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WDCM Workshop on GCM

WDCM Online Workshop of Global Catalogue of Microorganisms

Established in the 1960s, WFCC-MIRCEN World Data Centre for Microorganisms is a vehicle for networking of 815 microbial resource centers from 78 countries.

WDCM launched the Global Catalogue of Microorganisms (GCM) project in 2012. GCM program aims to provide a globally uniform data warehouse for valuable microbial resources scattered in various culture collections and in the hands of the scientists around the world. Currently, 146 microbial resource collection agencies in 51 countries and regions have officially participated in the program, providing effective data support for all aspects of physical resources of microorganisms such as gathering, collection, transnational transfer, academic and commercial applications, and benefit sharing, and offering the most important support to the implementation and enforcement of the Convention on Biological Diversity in the field of microorganisms.

On the basis of GCM international cooperation program, WDCM launched GCM2.0 international cooperation program — Global Microbial Type Strain Genome and Microbiome Sequencing Project — for complete coverage of microbial genomes, and established cooperation network for genome sequencing and function exploring of microbial resources covering 22 major culture collections in more than 16 countries, which is expected to complete genome sequencing of more than 10,000 microbial type strains, establish a set of International standard system in microbial resource sharing and exploration, and set up a globally authoritative reference database and data analysis platform of microbiome.

Since 2011, WDCM Symposium has been held over 10 times. WDCM will hold online workshop of Global Catalogue of Microorganisms on December 16, 2021. In the online workshop, microbiologists from culture collections and related fields are invited to discuss related research questions based on Global Catalogue of Microorganisms and Global Microbial Type Strain Genome and Microbiome Sequencing. Future cooperation between culture collections and microbiologists will be promoted by providing free sequencing and high-quality data analysis.

You are invited to attend the workshop on December 16, 2021. Scan the QR code below or send email to Jianyuan Zhang (zhangjy@im.ac.cn) to register for the workshop.

Dr. Ipek Kurtboke
President of World Federation of Culture Collections

Dr. Juncai Ma
Director of WFCC-MIRCEN World Data Centre for Microorganisms

MIRRI-IS Pairwise alignment movie

A new instruction movie showing how to use the pairwise alignment on the MIRRI-IS website has been made available.
See also the list of available instruction movies.

IBBR Webinars: UMCC, L. De Vero

Abstract

In Italy, the food and beverage industry represents the third most important sector of the National manufacturing sector in terms of added value produced. Even during the emergency due to Covid-19, the Italian food industry has proven to be a sector capable of supporting the Country’s economy, while highlighting the strong need to urgently develop a pluriannual plan of actions able to promote investments for technological innovations. Indeed, there is a growing consumers awareness towards food quality, food safety and health aspects. Moreover, a strong preference for “clean label” foods with high added value and low environmental impact has emerged.
In this regard, the study and preservation of microbial biodiversity are fundamental for the research and biotechnological applications of microorganisms in various fields, including food. In fact, some microbial cultures are particularly useful to produce enzymes, antibiotics, prebiotics, probiotics, polymers, antimicrobial agents and much more. Therefore, the qualified microbial collections have a fundamental role in research, selection and preservation of microorganisms of food interest.
Among the Italian collections, UMCC, located in Reggio Emilia (Italy) and belonging to the University of Modena and Reggio Emilia (Department of Life Sciences), boasts a long experience in the acquisition, study and ex-situ conservation of “authenticated biological material” and associated genomic data, with the aim of offering services to support research, teaching and technology transfer to industry and private institutions.
Specifically, UMCC holds about 3,000 microbial cultures including yeasts, lactic acid bacteria and acetic acid bacteria used for the implementation of functional starter cultures to be applied in food and industrial fermentation processes. UMCC is an Internationally recognized collection, affiliated to the World Federation for Culture Cultures (WFCC) and the European Culture Collection Organization (ECCO). Moreover, UMCC is one of the five founding partners of the Joint Research Unit MIRRI-IT (http://www.mirri-it.it/) and is involved in the European project Horizon 2020 IS_MIRRI21 aimed at the development of a pan-European research infrastructure for access to collections of certified microorganisms and their derivatives

