obesity Structural segregation of gut microbiota

Shanghai Jiao Tong University 高脂食物诱发的肥胖的发展 Shanghai Jiao Tong University during obesity progression 肠道菌群结构随肥胖发展而变化 week 2nd 3rd 4th 5th 6th 7th 8th 9th Average HFD CD HFD CD Weight (g) week* week* week* week* week* week** week*** Week*** M H1 H2 H3 H4 H5 H6 H7 M C1 C2 C3 C4 C5 C6 M M H2 H3 H4 H5 H6 H7 M C1 C3 C4 C5 C6 M group HFD 187±2225±12 315±17 368±20 399±21 437±24 485±31 502±32

CD 185±3212±7299±21 344±30 365±38 386±41 416±47 424±48

*P>0.05 **0.01

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

V3-1 V3-2 V3-3 V3-4 V3-5 V3-6

th D 9 week C 8th week Structural segregation of gut microbiota Gram-positive Shanghai Jiao Tong University during obesity progression Shanghai Jiao Tong University 肠道菌群结构随肥胖发展而变化 6 5 4 Normal diet 3 2 1 7 6 th A 2nd week B 5 week 5 High-fat diet 4 3 2 1 P Ru Ru D An An a m o a a p m r e e i i i e r ll n n a ro o i o o v v b c c i i a o o b b c c c r r t c c i io e u u o r s s o b th th e D 9 week C 8 week u m Development of Colorectal cancer Shanghai Jiao Tong University

Structural shifts of gut microbiota induced by carcinogen during precancerous lesion development 致癌剂诱导癌前病变过程中 ACF under a light microscopy（×40） Dysplasia 肠道菌群结构的动态变化

adenocarcinoma polypous adenoma

结肠癌的癌前病变模型 肠道菌群与宿主代谢的监测 Shanghai Jiao Tong University Precancerous lesion of colon cancer Shanghai JiaoMonitoring Tong University of host metabolism and gut microbiota

50 L M The third week The ninth week 40 S control Mr model Mr Mr control model Mr * ** 30 ** ** 3 ** 4 3 20 ** ** 4

10 Aberrant crypt foci 19 19 25 25 0 26 26 u lian trol g uy n DMH h Co uan H Wuz Herb pair

Aberrant crypt foci (ACF) induced Reduction of ACF formation by by 1,2-dimethylhydrazine (DMH) TCM herbal extracts DNA fingerprinting of gut microbiota GC/MS profiling of host metabolism

Wu group, Jia group, Zhao group 癌前病变动物菌群结构和 区别癌前病变动物和健康动物的关键代谢物 Shanghai Jiao Tong University 整体代谢特征的变化 Shanghai Jiao Tong University 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. 菌群结构变化 整体代谢变化 Gut microbiota structure Global metabolism Concomitant shifts of gut microbiota and host global metabolism away from healthy control during precancerous lesion formation in DMH treated group

结肠癌的癌前病变模型

Shanghai Jiao Tong University区别癌前病变动物和健康动物的关键细菌 Shanghai Jiao Tong University Precancerous lesion of colon cancer Key gut bacteria for differentiation between healthy and precancerous animals

Band Closest relative 50 L M Similarity Organism S No. Phylogenetic affiliation 40 （%） (Acession no.) * ** 30 ** ** ** 20 ** ** Ruminococcus obeum (AY169419) 19 98 Firmicutes;Clostridia;Lachnospiraceae 10 Aberrant crypt foci

0 u lian trol g uy Allobaculum stercoricanis(AJ417075) n DMH h Co uan 25 95 Firmicutes; Mollicutes; Allobaculum. H Wuz Herb pair

97 uncultured bacterium(AY986052) Bacteroidetes;Porphyromonadaceae Aberrant crypt foci (ACF) induced Reduction of ACF formation by 26 by 1,2-dimethylhydrazine (DMH) TCM herbal extracts 93 Allobaculum stercoricanis(AJ417075) Firmicutes; Mollicutes; Allobaculum.

Wu group, Jia group, Zhao group 16S rRNA gene V3 fragment DGGE profiles

Shanghai Jiao TongCoptidis University rhizoma, Evodia rutaecarpa Shanghai Jiao Tong University herbal pair The ninth week The ninth week Coptidis Rhizoma Evodiae Fructus Mr model Herb pair Mr control

22 22

28 28

Major component: evodiamine、 Major component: Berberine 、 rutaecarpine、hydroxy- evodiamine、 palmatine、jatrorrhizine、coptisine limonin、synephrine、evodente

PCA scores plot of the 16S rRNA gene V3 region DGGE profiles of Shanghai Jiao Tong University different groups A Shanghai3D-PCA Jiao Tong sores University plot of GC/MS spectral data from the three group 15 rats at the 9th week (n=8 per control 9th group; DMH-induced, red dots; model 9th healthy, blue dots; herb treated, herb pair 9th 10 black dots; each dot denotes an individual rat

5

0 PC2 (17.32%) Time-dependent mean fold changes of those differential metabolites of healthy group, DMH-induced group -5 and herb treated group at 3rd, 5th, 7th, and 9th week .

