Edit
Microbial metagenomics: a 360º approach – Course and Conference Office

EMBO Practical Course

Microbial metagenomics: a 360º approach

Overview

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

Course overview

The course focuses on the highly interdisciplinary topic of metagenomics. During the course, participants will receive an overview of state-of-the-art genomic technologies and bioinformatic tools. A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines.

The course will start with training the participants about experimental design and the preparation of their own metagenomic libraries with soil or their (environmental) samples. The metagenomic DNA will be sequenced onsite using third generation sequencing technologies and subsequent data analysis. Thus, the students have a unique opportunity to work on the complete workflow from sample preparation to data analysis. This updated course version will also address cutting-edge single-cell microbial genomics during practical. Bioinformatics analysis is a key part of the course, where students will learn how to process data from raw sequences to the application of algorithms for analysing metagenomic datasets. Trainers will provide short lectures with follow-up hands-on exercises in order to have the participants learning and assessing their knowledge.

Audience

This course is aimed at advanced PhD students and post-doctoral researchers who are doing or planning to start research in the field of metagenomics.

Modules/resources

  • Experimental design
  • Extraction of metagenomic DNA
  • Construction of metagenomic libraries
  • Single-cell microbial genomics
  • 3rd generation sequencing (Nanopore)
  • Bioinformatic analysis of metagenomic data: data standards and submission, processing of raw data, assembly, functional annotation, overview of databases, retrieval and analysis tools.

Learning outcomes

  • Construct your own metagenomic library
  • Analyse and organise your data
  • Interpret results, explore different databases, use different retrieval and analysis tools
  • Sequence analysis

What past participants say about the course

“This course gave me the opportunity to learn from my coursemates and understand the software used in metagenomics. The speakers were friendly and are always ready to answer our research questions, and provide us with valuable advice and comments.” – Lee Hwei Huih, The University of Hong Kong

Speakers

Speakers, trainers, and staff

Karine Clément

National Institute for Health and Medical Research (Inserm)

France

Scientific organisers

Course organisers

Preliminary programme

Got something to say? Tweet it! #EMBOMetaG 

  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 0 – Monday 3 March 2023
TimeSpeakerLocation
 Overview of pre-course work, introduction round, liberating course content on EMBL  eCampus 
 Introduction to EMBL eCampus 
 Pre-recorded Lecture 1
Introduction to Linux
Giuseppe D’Auria – FISABIO, Spain
 
 Pre-recorded Lecture 2
Introduction to R
Giuseppe D’Auria – FISABIO, Spain
 
 Pre-recorded Lecture 3
Diversity matters, a place for a classification of uncultured microorganisms in Taxonomy
Kostas Konstantinidis – Georgia Institute of Technology, USA
 
Day 1 – Monday 17 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15     Welcome and EMBL overview
Elisabeth Zielonka  – EMBL Heidelberg, Germany       
Courtyard Room
09:15 – 09:30    Introduction to Training Lab and House notes
TBA – EMBL Heidelberg, Germany         
Courtyard Room
09:30 – 09:45Welcome and Introductions
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain    
Courtyard Room
09:45 – 10:45      Flash talks participants
Elisabeth Zielonka – EMBL Heidelberg, Germany    
Courtyard Room
10:45 – 11:00      BREAKFlex Lab
11:00 – 12:00      Metagenomics: Concepts, historical milestones and next advance
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain     
Courtyard Room
12:00 – 13:00     LUNCH     Canteen
13:00 – 14:00      Metagenomics library preparation for NGS
Vladimir Benes – EMBL Heidelberg, Germany
Courtyard Room
14:00 – 15:00      Group Activity    Rooftop lounge
15:00 – 16:00      The impact of Metagenomics, on genes and genomes discovery
Gabrielle Potock i- Veronese – INRA-LISBP, France
Courtyard Room
16:00 – 16:30      BREAKFlex Lab
16:30 – 17:30      What brings a metagenomic approach in cardiometabolic and nutrition-related disorders?
Karine Clement – ICAN INSERM, France 
Courtyard Room
17:30 – 19:30      POSTER SESSION 1 Helix A
19:30 – 20:30      DINNER     Rooftop Lounge
Day 2 – Tuesday 18 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15      Quick overview of the day
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain     
Courtyard Room
09:15 – 10:30      PRACTICAL 1      
Extraction of metagenomic DNA in groups from soil samples

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain     
Training Labs
10:30 – 11:00 BREAKFlex Lab
11:00 – 12:30 PRACTICAL 2
Quality control of DNA samples and Nanopore 16S PCR set up

