International Human Microbiome Congresshuman-microbiome.org/fileadmin/Content/Paris... · 2012...

19‐21 March Paris ‐ France

2012 International Human Microbiome Congress

2012 International Human Microbiome Congress Paris 19‐21 Mars

The conference is the third event organized under the banner of the IHMC, and follows Shenzhen 2010 (organized by the MetaHIT consortium, with BGI Shenzhen) and Vancouver 2011 (organized by the NIH and the Foundation for the National Institutes of Health ‐ Canada?).

The goals of the International Human Microbiome Consortium (IHMC) is to work under a common set of principles and policies to study and understand the role of the human microbiome in the maintenance of health and causation of disease and to use that knowledge to improve the ability to prevent and treat disease. The Consortium's efforts are focused on generating a shared comprehensive data resource that will enable investigators to characterize the relationship between the composition of the human microbiome (or of parts of the human microbiome) and human health and disease. The IHMC is open, at any time, to the funders and PIs of human microbiome research programs that have the capacity to mount a comprehensive analysis of the human microbiome in health and/or disease, and that agree to carry out their efforts according to a set of commonly agreed‐upon IHMC policies The principles, structure and operating modes of the IHMC were defined progressively through several meetings organized since November 2005. The IHMC was officially launched at its meeting held in Heidelberg on October 15‐16 2008. For additional information about the IHMC, please visit www.human‐microbiome.org. The 2012 conference is

and supported by the European Commission (grant HEALTH‐F4‐2007‐201052).

Join the conversation on twitter using the hashtag #IHMC2012

Paris, France –March 19‐21 2012

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9:00 ‐ 11:00 REGISTRATION

11:00 ‐ 11:45 Welcome speeches Marion GUILLOU, President & CEO INRA, France Pascale BRIAND, General Director, ANR, France Rudolf STROHMEIER, Deputy Director General, DG Research and Innovation, European Commission

11:45 ‐ 12:30 Keynote

Chair: Julian DAVIES (UBC, Canada)

S. Dusko EHRLICH (INRA, France) Lessons from the MetaHIT project

12:30 ‐ 14:00 Lunch ‐ Posters

14:00 ‐ 16:30 APPROACHES TO MICROBIOME ANALYSIS

Chair: SØren BRUNAK (CBS Denmark Technical University, Denmark)

14:00 ‐ 14:30 Rob KNIGHT (University of Colorado, USA) Sources of variation in the human microbiome

14:30 ‐ 15:00 LI Junhua (BGI Shenzhen, China)Improvement of microbial gene catalog construction

15:00 ‐ 15:30 Karen E. NELSON (J. Craig Venter Institute, USA) Reference genomes for the study of the Human Microbiome

15:30 ‐ 16:00

16h00 ‐ 16:15

16h15 ‐ 16:30

H. Bjørn NIELSEN (CBS Denmark Technical University, Denmark) MetaGenomic Species: facilitating statistical and biological interpretation Mathieu ALMEIDA (INRA, France) From "meta‐genomic species" to high quality draft genomes Mircea PODAR (Oak Ridge National Laboratory ‐ Univ. of Tennessee, USA) Uncovering the dark matter of the human microbiota through high throughput single cell genomics and targeted pangenomics

16:30 ‐ 17:00 Coffee Break

19 March 2012


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17:00 ‐ 18:45 DATA ORGANISATION & INTERPRETATION

Chair: Lita PROCTOR (National Institutes of Health, USA)

17:00 ‐ 17:30

17:30 ‐ 18:00

Owen WHITE (University of Maryland, USA)The Human Microbiome Project analysis infrastructure Jens NIELSEN (Chalmers University of Technology, Sweden) Prospects for systems biology and modeling of the gut microbiome

18:00 ‐ 18:30 Manimozhiyan ARUMUGAM (EMBL, Germany)Towards petabase metagenomics : challenges and roadblocks ahead

18:30 ‐ 18:45 Dan KNIGHTS (University of Colorado, USA)Human‐associated microbial signatures: examining their predictive value

19:00 ‐ 21:00 Wine & Cheese Buffet ‐ Poster Session

20 March 2012

9:00 ‐ 10:45

MICROBIOME IN HEALTHY INDIVIDUALS 1

Chair: Jane PETERSON (National Institutes of Health, USA)

9:00 ‐ 9:30 Dirk GEVERS (The Broad Institute, USA) Baseline for a healthy human microbiome

9:30 ‐ 10:00 Mihai POP (University of Maryland, USA) Can we and should we assemble metagenomes?