Author’s Info: Luciana De Vero

MIRRI-IT and the BY-COVID project

Members of MIRRI-IT integrate the BY-COVID consortium

Braga (Portugal) and Turin (Italy), 29 October 2021
It has been officially launched a new €12 million Horizon Europe funded project, BeYond-COVID (BY-COVID), which will tackle the data challenges that can hinder effective pandemic response. The core aim of the project is to ensure that data on SARS-CoV-2 and other infectious diseases can be found and used by everyone.
BY-COVID is an interdisciplinary project that unites life science, medical, policy, social science and public health experts from across Europe. Led by ELIXIR, the project has 53 partners from 20 European countries. It will run for three years and is part of the European Commission’s HERA Incubator plan “Anticipating together the threat of COVID-19 variants”.
MIRRI, the pan-European distributed Research Infrastructure for the preservation, study, provision and valorisation of microbial resources and biodiversity, will take part in the project BY-COVID through the participation of three of the member organisations of its Italian node, MIRRI-IT, namely: Ospedale Policlinico San Martino (USMI), Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), and Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER).
According to its Executive Director, Luís Soares, “MIRRI has a pivotal role to play on the response to microbialrelated emergencies, since we bring together a comprehensive set of resources, data, services and expertise, coming from our many partner organisations, which provide real added-value for researchers and companies working in the field of human and human-animal infectious diseases, or in the development of new diagnostic or therapeutic solutions”.
Paolo Romano, principal investigator of MIRRI-IT in the project, adds that “The contribution provided by MIRRI partners to BY-COVID, while relatively limited in person-month effort, is very relevant for the best results of the project. The contribution of the Ospedale Policlinico San Martino will bring important knowledge and expertise in the health domain, while the other MIRRI-IT partners will provide a unique expertise in the domain of veterinary health and especially in infective diseases of zoonotic origin”.

The project BY-COVID, in a nutshell

BY-COVID will build and expand upon the successful COVID-19 Data Platform, a resource initiated in the early stages of the pandemic and led by EMBL-EBI. Since its launch, many countries have established their own national data hubs, which ensures that data produced locally can be instantaneously connected and shared with the main COVID-19 Data Portal. Rather than focus purely on providing technical solutions to the biological data, BY-COVID will work with partners such as the Versatile emerging infectious disease Observatory (VEO) and the Public Health Information Research Infrastructure (PHIRI) to incorporate data from a broader range of disciplines, including public health and social sciences.
The BY-COVID project strives to simplify data access and reuse through four key pillars:

  • Mobilise data – ensuring raw sequencing data from across the world can be easily submitted to core data hubs.
  • Connect data – build the technical capacity to allow linking of sequence data and metadata, expanding beyond scientific and medical data to broader metadata from, for example, public health and economics, and support integration to the COVID-19 Data Portal.
  • Standardise data – provide recommended data management protocols to encourage Findable, Accessible, Interoperable and Reusable (FAIR) data standards and interoperability among resources.
  • Expose and analyse data – support exposure and analysis of FAIR data on infectious diseases such as the regular VEO reports on mutations and variation in publicly shared SARS-CoV-2 data and the open COVID-19 Galaxy analysis platform.

For more information, visit the BY-COVID website at by-covid.org.

