Take home messages. Diet and antibiotics are major regulators of microbiota composition

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1 Mining Novel Therapeutic Bacterial Strains Using Fecal Microbiota Transplantation to Combat Metabolic Disease Seminar Infectious Diseases Guido Bakker MD, PhD student Department of Vascular Medicine Academic Medical Center, Amsterdam The Netherlands

2 Take home messages Personalized intestinal microbiota Diet and antibiotics are major regulators of microbiota composition Associations microbiota with disease, but causality has only been proven for few diseases! Fecal transplantation may be used to find therapeutic/ pathologic strains or metabolites

3 Background Gut microbiota kilogram feces in a human life produced! 1 Ley et al, Nature 2006, 444: Bäckhed et al, PNAS 2004, 101:

4 Background Gut microbiota kilogram feces in a human life produced! The gut microbiota (60% of the dry mass of feces) content consists of (!) bacteria 1 Ley et al, Nature 2006, 444: Bäckhed et al, PNAS 2004, 101:

5 Microbes Maketh Man 90% of the cells in your body are bacteria!

6 Gut microbiome in physiology

7 Personalized intestinal ti microbiome

8 Growing Up In A Microbial World The microbiota develops in the first 2 years Dominguez-Bello, PNAS 2010 (40-50% by parents, rest via lifestyle)

9 Impact of Diet on Microbiota Variation? Mice Diet explains 77% Zhang et al. ISME J :2 Diet explains 81% Faith et al. Science (6038) Diet has a dominating role in shaping the gut microbiota Humans Diet explains 40-50% Metagenomic study of 17 Europeans Tap et al EM 11:10 Individual Variation Large Habitual diet > Intervention Hildebrandt et al. Gastroenterology 137 (2009) Cani et al. Diabetes 56 (2007) Wu et al. Science 333 (2011) Walker et al. ISME J 55 (2011) Mouse & Human Metagenomes Share < 5% Identical Genes

10 Dogma shift: best infectious microbe is a dead microbe in the 1950 s.. Relation antibiotic prescriptions and obesity

11 Antibiotics Impact Microbiota Development in Children Nature 2012 Average child in USA 12 courses AB age of 7 (NL: 2 courses)

12 Fecal microbiota and obesity/type 2 diabetes mellitus: associations! Qin, Nature 2012 Le Chatelier, Nature 2013 Karlsson, Nature 2013 Ridaura, Science 2013

13 Shortcomings of current fecal sample centered approach 1. Small intestine is more involved in metabolism than the colon 2. Diet is not taken into account 3. Association is not causality!

14 Gut epithelium as barrier

15 Bacterial translocation

16 Postprandial endotoxemia parallels plasma triglyceride curves Harte, Diabetes Care 2012

17 Results of cohort based studies using fecal samples Smits/Nieuwdorp, Gastroenterology 2013

18 Causal role of microbiota in metabolism and diabetes

19 Association or causality of intestinal microbiota: visceral adipose tissue Inflamed visceral adipose tissue is strongly associated with DM2 Depres JC, Ann Int Medicine 2004 Causal driving factors? Bacterial translocation?

20 Koch s postulates for causality The microorganism must be identified/isolated from a diseased organ(ism). The cultured microorganism should induce beneficial i or adverse effects when introduced into an organism (inoculation). The microorganism must be reisolated after inoculation

21 Manipulating gut microbiota by fecal transplantation

22 De Vrieze, Science 2013

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25 Donors Screening donors: - Questionnaire (bowel habits, travel history, medication, etc) - Faeces (parasites, Clostridium difficile, il SSYC and viruses (rota etc)) - Bloodborn viruses (Hepatitis, HIV, HTLV, CMV, EBV) - Checklist day before treatment (been ill? different sexual contact? travelling? no antibiotics in last 3 months?)