10:00 ‐ 10:30 Curtis HUTTENHOWER (Harvard School of Public Health, USA) Reducing microbial unemployment: functional roles for the microbiome in health and disease

10:30 ‐ 10:45 Masahira HATTORI (University of Tokyo, Japan)Metagenomics of Japanese gut microbiomes



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20 March 2012

11:15 ‐ 12:30

MICROBIOME IN HEALTHY INDIVIDUALS 2

Chair: Maria GIOVANNI (National Institutes of Health, USA)

11:15 ‐ 11:45 Kristine WYLIE (Washington University Genome Institute, USA) Novel Bacterial Taxa in the Human and Vervet Microbiomes

11:45 ‐ 12:15 Paul W. O'TOOLE (APC University College Cork, Ireland) Diet‐health‐microbiota interactions in older persons

12:15 ‐ 12:30 Christian HOFFMAN (University of Pennsylvania, USA) Long term dietary patterns shape gut microbial enterotypes

12:30 ‐ 14:00 Lunch ‐ Posters 13:15 ‐ 13:45 Seminar power calculations for designing microbiome experiments

14:00 ‐ 16:15 MICROBIOME IN DISEASE 1Chair: Karsten KRISTIANSEN (University of Copenhagen, Denmark)

14:00 ‐ 14:30 Oluf PEDERSEN (Hagedorn Research Institute, Denmark) Deep metagenomic sequencing demonstrates marked differences in the gut microbiome between lean and obese people: evidence from the MetaHIT obesity study

14:30 ‐ 15:00 Karine CLEMENT (Institute of Cardiometabolism & Nutrition, INSERM‐UPMC‐APHP, France) Gut metagenome: clinical investigation studies

15:00 ‐ 15:30 Liping ZHAO (Shanghai Jiao Tong University, China) “Microbiome‐Wide Association studies,MiWAS” for dissecting the role of gut microbiota in metabolic syndrome, from animal models to human trials

15:30 ‐ 16:00

WANG Jun (BGI Shenzhen, China) A Metagenome‐Wide Association Study of gut microbiota identifies markers associated with Type 2 Diabetes

16:00 ‐ 16:15 LI Lanjuan (Zhejiang University, China) The intestinal dysbiosis and its contribution to NAFLD in human and the high‐fat induced rats

16:15 ‐ 16:30 Kjersti AAGAARD (Baylor College of Medicine, USA)A comprehensive metagenomic catalogue of microbiota across body sites in primates: a high fat maternal diet alters the offspring microbiome to 1 year of age

16:30 ‐ 17:00 Coffee break


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17:00 ‐ 19:15 MICROBIOME IN DISEASE 2

Chair: Per BRANDTZAEG (Oslo University Hospital, Norway)

17:00 ‐ 17:30 Francisco GUARNER (Hospital Univeristari Vall d’Hebron, Spain) Distortion of the gut microbial ecosystem in patients with ulcerative colitis

17:30 ‐ 18:00 Brandi L. CANTAREL (University of Maryland, USA) Identification of Crohn’s signatures in the human gut microbiota by meta‐omics

18:00 ‐ 18:30 James VERSALOVIC & Emily HOLLISTER (Texas Children’s Hospital, USA) Network analysis reveals altered community structure in the fecal microbiota of children with irritable bowel syndrome

18:30 ‐ 18:45 Jacques RAVEL (University of Maryland, USA) Transcriptional dynamics of the vaginal microbiome

18:45 ‐ 19:15 Melody SLASHINSKI (Baylor College of Medicine, USA) Ethical, legal and social dimensions of human microbiome research

19:45 Gala Dinner in the nave of Palais Brongniart

21 March 2012

9:00 ‐ 10:45 MICROBIOME MODULATION

Chair: Annick MERCENIER (Nestlé Research Center, Switzerland)

9:00 ‐ 10:30 Muriel DERRIEN (Danone Research, France) Impact of consumption of a fermented milk product on gut microbiota stability and functionality in ulcerative patients

9:30 ‐ 10:00 David A. RELMAN (Stanford University, USA) Stability and resilience in the human microbiome

10:00 ‐ 10:30 Willem de VOS (Wageningen University, The Netherlands) From associations to causality: effect of treatments targeting the human intestinal microbiome

10:30 ‐ 10:45 Paul COTTER (University College Cork, Ireland) Modulation of the gut microbiota; antibiotics vs. bacteriocins

10:45 ‐ 11:00 Coffee break


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11:15 ‐ 12:30 FUNCTIONS OF MICROBIOME 1

Chair: Emmanuelle MAGUIN (INRA, France)

11:15 ‐ 11:45 Joël DORÉ (INRA, France) Screening of metagenomic clones

11:45 ‐ 12:15 B. Brett FINLAY (University of British Columbia, USA) The role of microbiota in enteric and allergic diseases

12:15 ‐ 12:30 Marion LECLERC (INRA, France) Riboflavin production by a metagenomic clone from the human ileum mucosa: a new role for Faecalibacterium prausnitzii in vivo?

