In 2022, the project SUS-MIRRI.IT “Strengthening the MIRRI Italian Research Infrastructure for Sustainable Bioscience and Bioeconomy” was launched as part of the actions oriented towards Italy’s membership of MIRRI-ERIC, the pan-European distributed Research Infrastructure for the preservation, systematic investigation, provision and valorization of microbial resources and biodiversity. The project SUS-MIRRI.IT, funded by Italy’s National Recovery and Resilience Plan – PNRR, is granted by the European Commission’s “NextGenerationEU” program with a total budget of about 17M €. The main objective of SUS-MIRRI.IT is to implement the network of microbial biobanks distributed throughout Italy to increase the benefit(s) that society can derive from the knowledge and valorization of microbial biodiversity, which is a critical asset to face several of the greatest social, economic, and environmental challenges characterizing our time. Microbiomes are defined as a characteristic microbial community (microbiota) occupying a certain habitat (the so-called theater of activity) and exhibiting distinct and emergent physicochemical properties. Recently, several studies showed that microbiomes represent innovative and frontier tools to address current and future problems in the areas of agriculture, environment, food production, and animal and human health. However, despite this amazing potential of microbiomes, there is a huge gap to be filled in terms of how microbiomes are sampled, characterized, safely stored, and then cultured for further applications. In addition, the lack of standardization in the processes of sampling, extraction of genetic material, execution of -omics technologies, and bioinformatic analyses has resulted in the limited possibility of data comparison. Therefore, in the absence of international standards, the purpose of Work Package 4 of the SUS- MIRRI.IT project is to contribute to the definition and validation of microbiome quality standards to be applied globally in different scientific areas. Specifically, Standard Operating Procedures (SOPs) for sampling different ecosystems (which are: fermented solid and liquid foods, human feces, soil/plant environment, insects, water, and sediments) and the subsequent DNA extraction steps have been developed in this document. To properly construct the promised SOPs, the different research units participating in the WP4 gathered relevant information from their own experience/published articles or the available literature to create a solid body of knowledge, based on which to prepare SOPs. Here, we are thus providing different protocols with a homogeneous and consistent structure organization for the isolation and subsequent analysis of microbiome materials from different matrices. A total of 13 SOPs were created, specifically, 6 for sampling and 7 for DNA extraction.

STANDARD OPERATING PROCEDURES (SOPs) FOR SAMPLING OF MICROBIOME IN DIFFERENT ECOSYSTEMS

Luca Cocolin;Cristina Costa;Antonio Curtoni;Aya Elsayed;Giovanna Felis;Ilario Ferrocino;Alessia Fiore;Giuseppe Gallo;Marco Garello;Elena Gonella;Sahar Maghrebi;Narcisa Mandras;Marino Moretti;Antonino Pollio;Janira Roana;Federico Sbarra;Davide Spadaro;Irene Stefanini;Jacopo Tartaglia;Cristina Giovanna Varese
2023-01-01

Abstract

In 2022, the project SUS-MIRRI.IT “Strengthening the MIRRI Italian Research Infrastructure for Sustainable Bioscience and Bioeconomy” was launched as part of the actions oriented towards Italy’s membership of MIRRI-ERIC, the pan-European distributed Research Infrastructure for the preservation, systematic investigation, provision and valorization of microbial resources and biodiversity. The project SUS-MIRRI.IT, funded by Italy’s National Recovery and Resilience Plan – PNRR, is granted by the European Commission’s “NextGenerationEU” program with a total budget of about 17M €. The main objective of SUS-MIRRI.IT is to implement the network of microbial biobanks distributed throughout Italy to increase the benefit(s) that society can derive from the knowledge and valorization of microbial biodiversity, which is a critical asset to face several of the greatest social, economic, and environmental challenges characterizing our time. Microbiomes are defined as a characteristic microbial community (microbiota) occupying a certain habitat (the so-called theater of activity) and exhibiting distinct and emergent physicochemical properties. Recently, several studies showed that microbiomes represent innovative and frontier tools to address current and future problems in the areas of agriculture, environment, food production, and animal and human health. However, despite this amazing potential of microbiomes, there is a huge gap to be filled in terms of how microbiomes are sampled, characterized, safely stored, and then cultured for further applications. In addition, the lack of standardization in the processes of sampling, extraction of genetic material, execution of -omics technologies, and bioinformatic analyses has resulted in the limited possibility of data comparison. Therefore, in the absence of international standards, the purpose of Work Package 4 of the SUS- MIRRI.IT project is to contribute to the definition and validation of microbiome quality standards to be applied globally in different scientific areas. Specifically, Standard Operating Procedures (SOPs) for sampling different ecosystems (which are: fermented solid and liquid foods, human feces, soil/plant environment, insects, water, and sediments) and the subsequent DNA extraction steps have been developed in this document. To properly construct the promised SOPs, the different research units participating in the WP4 gathered relevant information from their own experience/published articles or the available literature to create a solid body of knowledge, based on which to prepare SOPs. Here, we are thus providing different protocols with a homogeneous and consistent structure organization for the isolation and subsequent analysis of microbiome materials from different matrices. A total of 13 SOPs were created, specifically, 6 for sampling and 7 for DNA extraction.
2023
https://zenodo.org/records/8430600
Microbiota, microbiome storage, host–microbe interactions, fecal microbiota, food microbiome, soil microbiome, interspecific interactions, sustainable agriculture
Luca Cocolin; Annamaria Bevivino; Rosa Alduina; Marco Andreolli; Angela Bianco; Vittorio Capozzi; Cristina Costa; Manuela Costanzo; Antonio Curtoni; L...espandi
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2318/1938271
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