-10 -15 -10 -5 0 5 10 15 Jia group PC1 (34.64%) 尿液的900 MHz 1H 核磁共振谱 METABONOMICS代谢组学 Shanghai Jiao Tong University Quantitative measurement of multivariate metabolic responses of 尿液中蕴含的生物信息: multicellular systems to pathophysiological stimuli or genetic 基因型 modification 生理状态 营养状态 多细胞系统在受到病理生理刺激或者遗传修饰后，其代谢反应 肠道微生物 的多参数定量测定 生物学年龄 疾病 AIMS TO MODEL HUMAN GLOBAL METABOLIC REGULATION -THE BASIC HOLISTIC PHILOSOPHY IS IN HARMONY WITH THEORY OF TRADITIONAL 可以用于临床的生物标识物 CHINESE MEDICINES 诊断 目标是人体整体代谢调控的建模，其基本哲学思想与中医是一致的 预测 毒性 GLOBAL SYSTEMS BIOLOGY IS THE TOP-DOWN INTEGRATION OF MULTI-OMICS DATA 疗效 TO DECIPHER GENE-ENVIRONMENT INTERACTIONS IN RELATION TO DISEASE DEVELOPMENT. 人体系统生物学是用自上而下的策略进行多种组学数据的整合，来解析疾病 发展过程中基因与环境的互作关系 Nicholson Nicholson Large Scale Metabonomic Screening of Human Populations FUNDAMENTAL METABOTYPE DIFFERENCES

Cystinuria/lysinuria Shanghai Jiao Tong University PCA-DA of population data (disease outliers removed) cystine Type 2 Diabetes

JAPANESE

Alcohol

“Normal”

AMERICAN Genetic defects Analgesics CHINESE

COMBINATION OF GENETIC ENVIRONMENTAL Nicholson Nicholson © Imperial College, 2005 © Imperial College, 2006 & NUTRITIONAL FACTORS NMR-based Trajectory plot of OSC-PLS model for individual subject pre and post exposure to Guangxi Shanghai Jiao Tong University Metabonomics of chamomile tea south and north Chinese Populations. 1.5 C d-28 A 1 d-01 d-05 主要是肠道菌群代谢物不同 0.5 d-30 d-21 creatine d-24 d-10 Shanxi 0 PC2 d-14 a -0.5 d-11 PCA Plot hippurate phenylacetyl glutamine -1 B d-20 b d-17 Loadings β-amino- iso-butyrate d-15 c plot -1.5 7.8 7.6 7.4 7.2 ppm -2 Subject does not return to pre-dose space Nicholson after-1.5 2 weeks- -1 changes-0.5 are0 in the0.5 gut microbiota 1 1.5 2 PC1 Nicholson Meta-GUT: Overall Project Aim Shanghai Jiao Tong University GutShanghai Microbiota-based Jiao Tong University Biomarker Discovery for Preventive Management of Metabolic Diseases via Nutritional Modulation

Early stage Late disease/ stage Nutrition, gut microbiota, disease host immunity and metabolism, and their Transition stage interactions in the development of obesity and related metabolic diseases Opening novel avenues to combat these conditions in Nutritional a predictive, preventive and intervention personalized manner Drug intervention Health stage Diet and life style Population-based Case-Control Study Data Collection Shanghai Jiao Tong University Shanghai Jiao Tong University

Dietary Pattern FFQ & 24-hr recall Study design:

500 pairs of age, sex and lifestyle matched overweight/obese and Name, Gender, Age, Household non-obese individuals Demographic members, Ethnicity, Marital status, Information Education level, Occupation, • Case： BMI ≥ 26 kg/m2 Income • Control：18 ≤ BMI ≤ 23kg/m2 Self-reported health status, Health Lifestyle & Health behavior, Medication, Family Inclusion criteria: Status history of diseases, Smoking status, Alcohol Drinking • Urban residents in Shanghai Physical Activities Frequency, Duration and Level • Residence ≥ 10 yrs (IPAQ-short form) • Age: 35-54, male > 40% Mental Health CES-D questionnaire • Without currently participating other study Height, Weight, Blood pressure, • Without physical disabilities and mental disorder Anthropometrics Waist circumferences, Hip Body circumferences Composition DEXA: Fat, lean mass and bone density, % body fat, % trunk fat

DataLaboratory Collection Assays DataLaboratory Collection Assays Shanghai Jiao Tong University Shanghai Jiao Tong University

CategoryDietary Pattern FFQ & 24-hrBiomarker recall CategorySamplesDietary Pattern FFQ & 24-hrAnalysisBiomarker recall