12:30 ‐ 14:00

Lunch – Posters

14:00 ‐ 15:30 FUNCTIONS OF MICROBIOME 2

Chair: Baghi SINGH (Canadian Institutes of Health Research, Canada)

14:00 ‐ 14:30 Stephen M. COLLINS (McMaster University Medical Center, Canada) The influence of the intestinal microbiota on the gut‐brain axis

14:30 ‐ 15:00 Martin J. BLASER (New York University, USA) Effects of early‐life antibiotics on murine developmental phenotypes and immunity

15:00 ‐ 15:15 James GOEDERT (National Cancer Institute NIH, USA) Fecal microbial determinants of fecal and systemic estrogens

15:15 ‐ 15:30 Iradj SOBHANI (UPEC‐Paris XII, France) Putative role of gene mutation and environment in colon cancer inflammation in host

15:30 ‐ 16:15 MICROBIOME DATA CHALLENGES

Peer BORK (EMBL, Germany)Complexity and individuality of human gut microbiomes



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21 March 2012

16:45 ‐ 18:30 MICROBIOME FUTURE Panel discussion on the future of Human Microbiome Research

Debate moderator: Ed YONG, UK Funding agencies…

Patrik KOLAR, European Commission Marc OUELETTE, Canadian Institutes of Health Research, Canada Lita PROCTOR, National Institutes of Health, USA …Industry… Pierre BELICHARD, Entérome, France Christian BRECHOT, Institut Mérieux, France Johan VAN HYLCKAMA VLIEG, Danone Research, France ...Ethical & social issues Lucy HOAREAU, UNESCO Richard SHARP, Cleveland Clinic, USA

18:30 Closing remarks

2012 International Human Microbiome Congress Posters

All posters will be on exhibition on the ground floor of the Palais throughout the conference.

Posters 1-91, Notre Dame des Victoires Author Title Number Abdollahi-Roodsaz S. Critical role of mouse microbiota and efficacy of dietary non-digestible oligosaccharide

treatment in Th17-dependent autoimmune destructive arthritis 81

Alexeev D.G. Human gut microbiota analyzed by mass-spectrometry and sequencing 57

Azad M.B. Exclusive breastfeeding protects against Clostridium difficile colonization by promoting lower relative abundance of Lachnospiraceae in gut microbiota.

5

Ballarini A. Species-level profiling of human microbiomes with the BactoChip microarray 68

Beighton D. In vivo expression of glycan utilization genes by Streptococcus oralis and Streptococcus mitis in the oral cavity.

15

Belzer C. Function and importance of Akkermansia spp. in the intestinal tract 28

Brown J.R. Antibacterial Drug Modulation of the Gut Microbiome in Obesity and Diabetes Animal Models

82

Budding A.E. Evaluation of rectal swabs for the analysis of human intestinal microbiota 54

Budding A.E. Automated high througput analysis of the intestinal microbiota by IS-pro 53

Bülow E. Functional metagenomic analysis reveals selection for antibiotic resistance in the gut microbiota during Intensive Care hospitalization

86

Campbell A.G. Single cell genomics of uncultured oral Chloroflexi, Deltaproteobacteria and Synergistes 39

Campbell J.H. Single-cell genomic characterization of human oral representatives of the incultured SR1 and TM7 bacterial phyla.

47

Chen Yu Association of oral health, oral bacterial infection, and gastric precancerous lesions 70

Chunlei Chen Antioxidant-Protective Effects of Lactitol against Endotoxemia in Patients with Chronic Viral Hepatitis

85

Claesson M.J. Resolving Additional Microbiota Subtypes in Intestinal Microbiota of Older Subjects 4

Couvigny B. The commensal bacterium Streptococcus salivarius inhibits PPARγ activity and its target genes in human intestinal epithelial cells.

33

Cox L.M. Early life microbiota alters adult metabolism and body composition 1

Danilenko V.N. The Toxin-Antitoxin System Gene Polymorphism As A Marker for Species and Strain Identification of the Probiotic Component of Human Microbiome

19

Davenport E. Examining the genetic basis of interindividual variation in the human fecal microbiome 12

de Leeuw M. 16S metagenomics profiling 72


Author Title Number Di Liberto G. Functional analysis of the predicted surface proteome of Gram+ bacteria from the human

GI tract. 59

Do Thuy Evidence of ethanolamine catabolism by Fusobacteria. 29

Earl A. The Most Wanted Bacteria from the Human Microbiome 73

Eloe-Fadrosh E.A. Effects of oral immunization with the Ty21a typhoid vaccine on the gut microbiota and local and Systemic immune responses

87

Feehery G.R. Novel purification reagents for the study of the human microbiome 48

Flores R. Effect of Delayed Freezing on Microbial Composition in Human Feces: Lessons for Epidemiological Studies

42

Francino P. Meconium microbiota types: relation to maternal and childbirth determinants and to health outcomes in early childhood

2

González A. Assessing temporal changes in microbial communities. 6

Guédon E. Relationship between self-aggregation property of the human commensal bacterium Streptococcus salivarius and its ability to interact with intestinal epithelial cells

20

Haiser H.J. Characterizing the inactivation of the cardiac drug, digoxin, by a member of the human gut microbiota

30

Han S. Artificial Polyploidy Improves Genome Coverage from Single Cell 56

Hao Qin A mouse fecal microbial gene catalogue established by Illumina-based sequencing 55