26 Effects of fecal transplantations in clostridium difficileil diarrhea Van Nood, NEJM 2013

27 Emerging indications (ESBL and VRE)

28 Metabolic syndrome Increased wais Dyslipidemia id i Insulin resistance Hypertension Hyperglycemia

29 Effect donor faeces on peripheral insulin sensitivity A.Vrieze, Gastroenterology 2012

30 Eiseman (Surgery 1958) Fecal transplant doesn t induce a definite cure! The cultured microorganism should induce beneficial or adverse effects when introduced into a healthy organism (3rd postulate)

31 Small intestinal gut microbiota composition A.Vrieze, Gastroenterology 2012

32 Bacterial strains as novel probiotics: Eubacterium hallii

33 Eubacterium hallii Belongs to Firmicutes phylum (spore former) Anaerobic gram positive lactate-utilizing SCFA butyrate- producing bacterial strain, natural inhabitant of duodenum Can produce butyrate at ph 4 (small intestine) as well as p y p ( ) at ph 6-7 (colon)

34 Study protocol I Db/db male mice (8 weeks old), n=8 per group Daily gavage (100ul/mouse) with E. Hallii (stored in 10% glycerol l at -80C), gavage within ihi 1 hour after thawing for 4 weeks with: - 10^6 CFU/ml - 10^8 CFU/ml - 10^10 CFU/ml - Placebo (dissolvens = 10% glycerol)

35 Caecal E.hallii levels upon 1 month daily gavage Udayappan/Manneras, submitted Mean ±SEM

36 E. Hallii improves insulin sensitivity (insulin tolerance test ) placebo (10% glycerol) 10 6 CFU/ml E.Hallii 10 8 CFU/ml E.Hallii CFU/ml E.Halii * * Time (min) E. Hallii normalises insulin sensitivity (ITT) compared to placebo Udayappan/Manneras, submitted

37 Study protocol II Db/db male mice (8 weeks old), n=7-9 per group Daily gavage (100ul/mouse) with alive or heat inactivated E. Hallii 10x8CFU/ (stored in 10% glycerol at -80C), gavage g within 1 hour after thawing for 4 weeks followed by: - 48h in Metabolic cages (Somedic cages) - hyperinsulinemic normoglycemic clamp

38 E.hallii treatment metabolism and insulin sensitivity (clamp) in db/db P=0.06 Insulin sensitivity P=0.06 Udayappan/Manneras, submitted

39 Challenges for these novel strains Strain stability (storage, glycerol vs freezedrying) under Nitric oxide for anaerobics Industrial level (30-40liters) anaerobic culturing Human phase 1-2 dosefinding trial with GMP produced d E.hallii in MetSyn started t in 2014 Eubacterium hallii De Vos WM and Nieuwdorp M. Nature 2013; 498(7452):48-9

40 A deeper understanding of the gut microbiota in disease At AMC >300 FMT s since 2006, predominantly in RCT: long term side effects not observed yet At AMC ongoing/finished RCT s with single/multiple FMT using hard clinical endpoints for: - VRE/ESBL POSTIVE - Insulin resistance/dm2 POSITIVE - IBD (Colitis ulcerosa, TURN trial) NEG - Vascular inflammation ONGOING - NAFLD/NASH ONGOING - Type 1 diabetes ONGOING Smits/Nieuwdorp, Gastroenterology 2013 [; van Nood/Nieuwdorp, NEJM 2013

41 Take home messages Personalized intestinal microbiota Diet and antibiotics are major regulators of microbiota composition Associations microbiota with disease, but causality has only been proven for few diseases! Fecal transplantation may be used to isolate therapeutic/ pathologic strains or metabolites

42 Willem de Vos WUR/Helsinki Fredrik backhed Gothenborg Max Nieuwdorp AMC Anne Vrieze AMC Acknowledgements Nieuwdorp Diabetes research center PhD students Ruud Kootte MD Fleur van der Valk, MD Pim Gilijamse, MD Kasper ter Horst, MD Loek Smits, MD Sophie Bernelot Moens, MD Kristien Bouter, MSc Pieter de Groot, MD Annick Hartstra MD Guido Bakker, MD Mark Smits, MD Marcel Muskiet MD Lennaert Tonneijk, MD Shanti Udayappan, Msc Postdocs Han Levels PhD Daniel van Raalte, MD PhD Hilde Herrema PhD Jing Zhao PhD Geesje Dallinga, PhD Hans Romijn AMC Loek Smits AMC Erik Stroes AMC Geesje Dallinga- Thie AMC