Summer School 2016 in Metagenomics

 

The French Institute of Bioinformatics, France Génomique  and Institut Pasteur are organizing the First Summer School 2016 in Metagenomics

Les participants sont invités à se présenter à partir de 13h15 au 28 rue du Docteur Roux avec une pièce d'identité.

 

Date: Monday 12 – Friday 16 September 2016

Venue: Institut Pasteur, 28 rue du Docteur Roux, 75015 PARIS (France) – Auditorium François Jacob

Application opens: Thursday May 13 2016

Application deadline: Monday July 11 2016

Participation: Open application (120 participants), with selection for the hands-on tutorials (30 places)

Contact: Scientific contact :
summer_school_metagenomics_cs@groupes.france-bioinformatique.fr 
Organization contact : 
summer_school_metagenomics@groupes.france-bioinformatique.fr

Registration free of charge. Tutorials registrations are closed.

Overview:

Metagenomics, the sequencing of DNA directly from a sample without first culturing and isolating the organisms, has become the principal tool of “meta-omic” analysis. It can be used to explore the diversity, function, and ecology of microbial communities.

The aim of these 4 days workshop will be to give researchers and students an overview of the tools and bioinformatics techniques available for the analysis of next generation sequence data from microbial communities. Its content will focus on the taxonomic assignment and the functional analysis of metatranscriptomic and metagenomic data. The format will comprise a mixture of lectures and hands-on practical tutorials where students will process example data sets in real-time.

Summer School on the website of Institut Pasteur

The workshop comprises two parts

 

Part I: lectures
(Monday 12/09 2 p.m to Wednesday 14/09 12.30 am)

The conferences will focus on the state-of-the-art analysis tools for de novo similarity- and composition-based tools for the taxonomic assignment (binning) of unassembled and assembled samples, draft genome recovery for abundant community members, metatranscriptomic analysis, and an overview of functional annotation methods. These methodological presentations will be illustrated by several applications in the domain of marine, soil, clouds, and microbiotes metagenomics.

 

Invited Speakers:                                                                                                                      

» Matthieu Almeida (Center for Bioinformatics and Computational Biology, College Park, MD, USA)
» Karine Clement (l'Institut hospitalo-universitaire de Cardiologie, Paris, FR)
» A Murat Eren (Université Chicago, USA) 
» Sebastian Luecker (Department of Microbiology, Radboud University Nijmegen, NL)
» Folker Meyer (Institute for Genomics and Systems Biology, Argonne National Laboratory, Chicago, USA)
» Alex Mitchell (The European Bioinformatics Institute, InterPro and EBI Metagenomics database, UK)
» Pascal Simonet (Ecole Centrale de Lyon, FR)
» Gabriel Valiente (Technical University of Catalonia, Department of Computer Science, ES)
» Patrick Wincker (CEA/Genoscope, Evry, FR)

 

 

Part II: hands-on tutorials
(Wednesday 14/09 2 p.m to Friday 16/09 12.30  am) 

These tutorials are designed as self-contained units that include example data and pre-installed bioinformatics tools.  These hands-on practical tutorials will demonstrate the use of the following metagenome analysis tools:

FROGS: Find Rapidly OTU with Galaxy Solution [Géraldine Pascal et al. INRA Toulouse & Olivier Rué, Jouy, FR]
cDPCoA: Constrained DPCOA for community comparison [Stéphane Dray, Lyon, FR]
SHAMAN: SHiny Application for Metagenomic ANalysis [Amine Ghozlane, C3BI, Institut Pasteur, FR]
EggNOG, fetchMG, iVireon and PICRUSt for the functional annotation of metagenomic data [Mathieu Almeida, Center for Bioinformatics and Computational Biology, College Park,  MD, USA]
Anvi’o: an advanced analysis and visualization platform for ‘omics data [A. Murat Eren, Univ. Chicago, USA]

 

Scientific committee:

Erwan Corre, ABiMS, Roscoff
Jean-Michel Claverie, PACA-Bioinfo, Marseille
Jean-François Gibrat, IFB, Gif/Yvette
Sean Kennedy, Institut Pasteur, Paris
Claudine Médigue, MicroScope, Evry
Eric Pelletier, GENOSCOPE, Evry
Guy Perriere, PRABI, Lyon
Pierre Peyret, AUDI, Clermont

 

Involved IFB/FG platforms:

IFB core (Gif-sur-Yvette), PRABI (CNRS, Lyon), C3BI (Institut Pasteur, Paris), ABiMS (CNRS/UPMC, Roscoff), Genotoul (INRA,Toulouse), MIGALE (INRA, Jouy), MicroScope (CEA/CNRS, Evry)

