My microbes and me: A live-long relationship 1. The first come to us - PowerPoint PPT Presentation

My gut microbes and me : Exploring this live-long and fragile relationship Peer Bork Structural and Computational Biology EMBL, Heidelberg Aiming at a functional understanding of biological systems

My microbes and me: A live-long relationship 1. The first come to us latest at birth (Caesarean delivery brings different bugs) Madan et al., JAMA Pediatr. (2016) 1 2. Mother milk brings another boost (Bifidobacteria 20%), bottle-fed different 3. It takes 3-4 years until microbial composition is stabilizing, in interaction with our immune system Müller et. al.,Trends Mol.Med 21(2015)109 4. In parallel, the “inherited” part is being replaced by individually acquired microbiota, thus environment plays a big role Bork et al., in preparation 5. The microbial composition still changes somewhat in childhood, seems relatively stable in adulthood and diversity reduces in elderly, presumably associated with settled life style Claesson et al., Nature 488(2012)178

Gut microbiome: 2010 not even basics known How many microbial species and genes are in the gut? More bacterial than human cells, 1.5kg, >1000 species per person First illumina-based metagenomics: 10x cheaper, large scale, ca 250 species Human gut reference catalogue of 3.3 Mio microbial genes from 124 Europeans 2014: >10 Mio genes in >1200 individuals, with a stable core Frequent genes saturate, but rare genes keep being added Collaboration with BGI (China) and the EU MetaHit consortium Qin et al, Nature 464(2010)59 Li et al, Nat.Biotech. 32(2014)834

How different are our gut microbes? Nature 473(2011)174 Enterotypes in the landscape of gut microbial community composition Paul I. Costea 1,* , Falk Hildebrand [1],[2],[3],* , Manimozhiyan Arumugam [4],[5] , Fredrik Bäckhed [6],[7] , Martin J. Blaser [8] , Frederic D. Bushman [9] , Willem M. de Vos [10],[11] , S. Dusko Ehrlich [12],[13] , Claire M. Fraser [14] , Masahira Hattori [15] , Curtis Huttenhower [16] , Ian B. Jeffery [17] , Dan Knights [18],[19] , James D. Lewis [20] , Ruth E. Ley [21] , Howard Ochman [22] , Paul W. O’Toole 17 , Christopher Quince [23] , David A. Relman [24],[25],[26] , Fergus Shanahan 17 , Shinichi Sunagawa 1 , Jun Wang 5,[28],[29],[30],[31] , George M. Weinstock [32] , Gary D. Wu [33] , Liping Zhao [34] , Jeroen Raes 2,3,[35],# , Rob Knight [36],[37],[38],[39],# , Peer Bork 1,[40],[41],# ET1 ET3 ET2 3 distinct community types at genus level… …now in context of a complex composition landscape Paul Costea, Falk Hildebrand et al., in preparation

Enterotypen in the media ... and the phone kept ringing

Goal is Operates since 5000 Sep. 2011 samples Currently 500k Euro 600 Euro so far ... Sampling DNA extraction Sequencing Analysis my.microbes.eu www. bork .embl-heidelberg.de Donate or participate!

Personalized my.microbes report Version 2 Enterotypes approved by EMBL-ethics commission No approval for reporting antibiotics resistances, pathogen detection und some diseases

Our gut microbiome is linked to a multitude of different diseases Crohn’s Obesity • Gut 2006 • Nature 2006 disease • Nat. Rev. Arthritis Diabetes • Nature (2012) Rheumatology 2011 Autism NASH • J. Med. Microbiol. 2005 • Nature 2012 Multiple Athero- • Nature 2011 • Nature 2011 Sclerosis sclerosis Colo- Parkinson rectal • Eu. J. Neurosci. 2009 • Genome Res. 2012 Disease cancer Inflammatory diseases Neurological disorders Cardiovascular diseases Metabolic diseases Cancer

Association of microbiota with colon cancer Stool samples from 156 French individuals provided by Iradj Sobhani Study design (cancer detection) Per individual: on av. 9 Gb are currently sequenced, i.e. almost 3 human genome equivalents

Association of microbiota with colon cancer 22 Bacterial species in stool function as biomarkers in early cancer stages and can be utilized for non-invasive screening before colonoscopy 2014 In combination with the “fecal occult blood test” (FOBT) >45% more cancers detected as FOBT alone Zeller, Tap, Voigt et al, Mol.Sys.Biol. 10(2014)766 Problem: Full cost model for metagenomics ca 1000 Euro, FOBT = 6 Euro

Association of microbiota with colon cancer Of each of the 22 species, specific primers from marker genes are used only 2016 Cancer risk group: >50 years or >40 years, Stool sampling, 384 well plate screening for qPCR based if obese etc. preparation marker genes of 22 species readout Currently: ca 40 Euro total costs per sample (but can still be reduced)