Hettich R. A hybrid metagenomic sequencing and assembly approach increases proteome identification coverage in the human gut microbiome

49

Hooda S. Fecal microbiota of healthy adult men is affected by novel dietary fibers and correlated with fecal metabolites

89

Isaksen M.L. GA-map™ - a rapid, comprehensive gut microbiota analysis 51

Jalanka-Tuovinen J. Intestinal microbiota in healthy adults: dimensions of the common core and relation to intestinal symptoms

65

Jeffery I.B. Microbial diversity is highly correlated with the Healthy Food Diversity Index 90

Kaci G. Anti-inflammatory properties of commensal Streptococcus salivarius on human intestinal epithelial cells and in murine TNBS-induced colitis model

21

Keijser B.J.F. A public-private partnership that aims to establish a novel, multivariate view of oral health 43

Kolmeder C. Effects of a probiotic intervention on the human intestinal metaproteome 91

Kong, Ling-Chun Associations between gut microbiota and adipose tissue gene expression during bariatric surgery induced weight loss in morbid obesity

18

Konya T. Is house dust a reservoir for gut bacteria? 7

Kotowska D. Changes in gut microbiota in resveratol treated and exercised aged mice. 75

Kushugulova A.R. Study of the properties of bacteria of the genus Lactobacillus, representatives of intestinal microbiota

22


Author Title Number Lahti L. Global characterization of the human intestinal microbiota by integrative meta-analysis 67

Langella P. Analysis of anti-inflammatory effects of FaecalibacteriumI prausnitzii using gnotobiotic mice

24

Layec S. Impact of surface-exposed proteins on the commensal life in Streptococccus salivarius. 23

Lewis C.M. Characterizing Extinct Gut Microbiomes 50

Li Huiying Propionibacterium acnes strain populations in the skin microbiome associated with acne 32

Luang-In V. Influence of human gut microbiota on the metabolic fate of glucosinolates 34

Luna R.A. Temporal characterization of the gut microbiome in a cohort of hospitalized preterm infants

8

Ma Jun Initial association study of human microbiome profile with its host mitochondria genome variants

13

Mackie, R.I. Transcriptional analysis of wheat arabinoxylan hydrolysis and utilization by Bacteroides ovatus and Bacteroides intestinalis

38

Maukonen J. The currently used commercial DNA extraction methods give different results of Clostridial and Actinobacterial populations derived from human fecal samples

63

Maurice C.F. An active subset of the human gut microbiome responsive to xenobiotics 58

Morrison M. Weight loss associated dietary intervention affects the human gut microbiota in obese but otherwise healthy Australian males and changes in the growth of Faecalibacterium praunitzii in response to changes in nutrient profiles

83

Morrison M. A “metaparental mating” approach for the recovery of new transconjugant strains of human gut bacteria

84

Murugkar P.P. Mechanisms of Uncultivability in the Oral Microbiome 60

Pieper D. The anterior nare microbial community over space and time

31

Putignani L. Succession of early microbial consortia in the developing infant intestinal microbiota unveiled by meta-omics approaches

9

Renault P. Prevalence of Streptococci in the intestinal flora 25

Rho M. CRISPRs: Evolving immune systems in human microbiomes 44

Roeselers G. A Top-down microbial systems ecology view of the impact of prebiotic oligosacharides on Bifidobacteria in a Human gut microcosm

16

Roger L. Monitoring the Effects of Black Tea Polyphenols on the Human Intestinal Microbial Ecosystem in vitro

76

Salojärvi J. Meta-analysis of the Human Gut Microbiota - Focus on Enterotypes 66

Scheffer-Wong A. Massively Parallel Synthesis of Oligonucleotides Enables Fluorescence In Situ Hybridization (FISH) to Microbial Genomes

41

Schioppa T. Probiotic and postbiotic activity in health and disease: comparison on a novel polarized ex-vivo organ culture model.

77

Seekatz A. The Effect of an Oral Live-attenuated Shigella Vaccine and Wild type Shigella Infection on the Intestinal Microbiota of Cynomolgus Monkeys

74


Author Title Number Shah P. A biomolecular isolation framework for molecular Eco-Systems Biology of the human

microbiome 64

Sim K. Missing bifidobacteria: systematic undercounting in neonatal gastrointestinal microbiota resolved with novel, universal, barcoded 454 primers.

40

Sonne S.B. Modulation of the gut microbiota by diets and the anti-inflammatory drug indomethacin in obesity prone and obesity resistant mice

78

Spencer M.D. Robust data management and analysis strategies overcome sequencing platform idiosyncrasies

69

Spinler J.K. Pangenomic analysis of Lactobacillus reuteri highlights the evolution of a human-specific ecotype

35

Srivastava T. Complete genome sequences of rat and mouse strains of unculturable Segmented Filamentous Bacteria, a potent inducer of Th17 cell differentiation.