Part I: lectures

 

Monday 12/09/2016

1:45 pm Presentation of the workshop (Chairman: Claudine Médigue)
2:00 pm – 2:30 pm Pierre Peyret, EA 4678 CIDAM, Université d’Auvergne, Clermont-Fd, France
« Metagenomics to illuminate ecosystem functioning »
2:30 pm – 3:00 pm Sean Kennedy, Bio-Omics Pole, Pasteur Institute, Paris, FR
« From Samples to Data : Assuring Downstream Analysis with Upstream Planning »
3:00 – 3:45 pm Matthieu Almeida, Center for Bioinformatics and Computational Biology, College Park, MD, USA
« Deciphering the human intestinal tract microbiome using metagenomic computational methods »
3:45 pm – 4:15 pm Break
4:15 pm Session 2 (Chairman: Pierre Peyret)
4:15 pm – 5:00 pm Karine Clement, l'Institut hospitalo-universitaire de Cardiologie, Métabolisme, Nutrition (ICAN), Paris, FR
"Gut metagenomics in cardiometabolic diseases"
5:00 pm – 5:30 pm Romain Koszul, Spatial Regulation of Genomes, Pasteur Institute, Paris, FR
« Exploiting collisions between DNA molecules to characterize the genomic structures of complex communities »
5:30 pm – 6:00 pm Eric Dugat-Bony, Génie et Microbiologie des Procédés Alimentaires, INRA Grigon, FR
« Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses »

 

Tuesday 13/09/2016

9:00 am Session 3 (Chairman: Sean K.)
9:00 am – 9:45 am Gabriel Valiente, Technical University of Catalonia, Department of Computer Science, Barcelone, ES
« Taxonomic Assignment: From Amplicon to Shotgun Sequencing »
9:45 am – 10:15 am Jean Michel Claverie, Structural & Genomic Information Lab. (IGS), Marseille, FR
« Rationale and Tools to look for the unknown in (metagenomic) sequence data »
10:15 am – 10:45 am Eric Coissac, Laboratoire d’Ecologie Alpines (LECA), Grenoble, FR
"Sequencing 6000 chloroplast genomes : the PhyloAlps project"
10:45 am  – 11:15 am Break
11:15 am Session 4 (Chairman: Eric Pelletier)
11:15 am – 11:45 am Pascal Simonet, Environmental Microbial Genomics Group Laboratoire Ampère, Ecole Centrale de Lyon, FR
"Potentials and limitations of soil metagenomics for fundamental studies and industrial applications."
11:45 am – 12:15 pm Pierre Peterlongo, GenScale team, INRIA/IRISA, Rennes, FR
« Multiple Comparative Metagenomics using Multiset k-mer Counting »
12:15 pm – 12:45 pm Sébastien Terrat, Interaction Plantes Micro-organismes, Agroécologie, INRA, Dijon, FR
“Assessing microbial biogeography by using a metagenomic approach”
12:45 pm -  2:00 pm Lunch
2:00 pm Session 5 (Chairman: Damien Eveillard)
2:00 pm – 2:45 pm A. Murat Eren, The Univ. Of Chicago Department of Medecine Faculty, USA
« Reconstructing genomes from metagenomes: The holy grail of microbiology »
2:45 pm – 3:15 pm Violette Da Cunha, Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE) & Institute for Integrative Biology of the Cell (I2BC), Paris, FR
"Dr Jekyll and Mr Hyde: The dual face of metagenomics in phylogenetic analysis"
3:15 pm – 3:45 pm Guy Perrière, LBBE "Biométrie et Biologie Évolutive", Lyon, FR
« Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification »
3:45 pm – 4:15 pm Break
4:15 pm Session 6 (Chairman: J.M. Claverie)
4:15 pm – 5:00 pm Alex Mitchell, European Bioinformatics Institute (EBI), Cambridge, UK
« 200 billion sequences and counting: analysis, discovery and exploration of datasets with EBI Metagenomics »
5:00 pm – 5:30 pm Pierre Amato, Institut de Chimie de Clermont-Ferrand (ICCF/BIOMETA), Clermont-Ferrand, FR
"Structure and functioning of cloud microbiota"
5:30 pm – 6:00 pm Hélène Touzet,  BONSAI group at CRIStAL and INRIA, Bioinformatics and Sequence Analysis, Lille, FR
« Fast filtering, mapping and assembly of 16S ribosomal RNA »

