The gut microbiome and diabetes risk

Transcription

1 World Congress on Prevention of Diabetes and its Complications (WCPD10), Edinburgh, July 15 18, 2018 The gut microbiome and diabetes risk Oluf Pedersen Professor, MD, DMSCi Faculty of Health and Medical Sciences University of Copenhagen Novo Nordisk Foundation Center for Basic Metabolic Research University of Copenhagen

2 Do you like bacteria? Photo credi: Shutterstock.com

3 Of course we fear bacteria Tuberculosis Staphylococcus aureus Multiple resistant bacteria Cholera Yersinia Pestis Pertussis Salmonella Campylobacter and many others

4 But if you don t like bacteria you are on the wrong planet Photo art in a petri dish: Peta Clancy's Visible Human Bodies, 2005

5 You and I are borne on the planet of microbes Photo credit: Shutterstock.com

6 The original organic beings of this planet were archaebacteria and cyanobacteria Bacteria are estimated to have been here for 3 billion of years They outweigh all animals and plants on earth Photo credit:flickr Creative Commons

7 Man and his/her trillions of microbes: a holobiont = a super-organism Man consists of about 10 times more DNA-containing bacterial cells than human DNAcontaining nucleated cells The Human Microbiome Project

8 To understand human health or disease pathogenesis we likely need exploitations of our own genome, the hologenome and the environmental metagenome all influenced by the exposome Kevin R. Theis et al. msystems 2016;1:e

9 About 50,000,000,000,000 bacteria in each human adult gut (1-2 kg), split on > 1000 species and covering a gut surface of 32 square meters The far majority are commensal or mutualistic bacteria, i.e. they are not pathogenic when fenced in the gut

10 Gut microbiota and host benefits Metabolic functions Fermentation contributes to 5-10% of total daily energy infusion Synthesis of B and K vitamins and fatty acids Conversion of bile acids Protective functions Education of immune competences Protection against pathogens Elimination of toxins Trophic functions Regulation of mucosal cell proliferation and differentiation, vascularization, hormonal and neuronal signaling

11 Recent progress in basic human intestinal microbiome science Establishment of the first and second microbial gene catalogues of the human gut microbiome based upon shotgun whole microbiome sequencing Organization of microbial genes into metagenomics species and strains allowing deep taxonomic and functional microbiome analyses Integration of microbiomics and other omics read-outs with human physiology Natuer 2010 Mar 4;464(7285):59-65 Nature 2016 Jul 21;535(7612): Nature Biotechnol Aug;32(8): Nature Biotechnol Aug;32(8):822-8

12 Translational microbiome research in the general at risk population, in pre-diabetes and in overt Type 2 Diabetes

13 The case of Type 2 diabetes (T2D) The prevalence of T2D ranges between 3-15% of adult populations. Globally it is in epidemic growth The prevalence of pre-diabetes is between 10-40% The risk factors for pre-diabetes ( = pre-pre-diabetes ), i.e. insulin resistance and low grade inflammation are present in up to half of the adult population

14 A phenotype-staged resolution approach to dissect the natural course of T2D pathogenesis Stage A: the early subclinical and compensated stage = pre-pre-diabetes Overweight/Obesity with whole body inflammation, insulin resistance and compensatory hypersecretion of insulin. Blood glucose levels are still normal but hypertension and hyperlipidaemia may be manifest Stage B: intermediate stage = pre-diabetes Same phenotypes but meal-stimulated insulin secretion is declining and fasting blood glucose increasing to upper non-diabetic level. Often hypertension and hyperlipidaemia Stage C: overt type 2 diabetes Elevated fasting and/or meal-released blood glucose with impaired insulin secretion. Often hypertension and hyperlipidaemia. Relative high percentage with organ damages in heart, brain, legs, nerves, eyes and kidneys at time of diagnosis

15 Aetiology of T2D A complex interplay of genetics (hundreds of gene variants) and multiple environmental risk factors some of which mediate their diabetogenic impact via the intestinal microbiome

16 Hypothesis An aberrant gut microbiota is a mediator of the diabetogenic impact from the environment Environmental risk factors, e.g. unhealthy diet, smoking, chronic subclinical infections, toxins and drugs cause intestinal dysbiosis Altered gut microbial communities cause subclinical inflammation and insulin resistance In individuals with an accumulation of risk genes primarily causing impaired insulin secretion, this genetic susceptibility is activated under the pressure of inflammation and insulin resistance and T2D presents itself The T2D phenotype is reproduced in animals with genetic susceptibility to a T2D-like disorder via transplantation of stools from treatment-naïve T2D patients. In other words, a diseased microbiota has become autogenic