Lipid profile Total cholesterol, HDL, LDL, triglyceride; LipidBlood profile ProteinTotal cholesterol, profiling HDL, LDL, triglyceride; Name, Gender, Age, Household Name, Gender, Age, Household Demographic members, Ethnicity, Marital status, DemographicMetabolic members, profiling Ethnicity, Marital status, GlucoseInformation Fasting plasmaEducation glucose level, Occupation, GlucoseInformation Fasting plasmaEducation glucose level, Occupation, Income Urine NMR spectroscopicIncome profiling Hormone Fasting InsulinSelf-reported health status, Health Hormone MS-basedFasting InsulinSelf-reported profiling health status, Health Lifestyle & Health behavior, Medication, Family FecalLifestyle matters & HealthMetabolic behavior, profiling-fecal Medication, water Family AdipocytokinesStatus Adiponectin,history Resistin, of dis PAI-1,eases, RBP4 Smoking AdipocytokinesStatus Adiponectin,history Resistin, of dis PAI-1,eases, RBP4 Smoking status, Alcohol Drinking Fragment-basedstatus, Alcohol profiling Drinking α α InflammatoryPhysical ActivitiesCRP, TNFFrequency,-R1,R2, IL-6 Duration and Level InflammatoryPhysical ActivitiesSequence-basedCRP, TNFFrequency,-R1,R2, IL-6 profilingDuration and Level factors (IPAQ-short form) factors (IPAQ-short form) Metagenomic sequencing Gene variantsMental HealthHNF4A, PPARG,CES-D PCK1,questionnaire G6PC, PPARGC1A, Gene variantsMental HealthHNF4A, PPARG,CES-D PCK1,questionnaire G6PC, PPARGC1A, Pattern Unsupervised classification NR3C1, ESRRA,Height, ADIPOQ, Weight, Blood RBP4, pressure, ENPP1,etc. NR3C1, ESRRA,Height, ADIPOQ, Weight, Blood RBP4, pressure, ENPP1,etc. Anthropometrics Waist circumferences, Hip recognitionAnthropometricsSupervisedWaist classification circumferences, Hip Body circumferences Body circumferences OthersComposition Ferritin, HbA1CDEXA: Fat, lean mass and bone OthersComposition Co-variationFerritin, HbA1CDEXA: analysis Fat, lean mass and bone density, % body fat, % trunk fat density, % body fat, % trunk fat Study Overview 粪、尿液采集情况汇总 Shanghai Jiao Tong University Fecal and urine samples Envir factors •Diet Obese • Body fat • Structural 受试者人数 合格粪样数量 合格夜尿数量 合格晨尿数量 ones •Lifestyle distribution differences of gut flora (500) • Glucose Number of Fecal Night Urine Morning metabolism • Functional bacteria Participants samples samples urine Glucose, insulin, associated with obesity samples • Gut HOMA-IR microbiota • Lipid level • Major diet/nutrients 卢湾 596 590 581 578 structure Tch，LDL， associated with • Key obesity Luwan bacteria HDL，TG • Inflammatory • Genetic 闸北 579 571 568 564 factors：CRP、 susceptibility and obesity-associated Zhabei Genetic IL6、TNFR1/R2, mutation RBP4 gut microbiota Fat • Mechanisms of 合计 1175 1167 1149 1142 Normal • Adipocytokines: metabolism Adiponectin, obesity-associated ones Total PPARA、 Resistin, PAI， gut microbiota 、 (500) PPARD RBP4 affecting PPARGC1B metabolism Energy 粪尿样均合格者共1131人，卢湾574人，闸北557人 metabolism ADIPOQ、 INSIG2, ADIPOR1/2 Specific Aims 疾病中后期 Shanghai Jiao Tong University Shanghai Jiao Tong University疾病早期 Scientific • Build a reference database 病前阶段 • Develop high-throughput methodologies • Define the pattern of nutritional transition • Identify and understand host-microbe metabolic interactions Nutrition

Products for Personalized nutrition drug Health risk assessment • 7-1000-25000-600000 • Databases and kits 健康人群 • Diet-based prevention of metabolic diseases 人群健康状况的分类与监测 • The beverage or additive that works just for you 基于人体分子测量的病人分型与健康监测 疾病中后期 Understanding how TCM works Shanghai Jiao Tong University疾病早期 Shanghai Jiao Tong University

TCM Whole-body systems biology

病前阶段 Signs and symptoms at the whole body level Urine and Stool samples Whole-body systems biology-enabled, large scale cohort study Four diagnostic techniques Wang, Wen, Wen, Qie Metabonomics, for discovery of pre-disease biomarkers with predictive power 四診 “望聞問切 ” Metagenomics for preventive management of public health Eight guiding principles Yin, Yang, Han, Re Multivariate statistics Nutrition Biao, Li, Xu, Shi for pattern extraction 八纲“陰陽，表裏，寒熱，虛實 ” drug “Biomarker profiles” “ZHENG證 ” differentiation for patient stratification for patient stratification 健康人群 7-1000-25000-600000 Diagnosis and Prognosis, 人群健康状况的分类与监测 Efficacy and Safety Evaluation, Drug Discovery

基于人体分子测量的病人分型与健康监测 Cellular and Molecular Mechanisms

Emerging of New Medicine

Shanghai Jiao Tong University东西方医学的汇聚与新医学模式的出现

Traditional medicine Western medicine New medicine

Holistic but Molecular-based but Molecular-based and empirical fragmentary holistic 传统医学－ 西方医学－ 新医学－ 模糊的整体 精细的局部 精细的整体