 

 

Wednesday 14/09/2016

8:45 Session 7 (Chairman: J.F. Gibrat)
8:45 am – 9.30 am Patrick Wincker, CEA/GENOSCOPE, Laboratoire d’Analyses Génomiques des Eucaryotes (LAGE), Evry, FR
“ Holistic metagenomics in marine communities »
9:30 am – 10:00 am Chantal Abergel, Structural & Genomic Information Lab. (IGS), Marseille, FR
« Hidden in the permafrost »
​10:00 am – 10:45 am Folker Meyer, Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, USA
« MG-RAST — experiences from processing a quarter million metagenomic data sets »
10:45 am – 11:15  am Break
11:15 am Session 8 (Chairman: Guy Perrière)
11:15 am – 11:45 am Sebastian Luecker, Department of Microbiology, IWWR, Radboud University, NL
« New perspectives on nitrite-oxidizing bacteria - linking genomes to physiology »
11:45 am – 12:15 pm Eric Pelletier, CEA/GENOSCOPE, Laboratoire d’Analyses Génomiques des Eucaryotes (LAGE), Evry, FR
"Marine planktonic eukaryotic metatranscriptomics : the Tara Oceans project"
12:15 pm – 12:45 pm Damien Eveillard, Laboratoire d'Informatique de Nantes Atlantique, irisa, Nantes, FR
« Revealing and analyzing microbial networks: from topology to functional behaviors »
12:45 pm end of the first part of the workshop

Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification
Guy Perrière - CNRS, Lab. BBE, Lyon

PPF (Prokaryotic Phylogeny on the Fly) is an automated pipeline allowing to compute molecular phylogenies for prokarotic organisms. It is based on a set of specialized databases devoted to SSU rRNA, the most commonly used marker for bacterial txonomic identification. Those databases are splitted into different subsets using phylogenetic information.   The procedure for computing a phylogeny is completely automated. Homologous sequence are first recruited through a BLAST search performed on a sequence (or a set of sequences). Then the homologous sequences detected are aligned using one of the multiple sequence alignment programs provided in the pipeline (MAFFT, MUSCLE or CLUSTALO). The alignment is then filtered using BMGE and a Maximum Likelihood (ML) tree is computed using the program FastTree. The tree can be rooted with an outgroup provided by the user and its leaves are coloured with a scheme related to the taxonomy of the sequences.  The main advantage provided by PPF is that its databases are generated using a phylogeny-oriented procedure and and therefore much more efficient for phylogentic analyses that "generic" collections such as SILVA (in the case SSU rRNA) por GenBank. It is therefore much more suited to compute prokaryotic molecular phylogenies than related systems such as the Phylogeny.fr online system.  PPF can be accessed online at https://umr5558-bibiserv.univ-lyon1.fr/lebibi/PPF-in.cgi

 

Exploiting collisions between DNA molecules to characterize the genomic structures of complex communities
Romain Koszul, Spatial Regulation of Genomes, Institut Pasteur, Paris

Meta3C is an experimental and computational approach that exploits the physical contacts experienced by DNA molecules sharing the same cellular compartments. These collisions provide a quantitative information that allows interpreting and phasing the genomes present within complex mixes of species without prior knowledge. Not only the exploitation of chromosome physical 3D signatures hold interesting premises regarding solving the genome sequences from discrete species, but it also allows assigning mobile elements such as plasmids or phages to their hosts.

 

Multiple Comparative Metagenomics using Multiset k-mer Counting 
Pierre Peterlongo, Scalable Optimized and Parallel Algorithms for Genomics, INRIA, Rennes

Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole set of sequences, do not scale up on ambitious metagenomic projects.
These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecology distances by replacing species counts by k-mer counts. Simka scales-up today metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets.
Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecology distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy.

 

Structure and functioning of cloud microbiota
Pierre Amato - CNRS, UMR 6296, ICCF, BP 80026, F-63178 Aubière, France.
Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand (ICCF), BP 10448, F-63000 Clermont-Ferrand, France.

