Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 533693
Title The multi-omics promise in context : from sequence to microbial isolate
Author(s) Gutleben, Johanna; Chaib De Mares, Maryam; Elsas, Jan Dirk van; Smidt, Hauke; Overmann, Jörg; Sipkema, Detmer
Source Critical Reviews in Microbiology 44 (2018)2. - ISSN 1040-841X - p. 212 - 229.
DOI https://doi.org/10.1080/1040841X.2017.1332003
Department(s) Microbiological Laboratory
VLAG
WIMEK
Publication type Refereed Article in a scientific journal
Publication year 2018
Keyword(s) Bacterial cultivation - metagenomics - metatranscriptomics - multi-omics
Abstract The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.
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