About MIRRI:

The Microbial Resource Research Infrastructure (MIRRI) is the pan-European distributed Research Infrastructure for the preservation, systematic investigation, provision and valorisation of microbial resources and biodiversity. It brings together 50+ microbial domain Biological Resource Centres (mBRCs), culture collections and research institutes from ten European countries and one associated country, namely: Belgium, France, Greece, Italy, Latvia, Netherlands, Poland, Portugal (headquarters), Romania, Russia and Spain.
MIRRI serves the bioscience and the bioindustry communities by facilitating the access, through a single point, to the broadest range of high-quality microorganisms, their derivatives, associated data and services, with a special focus on the domains of Health & Food, Agro-Food, and Environment & Energy. By serving its users, by collaborating with other research infrastructures and by working with public authorities and policy makers, MIRRI contributes to the advancement of research and innovation in life sciences and biotechnology, as well as for a sustainable, competitive and resilient bioeconomy.
More information and contacts: mirri.org | linkedin.com/company/microbial-resource-researchinfrastructure/ | info@mirri.org.

About MIRRI-IT:

The Joint Research Unit MIRRI-IT is aimed at the implementation of the Italian node of MIRRI and at the development of the Italian network of collections of microbial resources. Its mission is to overcome fragmentation in availability of resources and services, enhancing the quality management system of the collections, while focusing on needs and challenges of the stakeholders interested in the biotechnological transfer of these resources. MIRRI-IT currently incudes five partners and 18 associated partners from Universities, Public Research Institutes and Hospitals. Partners are active in many domains of interest for microbial resources, including food and nutrition, agriculture, forestry and environment, as well as human and animal health.
For more information see mirri-it.it or get in touch by email with info@mirri-it.it.

BY-COVID is funded by the European Union’s Horizon Europe research and innovation programme under grant agreement number 101046203.

Supporting biodiversity and ecosystem protection across land and sea – Open Call

2021-2022 Joint Call
“Supporting the protection of biodiversity and ecosystems
across land and sea”

Biodiversa+, the European Biodiversity Partnership, is pleased to announce that its 2021-2022 joint Call for Transnational Research Proposals on “Supporting biodiversity and ecosystem protection across land and sea” is now open.

CALL PRIORITIES
THEME 1: Knowledge for identifying priority conservation areas, establishing effective and resilient ecological networks, enhancing species-based protection and preserving genetic diversity
THEME 2: Multiple benefits and costs of biodiversity and ecosystem protection: synergies and trade-offs
THEME 3: Effective management and equitable governance to deliver bold conservation outcome

The call covers all environments, i.e. terrestrial, freshwater and marine. It also covers research on biodiversity conservation in the Outermost Regions (ORs) and Overseas Countries and Territories (OCTs) of the EU.

CALL SCHEDULE
A two-step process will apply, with a mandatory submission of pre-proposals at the first step and submission of full proposals at the second step.

  • Deadline for pre-proposals submission (mandatory): Tuesday 30 November 2021, 15:00 CET (local time in Brussels)
  • Deadline for full-proposals submission: Thursday 14 April 2022, 15:00 CEST (local time in Brussels)

FURTHER INFORMATION
For further information, see the Open Call web site at https://www.biodiversa.org/1772

For general information on the call, contact the Call Secretariat: biodiversa.cs@agencerecherche.fr (Juliette Bettus, Céline Billière and Sophie Germann)

IT Officer position for MIRRI

IT officer position available at the Spanish Type Culture Collection – University of Valencia (CECT-UV), UV Science Park, Catedràtic Agustín Escardino Benlloch, 9, Paterna, Valencia.

Gross salary 38.000 €

The contract will be bounded to the project IS_MIRRI21, funded by Horizon 2020, to implement the Microbial Resource Research Infrastructure (MIRRI).

Official call and procedure to apply: Soon available.
For contact information see below.

Estimated commencement date and duration: From November 2021 to February 2023. Prolongation possible subject to the availability of funds and extension of the project.

REQUIREMENTS
Bachelor’s degree in Information Technology, Computer Science, Information Systems, or a related field. Bachelor’s degree in Biology, Biotechnology or a related field.

PROFILE OF THE WORKING POSITION
IT officer specialized in programming and database management.

