, 14:43 | Cite as

Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

  • Farhana R. Pinu
  • Ninna Granucci
  • James Daniell
  • Ting-Li Han
  • Sonia Carneiro
  • Isabel Rocha
  • Jens Nielsen
  • Silas G. Villas-Boas
Review Article



Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies.

Materials and Methods

The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow.


Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.


Microbial metabolism Microorganisms Active efflux Secretion Metabolic engineering Metabolic modeling Systems biology 



The authors are thankful to Mia Jüllig for assistance with Fig. 2. Callaghan Innovation and Bioresource Processing Alliance provided PhD stipends for James Daniell and Ninna Granucci respectively.

Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary material

11306_2018_1339_MOESM1_ESM.docx (1.1 mb)
Supplementary material 1 (DOCX 1168 KB)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Farhana R. Pinu
    • 1
  • Ninna Granucci
    • 2
  • James Daniell
    • 2
    • 3
  • Ting-Li Han
    • 2
  • Sonia Carneiro
    • 4
  • Isabel Rocha
    • 4
  • Jens Nielsen
    • 5
    • 6
  • Silas G. Villas-Boas
    • 2
  1. 1.The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
  2. 2.School of Biological SciencesUniversity of AucklandAucklandNew Zealand
  3. 3.LanzaTechSkokieUSA
  4. 4.Center of Biological EngineeringUniversity of MinhoBragaPortugal
  5. 5.Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
  6. 6.Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkHørsholmDenmark

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