Rajna Hercog – EMBL Heidelberg, Germany
Ferris Jung – EMBL Heidelberg, Germany
Training Labs
12:30 – 13:30 LUNCHCanteen
13:30 – 14:30Discussion of metagenomic DNA Extraction Results
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain
Courtyard Room
14:30 – 15:30Metagenomics and other culture-independent tools to study virus communities
Josefa Antón Botella – University of Alicante, Spain
Courtyard Room
15:30 – 16:45PRACTICAL 2
Nanopore: 16S PCR cleanup, finishing library preparation and starting sequencing run, followed by Genomics Core Facility Tour

Rajna Hercog – EMBL Heidelberg, Germany
Ferris Jung – EMBL Heidelberg, Germany
Training Labs
16:45 – 17:00BREAKFlex Lab
17:00 – 19:00PRACTICAL 2
Nanopore: 16S analysis/ DNA cleanup and Sequencing start

Rajna Hercog – EMBL Heidelberg, Germany
Ferris Jung – EMBL Heidelberg, Germany
Training Labs
19:00 – 19:15Group activity: Description of Case Studies
Elisabeth Zielonka – EMBL Heidelberg, Germany
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Giuseppe D’Auria – FISABIO, Spain
Courtyard Room
19:15DINNER Hotel ISG
Day 3 – Wednesday 19 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15Quick overview of the day
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Courtyard Room
09:15 – 09:45PRACTICAL 1
Test digestion conditions for metagenomic DNA and preparation of agarose gels

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain
Training Labs
09:45 – 11:00PRACTICAL 3
Practical introduction: Single cells genomics in droplets

Tobias Wenzel – EMBL Heidelberg, Germany
Training Labs
11:00 – 11:15BREAKFlex Lab
11:15 – 12:30PRACTICAL 1
Digestion of metagenomic DNA for cloning in the libraries (once that digestion conditions are determined)

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain
Training Labs
12:30 – 13:30LUNCHCanteen
13:30 – 14:30PRACTICAL 1
Purification from gel of the digested metagenomic DNA

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain
Training Labs
14:30 – 15:00BREAKFlex Lab
15:00 – 17:00PRACTICAL 1
Cloning of the metagenomic DNA + overnight ligation

Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain
Training Labs
17:00 – 19:30 PRACTICAL 3
Practical (single cell microbial genomics): Droplet generation for single cell genomics and PCR set-up

Tobias Wenzel – EMBL Heidelberg, Germany
Training Labs
19:30 – 20:30DINNER Hotel ISG
Day 4 – Thursday 20 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15 Quick overview of the day
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Courtyard Room
09:15 – 11:00 PRACTICAL 1
Transformation in E. coli of the library

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain
Training Labs
11:00 – 12:00 Methodological discussion of practical session 1: Metagenomics experimental design: Common shortcoming and pitfalls
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Courtyard Room
12:00 – 13:00 LUNCHCanteen
13:00 – 14:30PRACTICAL 4
Solving problems and questions: Introduction to Linux and R based on pre-recorded lecture 1 and 2

Giuseppe D’Auria – FISABIO, Spain
Training Labs
14:30 – 15:30Metabolomic profiling of microbial communities
Mariana Reyes Prieto – FISABIO, Spain
Courtyard Room
15:30 – 16:00 BREAKFlex Lab
16:00 – 17:00 Pacific Bioscience (PacBio) sequencing for metagenomics
Vladimir Benes – EMBL Heidelberg, Germany
Courtyard Room
17:00SOCIAL ACTIVITYFree evening with tour of Heidelberg
Day 5 – Friday 21 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15 Quick overview of the day
Giuseppe D’Auria – FISABIO, Spain
Courtyard Room
09:15 – 10:00 PRACTICAL 1
Analysis of some colonies from the metagenomic libraries -Interpretation of results

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez – Hospital Can Misses, Spain
Training Labs
10:00 – 10:30 BREAKFlex Lab
10:30 – 12:00 Metatranscriptomics applied to the study microbial communities
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Courtyard Room
12:00 – 13:30 LUNCHCanteen
13:30 – 14:30 Functional and taxonomic analysis with Mgnify
Lorna Richardson – EMBL-EBI, Hinxton, UK
Courtyard Room
14:30 – 15:30PRACTICAL 5
Functional and taxonomic analysis with Mgnify

Lorna Richardson – EMBL-EBI, Hinxton, UK
Training Labs
15:30- 18:30 PRACTICAL 3
Visualization of droplets and single cell analysis with flexible coffee break

Tobias Wenzel – EMBL Heidelberg, Germany
Training Labs
18:30-19:30 PRACTICAL 5
Functional and taxonomic analysis with Mgnify