Test for many confounding factors (diet, drug treatment etc.) Metformin induces gut microbial composition changes in type II diabetes individuals Chinese: Qin et al., Nature 2012; AUC 0.81 Combined cohort after omission of metformin-treated individuals: Swedish: Karlsson et al., Nature 2013; AUC 0.83 AUC = 0.53 Danish: unpublished (54 T2D+75Ctrl); AUC 0.81 Metformin is strongest signal, Some proteobacteria up distinct from T2D which alone is after/during metformin weak treatment Forslund, Hildebrand et al., Nature 228(2015)262 (Metahit)

Drug-bug interactions Screen of 40 prevalent gut bacterial species with ca 1200 FDA- approved drugs shows widespread fitness effects Chemical library Bacterial growth patterns Antibiotics (~15%) Antiparasitic, antifungal, antiviral (~8%) Human-targeted drugs (~77%) OD (578 nm) Anaerobic incubation and 96 and 384-well plates/species, all optical density readout measures in triplicates Time (hours) Measuring growth differences after drug perturbation >> 10% of human non-antibiotics drugs inhibit or reduce growth of gut bacteria, already at low dosages In progress: With Zeller, Typas and Patil groups at EMBL

High resolution microbiomics: From species to strains Each of us carries individual bacterial strains and at least healthy keep them for a long time SNPs Gene content Human – Human ca 0.2% Human – Human ca 0.3% Human – Chimpanzee ca 1% Human – Chimpanzee ca 2% E.coli – E.coli ca 5% E.coli – E.coli ca 20% Schloissnig et al., Nature 493(2013)45 Zhu et al., Genome Biol. 16(2015)82 Our microbial strains are individual, even in monozygotic twins Thus microbiome amplifies genetic individuality (e.g. in digestion) and could be target for personalized therapies

Faecal Microbiota Transplantation (FMT) Transfer of stool from a healthy donor to patient • Analysis usually at – Usually following antibiotics treatment or bowel lavage species level, but most Positive effects reported in GI and non-GI diseases • species are shared – Over 90% success in treating Clostridium difficile infection 1 • Mechanism is currently unknown, e.g. fate of native and introduced strains 1. van Nood, E. et al. (2013). N Engl J – Specific bacteria introduced in patient 2 Med, 368, 407-15. 2. Lawley, TD., et al. (2012). PloS – Replacement or ‘repair’ of ‘bad’ microbial species Pathog, 8, e1002995.

Donor species and strain colonization after FMT for metabolic syndrome 5 time points up to 3 months after FMT, 164 metagenomes incl. donors Collab. with W. de Vos and M. Nieuwdorp Species Strains Measured using Measured using marker genes discriminative SNVs, (mOTUs) modified from Schloissnig et al., Sunagawa et al., Nature Meth. Nature 493(2013)45 10(2013)1196

Strain replacement after faecal microbiota transplantation (FMT) is easier than acquisition of new species Species Strains Donor species Donors strains barely above with durable random colonization, often fluctuation in coexistence 1. There is no “ superdonor ” – 1 donor has 3. New donor strains colonise better different outcomes than new donor species, perhaps by being invisible to the host immune 2. Donor strains can colonise and persist system over at least 3 months Strain replacement implies personalized treatment options, e.g. by replacing multidrug resistance. Li et al., Science 352(2016)586

Screen for presence of helpful/harmful gut microbes Basis for powerful health screenings in the future

Acknowledgements Gut team Collaborators IHMC IHMS, Metacardis, MetaHit (EU) D.Ehrlich W. De Vos (NL/FL) S.Sunyaev (Harvard) Renato Marja Ana Paul I. Sobhani, (UPEC, F) Alves Driessen Zhu Costea M. von Knebel (HD) W. de Vos (Helsinki) Genecore facil. (EMBL) TARA Oceans consort. R. Pepperkok (EMBL) Shini Kristoffer Falk Simone Tools Sunagawa Forslund Hildebrand Li Ece Georg Matt Anita Jens Luis Kartal Zeller Hayward Voigt Kultima Coelho www. bork .embl-heidelberg.de + All other current and former group members as well as visitors ….

For details see: www.bork.embl.de Thank you!

The Microbial Environment and its Influence on Allergy and Asthma in Early Life Sabina I lli On behalf of Erika von Mutius Dr. von Hauner Children‘s Hospital Ludwig Maximilians University Munich, Germany

GABRIEL Study: Prevalences between farm and non farm children % 45 Farm 40 Non farm 35 30 25 20 15 10 5 0 asthma current severe atopy hay fever atopic asthma wheeze dermatitis

European PASTURE Birth Cohort (N=1,133) Cord blood immune CrP asthma responses atopy atopy atopy postnatal Recruitment questionnaire in pregnancy birth 2mo 1y 2y 3y 4y 5y 6y diary yearly questionnaires until age 6 years