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WORKSHOP (4TH SEPTEMBER - 5TH SEPTEMBER 2019)

This meeting aims to bring together a community of experts and those with interests in how proteins can provide invaluable insight into the functionality of microbiomes. It will run from lunch time 4th September, through to mid afternoon on Thursday 5th September.

 

Metaproteomics and microbiomes

Workshop Details

Guest Speaker: Dirk Benndorf (Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany).

Organisers: Dr. Jags Pandhal (The University of Sheffield) and Professor Liz Wellington (The University of Warwick)


Where: The Diamond, The University of Sheffield, 32 Leavygreave Rd, Sheffield S3 7RD, UK

Understanding interactions between organisms in an ecosystem is a critical part of ecological research and facilitates our understanding of how ecosystems function, and this is particularly important for microorganisms and microarthropods as they are often difficult to study in situ in real time. Currently the natural environment faces many challenges and we need to be able to measure the impacts of changes in climate, pollutant levels, intensive farming and development of ley systems to understand how resilient communities are and how carbon, nitrogen and phosphorous cycles are affected. Moreover, there is a growing appreciation within industry, for controlling and optimising microbial community function.


Microrganisms play a vital role in our environment. They occupy a wide range of habitats from our gut and body surfaces all

the way to hot vents under the sea, they are critical in the soil for recycling of nutrients and plant health and responsible for

the essential digestion of cellulose from grass being broken down in the specialised stomach of the cow termed the rumen  

to the global cycling of carbon in the oceans via harvesting of sunlight as many bacteria can photosynthesize and thus

harvest light energy to fix carbon dioxide. A major problem exists in our ability to study the physiology and overall activities

of these microbes due to the fact that we cannot isolate and cultivate (yet) the vast majority (probably over 98%) of them in

the laboratory. We know they exist because we have used methods similar to DNA forensic approaches to detect them

solely based on their DNA using signature genes which allow us to identify and group them. Most of this diversity is

bacterial but there are also many groups of fungi and algae. New methods are constantly being developed for the study of these microbial populations, with metagenomics being the most commonly applied. It is now possible to use deep sequencing and assemble thousands of bacteria into near complete genomes from metagenomic data (MAGs). This technique allows us to gain insight into the composition of the population (Who's there?) and well as enable us to predict fucntion (What could they be doing?). However, this meeting is largely focussed on the proteins produced by these microbes, a field termed metaproteomics. Proteins equate with activity in cells, as enzymes are proteins and act as catalysts for reactions. Therefore, characterising proteins produced in microbial populations really enables us to look at function (What are they doing?). In the UK, there are outdated perceptions on metaproteomics, and its often the "last to be included" omics analysis.


This meeting aims to bring together researchers with an interest in improving overall 

understanding of environmental and industrially relevant microbiomes. We will focus on linking metagenomes to metaproteomes to demonstrate the power of rapidly advancing technology.


To achieve this we aim to:

1. Share latest metaproteomics workflows, with emphasis on open source computational pipelines for protein identification

2. Demonstrate processes for assembly of metagenome sequences as well as metagenome assembled genomes (MAGs). 

3. Discuss intergration with other omics data and traditional (microbial) ecology datasets.

4. Present details of an open competition where the winner will be able to submit environmental samples for metaproteomic analysis

The overall aim of this workshop is to establish a network of academic/industry partners to build capacity in this important area of science to ensure that we are able to study and exploit all the interesting and exciting attributes of microbial populations and harness them for a sustainable future.

£25 per person. This cost includes two lunches and one dinner. Accommodation is not covered. If you want to stay at Leopold Hotel in the City Centre please request a University of Sheffield discount code from j.pandhal@sheffield.ac.uk

Register at: https://onlineshop.shef.ac.uk/conferences-and-events/faculty-of-engineering/chemical-and-biological-engineering/metaproteomics-the-gateway-to-microbial-community-structurefunction-analysis

 

TENTATIVE PROGRAM

Metaproteomics- the gateway to microbial community structure-function analysis


Day 1: 4th September


Venue: Diamond Building, Work Room 2


11.30 Arrival and registration


12.30-13.30 Lunch


13.30 Introduction to the workshop (Liz Wellington and Jags Pandhal)

14.00 Plenary Dirk Benndorf (Max Planck Institute for Dynamics of Complex Technical Systems) “Recent experimental and bioinformatic developments in metaproteomics”

15:00 Introductions from Workshop participants


16.00 Coffee/Tea


From metagenomes to metaproteomes

16.30 Chris Quince:

17.10 Seb Raguideau:


17.40 Richard Stark:

18.00 Summary (Jags Pandhal and Liz Wellington and Chris Quince)


20:00 Dinner


Day 2: 5th September


Venue: Diamond Building, Pam Liversage Building, D05 Design Studio



09:00 Coffee and networking


Applications of metaproteomics

09.30 Joseph Christie-Oleza: Viromics

10.10 Jags Pandhal and Caroline Evans: Polluted aquatic systems

10.40 Chiara Borsetto:


11.10 Coffee


11.40 Ian Lidbury: Metaexoproteomics and P-cycling in soil

12.10 Andrew Murphy and Liz Wellington discussions on methods for extraction


13.00 Lunch


14.00 Open Competition details

14:20 Highlighted discussion points


16.00 Tea and close