QUALIFICATIONS/SKILLS

  • Experience in web development tools (jQuery, Vue.js, Agilent, BootStrap, etc.)
  • Experience in web programming languages (php, Python, javascript, typescript, etc.)
  • Knowledge of cloud services PaaS and SaaS
  • Experience in relational (MySQL, PostgreSQL, etc.) and non-relational (MongoDB, etc.) database management systems
  • Working experience in Internationally Distributed Research Infrastructures in particular, or at least in Research Infrastructures in general
  • Participation in research projects related with biodiversity (preferably) or with Life Sciences (in general) would be an asset
  • Proficiency in English (oral and written)

TASKS AND RESPONSIBILITIES

  • Manage the MIRRI applications generated within the project
  • Manage users according to specifications to ensure access and availability of the system resources
  • Give IT support to MIRRI’s Central Coordinating Unit
  • Contribute to the design of an interoperable virtual platform providing the MIRRI service offer, ensuring data privacy and security, in collaboration with the Center for Computer Graphics (CCG) based in Braga (Portugal)
  • Contribute, together with CCG, in the development of a MIRRI virtual platform to compile, prepare, enrich, store and process a large amount of heterogeneous data (different sources and formats), allowing access to data services related to biological material (MIRRI-IS)
  • Contribute, together with the MIRRI ICT team, to export the catalogue data of MIRRI Culture Collection partners to be incorporated into the MIRRI-IS database
  • Act as a link of MIRRI-IS with CECT-UV, CCG and LifeWatch (Spain)
  • Participate in the project’s tasks (assistance to meetings, elaboration of reports, etc.)
  • Willingness to travel to different European cities, mainly to Braga

CONTACT: jmlopez@cect.org

Exhibition “Extraordinary microorganisms”

Extraordinary Microorganisms


Escovopsis aspergilloides (Credits: Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands)

Photo exhibition on the occasion of the International Day on Microorganisms
September 17, 2021 – October 31, 2021

On the occasion of the International Day on Microorganisms (September 17), the exhibition “Extraordinary Microorganisms” (open until October 31) was inaugurated at the Turin Botanical Garden. 44 photos taken at 27 European research centers with sophisticated microscopy techniques are exhibited.

The exhibition was organized by the Department of Life Sciences and Systems Biology and by the Mycotheca Universitatis Taurinensis (MUT) of the University of Turin with the collaboration of the European Culture Collections’ Organization (ECCO) and the support of the CRT Foundation.

The photographs are accompanied by a brief description in Italian and English of the role of that microorganism in the environment and in various biotechnological processes. Along the way, insights are offered through a QR-code system.



Aspergillus discoforus (credits Westerdijk Fungal Biodiversity Institute, Utrechts, Netherlands)

If you want to read more, see the following pages (in Italian):

Il futuro del cibo in 16mila ceppi

Da Repubblica, 17 settembre 2021, pag. 8, sez. CRONACA-BARI
Bari, nel Cnr il quartier generale dei microbi:
“Qui con 16mila ceppi studiamo il futuro del cibo”

La collezione di colture microbiche fra le più importanti in Italia, unica al Sud, è custodita nel seminterrato della sede barese del Cnr, il Centro nazionale delle ricerche Ispa: 16mila ceppi microbici tra funghi, batteri e lieviti – alcuni unici al mondo, come i lieviti dei vini del Salento – 8mila dei quali in catalogo e a disposizione della comunità scientifica internazionale, che costituiscono un patrimonio di inestimabile valore da tutelare e valorizzare.
Tre grandi frigoriferi, due di criocongelazione a quasi meno 150 gradi e l’altro di colture in fresco, conservano la biodiversità microbica dell’agroalimentare pugliese, ma non solo, al quale l’istituto barese lavora da trent’anni.
Dal quartier generale in via Amendola, con sedi secondarie a Lecce, Foggia, Sassari, Milano e Torino, i circa 600 tra scienziati, ricercatori e addetti, diretti da Antonio Francesco Logrieco, si dedicano alla ricerca nel campo della Scienza della produzione alimentare.
“Curiamo tutta la filiera dal campo alla tavola – spiega il direttore Logrieco – supportando anche le aziende agricole per produrre materie prime e alimenti sani e di qualità, partendo dai nostri prodotti tipici e dalla dieta mediterranea”

di Isabella Maselli

MIRRI Survey: maximizing its support for users’ projects

MIRRI needs to hear from you!