36

Stamboliyska R. Identification of prokaryotic transposable elements from metagenomic marine data 52

Thiele I. Systems biology approach to the human–Bacteroides thetaiotaomicron symbiosis 37

Thompson H. An in-vitro model system for the cultivation of previously uncultured human oral bacteria 61

Tims S. Development of a carbohydrate binding protein detection assay 45

Tomida S. The pan-genome and strain diversity of Propionibacterium acnes in the human skin microbiome

26

Tyler A.D. Interaction of IBD-associated genetic polymorphisms and the microbiome of the pelvic pouch

11

Ubeda C. Commensal anaerobic bacteria mediate Vancomycin-resistant Enterococcus clearance from the intestine.

17

Vallès Y. Acquisition and development of the gut microbiota 3

Wacklin P. Secretor genotype (FUT2 gene) is associated with composition of bacteria in the human intestine

14

Wang Duochun Genome sequencing reveals unique mutations in characteristic metabolic pathways and the transfer of virulence genes between V. mimicus and V. cholerae

10

Wang Xinhui Patterns on the composition of nasopharyngeal microbiota 27

Ward D.V. Impact of antibiotic administration on the establishment and development of infant gut flora

79

Witt K. Identifying mechanisms of bacterial unculturability in the human gut microbiome 62

Xiang C. Vaginal microbiota restoration for bacterial vaginosis treated with metronidazole and probiotic Lactobacillus intravaginally

88

Yamanishi S. Down-regulation of mucosal immune system in mice exposed to early life antibiotic treatments

80

Yang Liying Reproducibility and accuracy of amplicon-based 16S rRNA gene surveys 71

Yow M.A. Pathogen discovery in prostate cancer: a massively parallel sequencing approach 46


Posters 92-170, Espace Réaumur

Author Title Number Aagaard K. A 16S-Based Metagenomic approach to characterisation of the vaginal microbiome

signature in pregnancy 137

Abnet C.C. Upper digestive tract microbiome diversity is associated with total mortality in a prospective cohort study in China

164

Alban M. Life on human surfaces: skin metagenomics. 128

Alekseyenko A.V. Association of cutaneous microbiota with psoriasis 126

Alicki E. The impact of IgA on the intestinal microbiome 92

Aliferis C.F. Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison 136

Batto JM Optimizations to compute large correlation matrix onto GPU system of hybrid HPC clusters

108

Biesbroek G The nasopharyngeal microbiota in relation to 7-valent Pneumococcal Conjugate Vaccination: a randomized controlled trial in healthy children in The Netherlands

162

Biesbroek G Effect of Feeding type on the Composition and Dynamics of Nasopharyngeal Microbiota in Infants.

160

Biesbroek G Viral and Bacterial Interactions in the Upper Respiratory tract of Healthy Children: a metagenomic approach

161

Bylova N.A. Gut microbiota in chronic heart failure (CHF) 120

Charlson E.S. Biogeography of microbial populations in the respiratory tract of healthy and HIV-infected subjects

144

Cheng J. Duodenal epithelium associated microbiota in pediatric coeliac disease patients and healthy controls assessed by microbial phylogenetic microarray

171

Chiang H-I Hybrid assembly of metagenomic and single-cell genome sequencing data 150

Collison M. A data integration platform for the microbiota 110

Dols J.A.M. Bacteria associated with bacterial vaginosis in HIV-positive Tanzanian women: Correlation analysis between results from 16S-rDNA-based microarrays, microscopy and Whiff tests

140

Durbán A. Follow-up of faecal microbiota in irritable bowel syndrome patients. 148

Durbán A. Dynamics of faecal bacterial communities based on daily follow-up 147

Dutilh B.E. Towards the human colorectal cancer microbiome 151

Faust K. Prediction of relationships between microbial taxa in the human body 96

Fettweis J.M. The vaginal microbiome: disease, genetics and the environment 130

Fouad A.F. Transformation of oral microbiome from normal oral cavity to acute endodontic infections 127


Author Title Number Fricke W.F. The fungal and bacterial microbiome of the stomach 152

Gajer PM. Association between cigarette smoking and the vaginal microbiota 129

Ganu R. Linking barkers hypothesis on the developmental origins of adult disease with the hygiene hypothesis: maternal methyl-donor supplementation (MDS) significantly alters the fetal liver microbiome

141

Ganu R. Remote history of maternal infection or asymptomatic vaginosis alters the human placental microbiome

142

Garcia-Garcerà M. Staphylococcus prevails in the skin microbiota of long-term immunodeficient mice. 125

Gorkiewicz G. Dysbiosis and altered mucosal immune response in chronic inflammatory upper gastrointestinal (GI) diseases.