         The atmosphere carries microorganisms and connects distant ecosystems. In addition of the underlying epidemiological issues associated with the presence of living microorganisms in the air, it was shown recently that they can contribute to atmospheric physico-chemical processes. Clouds are thus now considered in some aspects as habitats for microorganisms, albeit temporary by essence. Our first culture-based studies led on cloud microflora recovered from the atmospheric observatory at the puy de Dôme mountain summit (1465 m asl.), in the early 2000’s, revealed a high diversity in the microbial community, dominated by a few genera of bacteria and fungi (Pseudomonas, Sphingomonas, Dioszegia…). The advent of new DNA amplification methods (MDA), associated with next generation sequencing tools allows clarifying our vision of cloud biodiversity and its functioning, while overcoming the difficulties raised by the low biomass in these environments (~104 cells m-3). Thereby, cloud water metagenomes, metatranscriptomes and amplicons libraries (16S and 18S rRNA genes) were investigated. The results clearly showed a high taxonomic diversity in both prokaryotes and eukaryotes, but a very uneven distribution with a few abundant and numerous rare OTUs. The large domination of Proteobacteria was confirmed, and the presence of noticeable groups such as viruses, Cyanobacteria and Archaea was revealed. The active biodiversity was largely related to some groups of bacteria, notably Alpha-Proteobacteria. Analyses of metatranscriptomes and mRNAs-enriched metatranscritptomes showed a large overrepresentation of functions related to metabolic regulation, genome reorganization, access to substrates and defense against oxidants. These new pictures of cloud microbial communities indicate that these environments are open to numerous taxa, but only a few can actually maintain. They must rapidly adjust their functioning for surviving in these inhospitable environments, suggesting that atmospheric transport probably operates strong selection on the microorganisms of outdoor surfaces, and thus drives in some extent microbial evolution.

Reconstructing genomes from metagenomes: The holy grail of microbiology 
A. Murat Eren, The Univ. Of Chicago Department of Medecine Faculty, USA

Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information about the organization of genes in cognate genomes. Several factors affect the assembly performance, and the feasibility of the assembly-based approaches varies across environments. However, increasing read lengths, novel experimental approaches, advances in computational tools and resources, and improvements in assembly algorithms and pipelines render the assembly-based metagenomic workflow more and more accessible. The utility of metagenomic assembly remarkably increases when contigs are organized into metagenome-assembled genomes (MAGs). Often-novel MAGs frequently provide deeper insights into bacterial lifestyles that would otherwise remain unknown as evidenced by recent discoveries. The increasing rate of the recovery of MAGs presents new opportunities to link environmental distribution patterns of microbial populations and their functional potential, and transforms the field of microbiology by providing a more complete understanding of the microbial life, ecology, and evolution.

 

Gut metagenomics in cardiometabolic diseases
Karine Clément, MD, PhD,Institute of Cardiometabolism and Nutrition (ICAN), Pitié-Salpetrière hospital,
INSERM/ Sorbonne University/ Université Pierre et Marie-Curie, Paris,Karine.clement@psl.aphp.fr, www.ican-institute.org

Cardio-metabolic and Nutrition-related diseases (CMDs) represent an enormous burden for health care. They are characterized by very heterogeneous phenotypes progressing with time. It is virtually impossible to predict who will or will not develop cardiovascular comorbidities. There is a clear need to intervene earlier in the natural cycle of the disease, before irreversible tissue damages develop. Predictive tools still remain elusive and environmental factors (food, nutrition, physical activity and psychosocial factors) play major roles in the development of these interrelated pathologies. Poor nutritional environment and lifestyle also promote health deterioration resulting in CMD progression. In the last few years, the characterization of the gut microbiome (i.e. collective bacteria genome) and gut-derived molecules (i.e. metabolites, lipids, inflammatory molecules) has opened up new avenues for the generation of fundamental knowledge regarding putative shared pathways in CMD. The gut microbiome is likely to have an even greater impact than genetic factors given its close relationship with environmental factors. In metabolic disorders, the discoveries that low bacterial gene richness associates with cardiovascular risks stimulate encourage these developments. Due to the complexity of the gut microbiome, and its interactions with human (host) metabolism as well as with the immune system, it is only through integrative analyses where metabolic network models are used as scaffold for analysis that it will be possible to identify markers and shared pathways, which will contribute to improve patient stratification and develop new modes of patient care.

3 References
- Aron-Wisnewsky J and Clément K The gut microbiome, diet, and links to cardiometabolic and chronic disorders. Nature Reviews, Nephrology, 2016
-Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E, Verger EO, Kayser BD, Levenez F, Chilloux J, Hoyles L; MICRO-Obes Consortium, Dumas ME, Rizkalla SW, Doré J, Cani PD, Clément K. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut. 2015 Jun 22
-Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, Almeida M, Quinquis B, Levenez F, Galleron N, Gougis S, Rizkalla S, Batto JM, Renault P; ANR MicroObes consortium, Doré J, Zucker JD, Clément K, Ehrlich SD. Dietary intervention impact on gut microbial gene richness. Nature. 2013 Aug 29;500(7464):585-8. 

