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Microbial cultivation and the role of microbial resource centers in the omics era


Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world’s culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the “Budapest Treaty” for establishment of an International Depositary Authority.

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This work was supported from the grant no. BT/PR/0054/NDB/52/94/2007 funded by Department of Biotechnology (DBT), Government of India, under the project “Establishment of microbial culture collection.” We are grateful to our colleagues, especially Kiran N. Mahale, and anonymous reviewers for critically reading the manuscript and providing valuable critics and comments for its improvement.

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Correspondence to Om Prakash.

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Prakash, O., Shouche, Y., Jangid, K. et al. Microbial cultivation and the role of microbial resource centers in the omics era. Appl Microbiol Biotechnol 97, 51–62 (2013).

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  • Cultivation
  • Preservation
  • Microbial resource centers
  • Budapest Treaty