17 General hypothesis for how dysbiosis of gut microbiota contributes to the pathogenesis of common polygenic diseases Lynch-S & Pedersen-O N Engl J Med 2016; 375: Healthy individuals each with genetic susceptibility to one or more polygenic disorders Combination of genetic susceptibility and environmental exposure results in manifest polygenic disorder Healthy gut microbiota Dysbiotic pathobionts Non-specific environmental triggering factors such as chronic infection and/or unhealthy diet Distinct disease phenotype is reproduced via transplantation of the dysbiotic disease-associated gut microbiota to a genetically susceptible rodent host

18 A phenotype-staged resolution in the natural course of T2D pathogenesis Implications for the studies of the potential pathogenic role of intestinal dysbiosis Stage A: the early subclinical and metabolically compensated stage - pre-pre-diabetes Featured by a subclinical inflammation and insulin resistance

19 Nature 500: , 2013 Photo credit: University of Buffalo Photo credit: Shutterstock

20 One in four of adults at the general population level has on average 40% less gut microbial genes These people are featured by altered structure and function of the remaining gut microbiome Low-richness people showed lowgrade inflammation, insulin resistance and increased adiposity Increased weight gain over 8 yrs Nature 500: , 2013

21 What are the causes of the missing gut microbiota? Antibiotics? Other drugs? Lack of food diversity? Food additives? Everyday chemicals? Lack of pets? Toxins? Chronic infections? Genetics?

22 A phenotype-staged resolution in the natural course of T2D pathogenesis Implications for the studies of the potential pathogenic role of intestinal dysbiosis Stage A: the early subclinical and metabolically compensated stage pre-pre-diabetes Featured by a subclinical inflammation and insulin resistance

23 Nature: , 2016 Photo credit: fishkeeping.co.uk Photo credit: MetaGenopolis

24 Analytical workflow integrating three domains of data: host physiology, fasting serum metabolome and gut microbiome Nature: 535; , 2016 Helle Krog Pedersen Valborg Gudmundsdottir

25 Insulin resistance was reflected in the serum metabolome and correlated with increased capacity of the gut microbiome for bacterial biosynthesis of Branched Chain Amino Acids (BCAAs) and lipopolysaccharides The insulin resistant gut microbiome was composed of 6 bacterial species with Prevotella copri as a major driver In high-fat fed mice Prevotella copri gavaging induced a rise in serum levels of BCAAs, which was associated with an aggravation of glucose intolerance and insulin resistance Nature: 535; , 2016

26 Phenotype-staged resolution in the natural course of T2D pathogenesis Implications for the studies of the potential pathogenic role of intestinal dysbiosis Stage B: Intermediate stage called prediabetes Same phenotypes as at stage A but meal-stimulated insulin secretion is declining and inadequate to maintain normal glucose homeostasis

27 Prediabetics are depleted in butyrate producing taxa and enriched in proinflammatory taxa Akkermansia muciniphila Roseburia hominis 28 species Kristine Allin Coprococcus comes Ruminococcus gnavus 8 species Valentina Tremaroli Diabetologia Apr;61(4):810 PMID:

28 The gut microbiome of women with gestational diabetes resembles the disrupted microbiota composition of prediabetic individuals 3 rd timester Mie Crusell 8 months postpartum OTUs present in at least 10% of samples and mean abundance of 0.01% Negative binomial Wald test with p-values adjusted for FDR 10% Microbiome May 15;6(1):89. PMID:

29 Phenotype-staged resolution in the natural course of T2D pathogenesis Implications for the studies of the potential pathogenic role of intestinal dysbiosis Stage C: unstratified overt Type 2 Diabetes exposed to polypharmacy

30 The majority of type 2 diabetes patients are prescribed 4-10 drugs: e.g. glucose lowering, blood pressure lowering, lipid lowering, antiplatelet aggregation drugs - all of which potentially influence the gut microbiota

31 Nature 528: , 2015

32 Metformin treatment was associated with a reduced Intestinibacter abundance across Danish, Chinese and Swedish samples and an increased Eschericia abundance in Danish and Swedish samples Study-source adjusted KW-test and post-hoc MWU test FDR < 0.1, *: FDR < 0.05; ***: FDR < Values corrected for differences in gender, BMI, and fasting levels of glucose and insulin Nature 528: , 2015

33 The changes in Eschericia and Intestinobacter genera were validated and extended in healthy individuals where 11 microbial taxa were significantly changed following metformin intervention

