The multi-omics promise in context: from sequence to microbial isolate

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 metaboli...

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Bibliographic Details
Published in:Critical reviews in microbiology 2018-03, Vol.44 (2), p.212-229
Main Authors: Gutleben, Johanna, Chaib De Mares, Maryam, van Elsas, Jan Dirk, Smidt, Hauke, Overmann, Jörg, Sipkema, Detmer
Format: Article
Language:English
Subjects:
Bacterial cultivation
Metabolomics - methods
metagenomics
Metagenomics - methods
metatranscriptomics
Microbiological Techniques - methods
Microbiota
multi-omics
Proteomics - methods
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Summary: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.
ISSN:1040-841X
1549-7828
DOI:10.1080/1040841X.2017.1332003