138

Hendriksen W.T. Modeling pathways of nasopharyngeal microbiota of young children based on 16S rRNA sequence data: an exploratory study

100

Hildebrand F. Combining a gut-specific annotation platform with a dedicated datamining pipeline towards understanding obese and IBD microbiota

114

Hunter C. EBI Metagenomics: Studying the Functions of Metagenomes. 101

Huot Creasy The Data Analysis and Coordination Center for the Human Microbiome Project 99

Joossens M. Functional Repercussions of Subclinical Intestinal Dysbiosis In Unaffected Relatives Of Crohn’s Disease Patients

157

Karlsson F. Atherosclerosis is associated with an altered gut metagenome 143

Kistler J.O Bacterial Composition of Dental Plaque during the Transition from Health to Experimentally Induced Gingivitis

145

Ko G.P. Investigation of Vaginal Microbiota in a Korean Twin Cohort 135

La Rosa P.S. Modeling and Clustering Taxonomic Trees from Human Microbiome Data using Statistical Object-Oriented Data Analysis

103

Langille M.G.I. Inferring microbial community function from taxonomic composition 102

Mai V. Fecal Microbiota Distortions Appear Associated with Late Onset Sepsis in Preterm Infants 153

Mändar R Effect of sexual intercourse on vaginal microbiome of infertile couples’ women 131

Manichanh C A robust microbiota: a key protagonist against functional intestinal disorders? 167

Manichanh C Storage conditions of intestinal microbiota matter in functional metagenomics 166

Miller C.S. EMIRGE: Sensitive, quantitative microbial community characterization via deep sequencing and assembly of full-length 16S amplicons.

105

Minot S. The human gut virome: Inter-individual diversity, genomic hypervariation, and dynamic response to diet

154


Author Title Number Nakayama J. Asian Microbiome Project: A pilot study on the basal microbiota profile of healthy Asian

youngsters 139

Nookaew I. Enterotype analysis of 317 gut genomes 113

Obregón-Tito A.J. Metagenomics and social inclusion in Peru 165

Ogilvie L.A. Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage ɸB124-14.

168

Patsantara G. Parasitic helminth Enterobius vermicularis as a commensal microorganism 169

Pérez-Brocal V. An approach to the characterization of the human virome in Crohn’s disease 155

Pesole G. SARMA: a web resource for species assignment of high-throughput sequencing reads from

Metagenomics Analysis

106

Philllips G.J. Dysbiosis characterised by reduced abundance of Roseburia is associated with increased

severity of colitis in Il-10-/- mice

146

Pinto J.M. Sinonasal Microbiota Vary with Disease Subtype: Implications for Mucosal Inflammatory

Disorders of the Upper Airway

156

Plichta D.R. Functional analysis of novel genetic structures indentified through metagenomics of

human gut.

115

Popenko A.S. MALINA - a Web-service for human gut microbiota whole-genome metagenomic reads

analysis

94

Potluri S. & Prifti E. Gut Microbiome and Immunome of NTR Twins 123

Qin Nan Analysis of gut microbiome in patients with liver cirrhosis 158

Raes J Microbiome variation in health and disease: how to get more out of your metagenome. 111

Redel H. Quantitation of cutaneous microbiota in diabetic and non-diabetic men 159

Riehle K. The Genboree Microbiome Toolset and Microbiome Analysis 107

Said H.S. Comparative Analysis of Salivary Microbiota of IBD Patients and Healthy Individuals using

Barcoded Pyrosequencing

116

Sanz A Genetic risk of developing coeliac disease and milk-feeding type influence the intestinal

colonization pattern in infants. The PROFICEL study

122

Saulnier D.M. Volatile metabolite production and microbiome composition in halitosis 117

Schmieder R. Tools for Detecting Antibiotic Resistance in the Human Microbiome 95

Segal L.N. Evaluation of the upper airway and lung microbiome in emphysema 118

Segata N. Efficient metagenomic community profiling enables species-level characterization of over 250 shotgun sequenced gut microbiomes

104

Sharma V.K. Comparative Analysis of MetaBin with Other Homology-based Methods for Taxonomic Assignments of Metagenomic Sequences

97


Author Title Number Sharpton T.J. Quantifying Human Microbiome Functional Variation using Operational Protein Families 109

Shoaie S. Saeed Modeling of human gut microbiome 93

Smith A.M. Development of a hierarchical taxonomy assignment pipeline for fungal microbiomics 98

Stahringer S.S. A longitudinal survey of the oral microbiota in adolescent twins 133

Tong M. Defining a mosaic of functional microbial communities at the human mucosal surface, and their association with IBD

149

Treangen. T. A modular and open source metagenomic assembly pipeline 112

Tyakht A.V. Examining composition of Russian human gut microbiota by assessing relative abundance of functional and taxonomical units

163

Vincent C. The intestinal microbiota as a predictor for nosocomial Clostridium difficile infection 119

Winek K. The impact of focal cerebral ischaemia on the composition of murine intestinal microbiota 121

Wylie K.M. The Human Virome in Healthy Adults 170

Youmans B. Alterations in the human gut microbiome during and after norovirus-associated travelers’ diarrhea

132

Zaura E. The relation between oral Candida load and bacterial microbiome profiles in Dutch elderly 124

Zhou Xia Characterization of Microbiota in External Urogenital and Perianal Areas of Women 134

2012 International Human Microbiome Congress Sponsors

The conference was organized with the support of our Sponsors. We are particularly grateful to Danone Research, HP, Proctor & Gamble, NIH HMP, Lenovo & NVIDIA, Major Sponsors of the 2012 edition.