How can we help delivering the maximum value
from your projects, technologies or products?

The Microbial Resource Research Infrastructure MIRRI is available to collaborate with researchers and companies on delivering the maximum value from research and innovation projects, technologies or products involving microbial resources. In order to continuously improve its positioning, it needs to hear from the (even potential) users of the resources and services that MIRRI provides.

MIRRI is now asking for your help. It would greatly appreciate if you could spend 10 minutes of your time to respond to its survey “How can we help delivering the maximum value from your projects, technologies or products”.

Fill the survey now at https://www.surveymonkey.com/r/YDHF7YD!

MD21: Advances in Microbial Diversity

The 6th Conference on Microbial Diversity (MD2021) will take place online from 14 to 15 December 2021. The Microbial Diversity Conference is a biennial international event that brings together researchers and professionals from all over the world working on agricultural, environmental and food microbiology.

Previous editions have seen a multidisciplinary audience and included academic and industrial researchers, as well as basic scientists from 36 Countries to make for an exciting forum. The 6th Edition of MD is organized by the Italian Society of Food, Agricultural and Environmental Microbiology (SIMTREA), in collaboration with the Institut National de la Recherche Agronomique (INRA, France).

MD2021 will be focused on emerging topics of microbiology, ranging from the study of the metabolome to microbial ecology and the impact of microbes on the human society. The online event will allow researchers from anywhere in the world to take part in the discussions, with the aim to create a connected and collaborative community of microbiologists.

Being a part of this first-of-its-kind virtual MD conference will allow to share experiences, knowledge, research outcomes and best practices, and to hear from the scientists how to explore the hottest topics in microbiology, like never before. The organizing committee is also excited to offer an advocacy and policy platform to communicate to decision makers and the general public the relevance and importance of microbiology.

Chairman of the Scientific Committee of MD 2021: Luca Cocolin

Invited speakers
Nicholas Bokulich (ETH Zürich, Switzerland); Bas Teusink (Vrije Universiteit Amsterdam, Netherlands); Rudolf Amann (Max Planck Institute, Bremen, Germany); Maria Marco (University of California, Davis, California); Sarah Lebeer (University of Antwerp, Belgium); Peter Vandamme (University of Ghent, Belgium); Korneel Rabaey (University of Ghent, Belgium); Pascal Saikaly (KAUST University, Saudi Arabia); Federico Aulenta (Italian National Research Council, Italy); Hadda Imene Ouzari (University Tunis El Manar, Tunisia); Loubna El fels (Cadi Ayyad University, Marrakech, Morocco); Petek Cakar (Istanbul Technical University, Turkey); Marcello Scalisi (Mediterranean Universities Union, Italy).

Scientific Committee
Chairman of the Scientific committee: Luca Cocolin President of SIMTREA, University of Turin;
Daniele Daffonchio, KAUST; Cinzia Caggia, University of Catania; Marilena Budroni, University of Sassari; Carlo Viti, University of Florence; Giovanna Felis, University of Verona; Maria Gullo, University of Modena and Reggio Emilia; Stéphane Chaillou, Institut National de la Recherche Agronomique – INRAE.

Organising Committee
SIMTREA Board
E-mail address: secretariatmd21@simtrea.org;
Website: https://md21.simtrea.org/it/

Registration fee
The registration fees are as follows: 50 Euros for PhD Students and Students; 100 Euros for SIMTREA members and 120 Euros for NON-SIMTREA members and includes the access to all Congress Sessions and digital proceedings. One day registration is fixed to 50 Euros for PhD Students, Students and SIMTREA members, to 70 Euros for NON-SIMTREA members. Please, check deadlines on our website https://md21.simtrea.org/it/

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