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      Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections

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          Abstract

          Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs.

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          Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

          The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.
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            A molecular view of microbial diversity and the biosphere.

            N Pace (1997)
            Over three decades of molecular-phylogenetic studies, researchers have compiled an increasingly robust map of evolutionary diversification showing that the main diversity of life is microbial, distributed among three primary relatedness groups or domains: Archaea, Bacteria, and Eucarya. The general properties of representatives of the three domains indicate that the earliest life was based on inorganic nutrition and that photosynthesis and use of organic compounds for carbon and energy metabolism came comparatively later. The application of molecular-phylogenetic methods to study natural microbial ecosystems without the traditional requirement for cultivation has resulted in the discovery of many unexpected evolutionary lineages; members of some of these lineages are only distantly related to known organisms but are sufficiently abundant that they are likely to have impact on the chemistry of the biosphere.
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              Health benefits of fermented foods: microbiota and beyond.

              Fermented foods and beverages were among the first processed food products consumed by humans. The production of foods such as yogurt and cultured milk, wine and beer, sauerkraut and kimchi, and fermented sausage were initially valued because of their improved shelf life, safety, and organoleptic properties. It is increasingly understood that fermented foods can also have enhanced nutritional and functional properties due to transformation of substrates and formation of bioactive or bioavailable end-products. Many fermented foods also contain living microorganisms of which some are genetically similar to strains used as probiotics. Although only a limited number of clinical studies on fermented foods have been performed, there is evidence that these foods provide health benefits well-beyond the starting food materials.
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                Author and article information

                Journal
                Microorganisms
                Microorganisms
                microorganisms
                Microorganisms
                MDPI
                2076-2607
                12 December 2019
                December 2019
                : 7
                : 12
                : 685
                Affiliations
                [1 ]Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; stefano.cassanelli@ 123456unimore.it (S.C.); maria.gullo@ 123456unimore.it (M.G.); andrea.pulvirenti@ 123456unimore.it (A.P.)
                [2 ]Biobank of Veterinary Resources, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, via Bianchi 9, 25124 Brescia, Italy; mariabeatrice.boniotti@ 123456izsler.it
                [3 ]Department of Agricultural Science, University of Sassari, viale Italia 39, 07100 Sassari, Italy; mbudroni@ 123456uniss.it (M.B.); imannazzu@ 123456uniss.it (I.M.)
                [4 ]Department of Agriculture, Food and Environmental Science, University of Perugia, borgo XX Giugno, 74, I-06121 Perugia, Italy; pietro.buzzini@ 123456unipg.it (P.B.); benedetta.turchetti@ 123456unipg.it (B.T.)
                [5 ]Agris Sardegna, Agenzia regionale per la ricerca in agricoltura, Loc. Bonassai, km 18.600 SS291, 07100 Sassari, Italy; rcomunian@ 123456agrisricerca.it
                [6 ]Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy; antonio.logrieco@ 123456ispa.cnr.it (A.F.L.); giancarlo.perrone@ 123456ispa.cnr.it (G.P.)
                [7 ]MicroMiB Culture Collection, Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy; rosario.musumeci@ 123456unimib.it
                [8 ]Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Torino, Italy; jolanda.perugini@ 123456unito.it (I.P.); cristina.varese@ 123456unito.it (G.C.V.)
                [9 ]Mass Spectrometry and Proteomics, Scientific Direction, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy; paolo.romano@ 123456hsanmartino.it
                Author notes
                [* ]Correspondence: luciana.devero@ 123456unimore.it ; Tel.: +39-0522-522-057
                Author information
                https://orcid.org/0000-0002-9887-9994
                https://orcid.org/0000-0001-6665-4574
                https://orcid.org/0000-0001-5929-4689
                https://orcid.org/0000-0003-0143-3601
                https://orcid.org/0000-0002-3841-6066
                https://orcid.org/0000-0003-4694-3883
                https://orcid.org/0000-0002-1455-6208
                Article
                microorganisms-07-00685
                10.3390/microorganisms7120685
                6956255
                31842279
                1629685f-824d-4b08-a3a7-d164684a0835
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 30 October 2019
                : 10 December 2019
                Categories
                Review

                biobanks,biological resource centres,biotechnology,bioeconomy

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