Danone was born out of a conviction that now lies at the very heart of its stated mission: "Bringing health through food to as many people as possible". The Group's strong ambitions rest primarily on the mobilisation and skills of its R&D teams. Its R&D know-how is housed by Danone Research, a worldwide organisation present in some 15 countries that brings together around 1,200 staff, with a network of almost 200 scientific collaborations worldwide generating knowledge in specific fields (prebiotics, probiotics, human breast milk, immunology, metabolic programming, etc). Danone is active in four fields: fresh milk products (No. 1 worldwide), water (No. 2 worldwide for bottled water), baby nutrition (No 2 worldwide) and medical nutrition. Visit us at www.danone.com

The NIH Human Microbiome Project is building a vast community resource of taxonomic and metagenomic sequences of microbiomes across major body regions of healthy adults, reference strain genome sequences and disease-specific properties of microbiomes in urogenital, skin and gut diseases. Computational tools and technologies along with microbiome-specific ELSI studies are providing additional resources for the field. Please visit commonfund.nih.gov/hmp/ for the latest information on the project.

HP for Health and Life Sciences helps organizations across the value chain deploy systems that improve business and health outcomes through the capture, management, and integration of information related to bioscience innovation, pharmaceuticals, medical technology, and patient data. HP's extensive portfolio of printing and personal computing products and IT services, software and solutions enable health and life science organizations to lower costs, speed innovation into practice, function more efficiently and improve the quality of care. HP Health and Life Sciences industry solutions enable collaboration across the entire ecosystem and mine more value from market players and information. More information about HP Health and Life Sciences is available at www.hp.com/go/healthandlifesciences

Lenovo (HKSE:992) (ADR: LNVGY) is a $US21 billion personal technology company serving customers in more than 160 countries, and the world's second-largest PC vendor. Dedicated to building exceptionally engineered PCs and mobile internet devices, Lenovo's business is built on product innovation, a highly-efficient global supply chain and strong strategic execution. Formed by Lenovo Group's acquisition of the former IBM Personal Computing Division, the company develops, manufactures and markets reliable, high-quality, secure and easy-to-use technology products and services. Its product lines include legendary Think-branded commercial PCs and Idea-branded consumer PCs, as well as servers, workstations, and a family of mobile internet devices, including tablets and smart phones. Learn more about Lenovo workstations at www.lenovo.com/thinkstation

Four billion times a day, P&G brands touch the lives of people around the world. P&G is marketing probiotics in the United States for Personal Health Care (Align®) and Pet Care (Prostora®) and is exploring additional new product possibilities. The company has one of the strongest portfolios of trusted, quality, leadership brands, including Pampers®, Tide®, Ariel®, Always®, Whisper®, Pantene®, Mach3®, Bounty®, Dawn®, Gain®, Pringles®, Charmin®, Downy®, Lenor®, Iams®, Crest®, Oral-B®, Duracell®, Olay®, Head & Shoulders®, Wella®, Gillette®, Braun® and Fusion®. The P&G community includes approximately 127,000 employees working in about 80 countries worldwide. Please visit www.pg.com for the latest news and in-depth information about P&G and its brands.

http://www.danone.com/

http://commonfund.nih.gov/hmp/

http://www.hp.com/go/healthandlifesciences

http://www.lenovo.com/thinkstation

http://www.pg.com/


Paris-based Enterome is a privately owned personalized medicine company dedicated to the development of drugs and biomarkers for chronic and challenging medical conditions relating to abnormalities of bacterial composition of the human intestine. Enterome's technology was developed initially in the INRA laboratory of S. Dusko Ehrlich at Jouy-en-Josas, France. Enterome is currently advancing an internal pipeline of biomarkers in chronic serious diseases i.e. metabolic diseases: NASH, type-2 diabetes, obesity and inflammatory bowel diseases, Crohn's disease and ulcerative colitis. Learn more about Enterome at www.enterome.com

LABIP, the Industry Platform for EU sponsored research programs on lactic acid bacteria, is a European Economical Association of industries involved in the production of products using lactic acid bacteria and probiotics and have production or research facilities within the EU. Companies that fulfill these criteria have the right to become a member and cannot be excluded. At the moment LABIP has 25 members. The focus of LABIP is on the interaction between Academia (universities and research institutions) and Industry (more specifically Industry R&D) in the field of (pre-competitive) scientific and technological research on lactic acid bacteria, gut microbiota and the interaction between microbiota and the host. LABIP aims to: • Secure EU-funding for LAB research on a long-term basis in Europe • Act as platform where industrial researchers in the area of LAB and microbiota

can meet and interact with scientist from Academia • Coordinate communication about topics of industrial relevance between

science, industry and EU authorities Visit for more information www.labip.com

Life Technologies Corporation is a global biotechnology company dedicated to improving the human condition. Our systems, consumables and services enable researchers to accelerate scientific and medical advancements that make life even better. Life Technologies customers do their work across the biological spectrum, working to advance the fields of discovery and translational research, molecular medicine, stem cell-based therapies, food safety and animal health, and 21st century forensics. The company manufactures both molecular diagnostic and research use only products. Life technologies' industry-leading brands are found in nearly every life sciences lab in the world and include innovative instrument systems under the Applied Biosystems and Ion Torrent names, as well as, the broadest range of reagents with its Invitrogen, GIBCO, Ambion, Molecular Probes and Taqman products.