34 Microbial gene analyses of the metformin-associated gut microbiome showed an increase of the functional potential for butyrate and propionate production pointing to an increase of intestinal gluconeogenesis The net result of an increased intestinal gluconeogenesis is a glucose lowering effect through reduction of appetite, body weight and hepatic glucose output Cell , 2014

35 Intestinal bacterial genera discriminant for development of intestinal side effects following metformin treatment in healthy individuals

36 Microbial gene analyses of the metformin-associated microbiome showed an increase of the functional potentials for hydrogen production and sulfate reduction which could be related to the known intestinal side effects of metformin Nature 528: , 2015

37 Based upon the outcome of our study we suggest that the most commonly used antidiabetic drug, metformin, shapes the human gut microbiota and contributes to: improved glucose homeostasis through an enhanced intestinal gluconeogenesis adverse effects as bloating and intestinal discomfort through increased hydrogen production and increased sulfate reduction Nature 528: , 2015

38 There is a general need to bear drug confounding in mind - when dissecting disease signatures of the gut microbiome - when developing microbiome-based diagnostic/prognostic tools - and when testing for phenotype transferability in gnotobiotic mice experiments Cell Metabolism 23:20, 2016

39 But what does the intestinal gut microbiome look like in metformin-untreated type 2 diabetes patients?

40 Studies of the intestinal microbiome of metformin-naive type 2 diabetes patients and controls from Denmark, Sweden and China At genus, level metformin-naive T2D was associated with a decrease of butyrateproducing Roseburia, Subdoligranulum and a cluster of Clostridiales Functional microbiome analyses showed increased degradation of several amino acids and increased lipopolysaccharide synthesis Nature 528: , 2015 Central cells of the map show Spearman correlations between abundance of bacterial taxa and microbial gene modules. Significance based upon study source adjusted KW-test and post-hoc MWU test FDR < 0.1, *: FDR < 0.05; +: FDR < 0.1

41 Gut microbiota lessons - learned from cross-sectional studies applying the phenotype-staged approach of at-risk individuals, pre-diabetics and patients with overt type 2 diabetes Stage A nondiabetics at risk with insulin resistance and inflammation - have low bacterial gene richness and certain bacterial species contribute to whole-body insulin resistance via biosynthesis of BCAAs and lipopolysaccharides Stage B prediabetics - are featured by a depletion of butyrate-producing bacteria and an enrichment in proinflammatory species Stage C patients with overt type 2 diabetes without treatment with metformin have a depletion of butyrate producing gut bacteria and increased microbial potential for BCAAs and lipopolysaccharide production

42 Is dysbiosis of intestinal microbiota a triggering component in the pathogenesis of T2D We still don t know

43 Ongoing efforts in treatment-naïve pre-diabetic individuals to elucidate a potential pathogenic impact of the intestinal microbiota IMI-DIRECT prospective studies of hundreds of individuals with prediabetes over several years to explore if dysbiosis of gut microbiota at strain level resolution alone or in combination with other markers (family history, physiological markers, genomics, epigenomics, metabolomics, proteomics etc.) do predict conversion from pre-diabetes to overt T2D Mechanistic studies to elucidate if gut microbiota from treatment-naïve diabetics and prediabetics cause metabolic decompensation in genetically susceptible animals with Western life-like behaviour

44 Severe limitations Only about one third of gut bacteria are known at species level Poor resolution at strain level Lack of relevant genetically susceptible rodents for bacterial transplantation

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46 The intestinal microbiota comprises bacteria (+ archaea), virus and fungi Bacteria Virus Fungi

47 Center for Basic Metabolic Research University of Copenhagen

48 Novo Nordisk Foundation Center for Basic Metabolic Research Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen

49 Henrik Bjørn Nielsen Helle K. Pedersen Valborg Gudmundsdottir Trine Nielsen Kristoffer Forslund Tuulia.Hyotylainen Falk Hildebrand Benjamin Jensen Gwen Falony Emmanuelle Le Chatelier Shinichi Sunagawa Edi Prifti Sara Vieira-Silva Manimozhiyan Arumugam Paul Igor Costea Jens Roat Kultima Torben Jørgensen Henrik Vestergaard Florence Levenez Joël Dore Susanne Brix Karsten Kristiansen Søren Brunak Jeroen Raes Jun Wang Matej Oresic Torben Hansen Peer Bork S. Dusko Ehrlich Metagenomics of the Human Intestinal Tract = MetaHIT EU

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51 To be a human in a world dominated by microbes? Photo by Mads Perch Consider yourself and your microbiome as one "holobiont = a super-organism This attitude may feed actions to take us to new dimensions of biological insights science knowledge with medical potentials

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