Lorna Richardson – EMBL-EBI, Hinxton, UK
Training Labs
19:30 – 20:00 DINNER
Dinner & drinks/ BBQ
Hotel ISG
Day 6 – Saturday 22 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15 Quick overview of the day
Giuseppe D’Auria – FISABIO, Spain
Courtyard Room
09:15 – 11:00Introduction to 16S rDNA profiling (Illumina/PacBio)
Giuseppe D’Auria – FISABIO, Spain
Courtyard Room
11:00 – 11:15 BREAKFlex Lab
11:15 – 12:15PRACTICAL 6
Practical to 16S rDNA profiling (Illumina/PacBio)

Giuseppe D’Auria – FISABIO, Spain
Training Labs
12:15 – 13:15 LUNCHCanteen
13:15 – 14:15PRACTICAL 6
Practice to 16S rDNA profiling (Illumina/PacBio)

Giuseppe D’Auria – FISABIO, Spain
Training Labs
14:15 – 16:00PRACTICAL 7
The MiGA web-server: the genome-equivalent of RDP/Silva SSU web-servers

Kostas Konstantinidis – Georgia Institute of Technology, USA
Training Labs
15:00 – 16:30 BREAKFlex Lab
16:30 – 18:30 PRACTICAL 8
Tools for specialized analyses of metagenomes

Kostas Konstantinidis – Georgia Institute of Technology, USA
Training Labs
18:30 – 19:30 DinnerHotel ISG
19:30 – 21:15 POSTER SESSION Helix A
Day 7 – Sunday 23 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15 Quick overview of the day
Kristian Vlahovicek – University of Zagreb, Croatia
Courtyard Room
09:15 – 11:15 PRACTICAL 9
Metagenomic assembly, ORF finding, functional annotation

Giuseppe D’Auria – FISABIO, Spain
Training Labs
11:15 – 11:30 BREAKFlex Lab
11:30 – 12:30 Analysis Tools Overview: INCA, MILC and MELP
Kristian Vlahovicek – University of Zagreb, Croatia
Courtyard Room
12:30 – 13:30 LUNCHCanteen
13:30 – 15:30 PRACTICAL 10
INCA

Kristian Vlahovicek – University of Zagreb, Croatia
Training Labs
15:30-16:00 BREAKFlex Lab
16:00 – 18:00 Student presentation preparation time: Case Studies
all trainers and speakers
Courtyard Room
19:00DINNER
 Downtown
Day 8 – Saturday 24 April 2023
Time (Europe/Berlin) Speaker Location
09:00 – 09:15 Quick overview of the day
Giuseppe D’Auria – FISABIO, Spain
Courtyard Room
09:15 – 10:15 Functional and taxonomic analysis
Georg Zeller – EMBL Heidelberg Germany
Courtyard Room
10:15- 10:45BREAKFlex Lab
10:45 – 12:00 PRACTICAL 11
MEGAN

Daniel Huson – University of Tübingen, Germany
Training Labs
12:00 – 13:00LUNCHCanteen 
13:00 – 14:00PRACTICAL 11
MEGAN

Daniel Huson – University of Tübingen, Germany
Training Labs
14:00 – 16:30Group activity and presentations: Case StudiesCourtyard Room
16:30 – 16:45BREAKFlex Lab
16:45 – 17:15Wrap-up and conclusionsCourtyard Room
18:00DINNERHotel ISG

Practical information

Registration fees and motivation letter

The course is limited to 20 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks. This EMBO course includes accommodation and transportation to and from the ISG Hotel to the venue.

Academia€500
PhD Student€500
Industry€1000

NO visa support letters will be issued until payment of the registration fee is confirmed.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles

Hotel

Accommodation has been pre-booked for you at the ISG Hotel for the default dates of 16 April to 24 April 2023 (8 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG. In case you would like to have a single room, please let us know and please note that you will be required to pay an additional cost of 21€ per night. This should be paid by you directly to the ISG during your stay. Any additional nights need to be booked and paid for by you. We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

Event supporter:

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

Social 1080×1920
Social 1080×1080
Social 1600×900
PPT Slide 16×9

Date: 17 - 24 Apr 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: 23 Jan 2023


Organisers:

  • Vladimir Benes
    EMBL Heidelberg, Germany
    • Giuseppe D´Auria
      FISABIO Sequencing and Bioinformatics Service, Spain
      • José Eduardo González-Pastor
        Center of Astrobiology (CSIC/INTA), Spain
        • Elisabeth Zielonka
          EMBL Heidelberg, Germany

        Contact: Diah Yulianti

        Download event poster


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

Edit