www.lifetechnologies.com

MO BIO offers a complete line of nucleic acid purification kits optimized for the isolation of microbial DNA and RNA from a variety of inhibitor rich sample types including gut, stool, cervical swabs, human skin, soil, biofilm, water, and bacterial cultures utilizing a patented enzyme Inhibitor Removal Technology®. We also offer the widest selection of bead homogenization options for lysis of any micro-organism including the multi-velocity high efficiency PowerLyzer™ sample homogenizer.

http://www.enterome.com/

http://www.labip.com/

http://www.lifetechnologies.com/


Nestlé, founded in 1866, is the world’s leading Nutrition, Health and Wellness Company. With headquarters in Vevey, Switzerland, Nestlé employs over 280,000 people, with factories and operations in almost every country of the world. The driving force of innovation within Nestlé is its dynamic network of Research, Development and Technology centres worldwide. Comprised of leading scientists, technicians and engineers, these centres cultivate diverse research and development expertise to respond to ever-changing consumer and business needs. At the heart of this Nestlé Research Network lies the Nestlé Research Center (NRC), the world’s largest private food and nutrition research institute and the centre of fundamental scientific research within Nestlé. Learn more about Nestlé Science & Research at www.research.nestle.com

NVIDIA awakened the world to computer graphics when it invented the GPU in 1999. From its roots in visual computing, the company expanded into parallel and mobile computing. One of the most complex processors ever created, the GPU is the engine of computer graphics: the science and art of using technology to create and enjoy beautiful, interactive experiences. NVIDIA has shipped over one billion GPUs.

Learn more about NVIDIA at www.nvidia.com

Headquartered in Basel, Switzerland, Roche is a leader in research-focused healthcare with combined strengths in pharmaceuticals and diagnostics. Roche is the world’s largest biotech company with truly differentiated medicines in oncology, virology, inflammation, metabolism and CNS. Roche is also the world leader in in-vitro diagnostics, tissue-based cancer diagnostics and a pioneer in diabetes management. Roche’s personalized healthcare strategy aims at providing medicines and diagnostic tools that enable tangible improvements in the health, quality of life and survival of patients. In 2011, Roche had over 80,000 employees worldwide and invested over 8 billion Swiss francs in R&D. The Group posted sales of 42.5 billion Swiss francs. Genentech, United States, is a wholly owned member of the Roche Group. Roche has a majority stake in Chugai Pharmaceutical, Japan. For more information: www.roche.com.

Unilever is one of the world's leading suppliers of fast-moving consumer goods. Our products are sold in over 180 countries and used by 2 billion consumers every day. Our vision is help people feel good, look good and get more out of life with brands and services that are good for them and good for others. We will inspire people to take small everyday actions that can add up to a big difference for the world. We will develop new ways of doing business that will allow us to double the size of our company while reducing our environmental impact. We work with 167,000 employees worldwide. We produce world leading brands such as Knorr, Lipton, Hellmann's, Becel, Dove, Axe and Pond's, and brands and innovation are at the heart of everything we do. Visit for more information www.unilever.com.

Visit our sponsors in the poster exhibition area

http://www.research.nestle.com/

http://www.nvidia.com/

http://www.roche.com/

http://www.unilever.com/

2012 International Human Microbiome Congress Acknowledgements

This conference was organized by the MetaHIT Consortium, as part of its task defined in the grant agreement HEALTH‐F4‐2007‐201052 financed by the European Commission under the 7th framework program. The consortium gathers 13 partners from academia and industry, from a total of 8 countries. Its total cost has been evaluated at more than 21,2 million € and the funding from the European Commission has been set with an upper limit of 11,4 million €. The project started 1 January 2008 and will last until 30 June 2012. To learn more about the project and our achievements, please visit www.metahit.eu

We wish to thank the following individuals for graciously contributing their time and expertise.

Scientific organization Committee

• Peer BORK • Julian DAVIES • Joël DORÉ • S. Dusko EHRLICH • Francisco GUARNER • Masahira HATTORI

• Karen E. NELSON • Jane PETERSON • Lita PROCTOR • Bhagirath SINGH • George WEINSTOCK • Liping ZHAO

Local organization : Jean‐Michel BATTO, Quitterie DUPUTEL, Florence HAIMET, Petar KOS, Rachel KOUANDA,

Marielle POUGNON & Yohanan WINOGRADSKY

Local organization was realized by coordinator of the MetaHIT project.

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