 

Soil metagenomics, potential and pitfalls
Pascal SIMONET, 
Environmental Microbial Genomics group, Ampère-UMR CNRS 5005, ECL and University of Lyon, 69134 Ecully cedex, France.
pascal.simonet@ec-lyon.fr

The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation). Nevertheless, genome structure information has been restricted by a large extent to a small fraction of cultivated species. This limitation can be circumvented now by modern alternative approaches including metagenomics or single cell genomics.  Metagenomics includes the data treatment of DNA sequences from many members of the microbial community, in order to either extract a specific microorganism’s genome sequence or to evaluate the community function based on the relative quantities of different gene families. In my talk I will show how these metagenomic datasets can be used to estimate and compare the functional potential of microbial communities from various environments with a special focus on antibiotic resistance genes. However, metagenomic datasets can also in some cases be partially assembled into longer sequences representing microbial genetic structures for trying to correlate different functions to their co-location on the same genetic structure. I will show how the microbial community composition of a natural grassland soil characterized by extremely high microbial diversity could be managed for sequentially attempt to reconstruct some bacterial genomes.

Metagenomics can also be used to exploit the genetic potential of environmental microorganisms. I will present an integrative approach coupling rrs phylochip and high throughput shotgun sequencing to investigate the shift in bacterial community structure and functions after incubation with chitin. In a second step, these functions of potential industrial interest can be discovered by using hybridization of soil metagenomic DNA clones spotted on high density membranes by a mix of oligonucleotide probes designed to target genes encoding for these enzymes. After affiliation of the positive hybridizing spots to the corresponding clones in the metagenomic library the inserts are sequenced, DNA assembled and annotated leading to identify new coding DNA sequences related to genes of interest with a good coverage but a low similarity against closest hits in the databases confirming novelty of the detected and cloned genes.

 

Taxonomic Assignment: From Amplicon to Shotgun Sequencing
Gabriel Valiente, Technical University of Catalonia, Department of Computer Science, Barcelone, ES

TANGO and BioMaS are a tool and a pipeline for microbiome classification from amplicon metagenomic data, and MetaShot is a pipeline for host-associated microbiome classification from shotgun metagenomic data. They combine coarse grained sequence similarity (fast sequence read screening) and fine grained sequence similarity (sequence read mapping and optimal taxonomic classification) based aproaches to attain the best compromise between computational efficiency and assignment accuracy, and allow for the classification of ambiguous sequence reads to archaeal, bacterial, fungal, protozoan, and viral species at the best possible taxonomic rank.

MG-RAST — experiences from processing a quarter million metagenomic data sets
Folker Meyer, Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, USA

MG-RAST has been offering metagenomic analyses since 2007. Over 20,000 researchers have submitted data. I will describe the current MG-RAST implementation and demonstrate some of its capabilities. In the course of the presentation I will highlight several metagenomic pitfalls. MG-RAST: http://metagenomics.anl.gov MG-RAST-APP: http://api.metagenomics.anl.gov/api.html
 

New perspectives on nitrite-oxidizing bacteria - linking genomes to physiology
Sebastian Lücker, Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.

It is a generally accepted characteristic of the biogeochemical nitrogen cycle that nitrification is catalyzed by two distinct clades of microorganisms. First, ammonia-oxidizing bacteria and archaea convert ammonia to nitrite, which subsequently is oxidized to nitrate by nitrite-oxidizing bacteria (NOB). The latter were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is contrasted by new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate), a process that had been postulated to occur under conditions selecting for low growth rates but high growth yields.

The existence of Nitrospira species that encode all genes required for ammonia and nitrite oxidation was first detected by metagenomic analyses of an enrichment culture for nitrogen-transforming microorganisms sampled from the anoxic compartment of a recirculating aquaculture system biofilter. Batch incubations and FISH-MAR experiments showed that these Nitrospira indeed formed nitrate from the aerobic oxidation of ammonia, and used the energy derived from complete nitrification for carbon fixation, thus proving that they indeed represented the long-sought-after comammox organisms. Their ammonia monooxygenase (AMO) enzymes were distinct from canonical AMOs, therefore rendering recent horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. Instead, their AMO displayed highest similarities to the “unusual” particulate methane monooxygenase from Crenothrix polyspora, thus shedding new light onto the function of this sequence group. This recognition of a novel AMO type indicates that a whole group loned gene chiti6alysi disco, 2016oupem>Strucs.
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