Trends in Biotechnology
ForumDesigning Reactor Microbiomes for Chemical Production from Organic Waste
Section snippets
Mixed Culture Fermentation
Most biotechnological processes use pure culture fermentations because process parameters can be optimized for specific strains of microorganisms. However, pure culture fermentation has some fundamental disadvantages – it requires sterile operating conditions and high-quality and high-purity raw materials. Mixed culture fermentation does not rely on specific microorganism strains and can be operated in nonsterile conditions without a significant risk of contamination. The mixed microbial
Reactor Microbiome
A reactor microbiome can be defined as a group of microorganisms living in a certain setting adapted to the artificial (bioreactor) environment. Through natural selection, microorganisms adapt to the surrounding conditions, and only the most efficient and profitable metabolic interactions occur between them. In the bioreactor, the microorganisms cooperate and interact with one another, showing a higher resilience level of functionality and organization [3].
Culture-dependent methods, which are
Structure of Mixed Microbial Communities
Nowak and colleagues [5] stated that the fundamental aspect of any biological systems is cooperation. The authors hypothesized that in complex communities, the ‘who-meets-whom’ is not random but it is determined by spatial relationships (Box 1). Verstraete [6] published an influential opinion on the potential active drivers of the mixed culture community. One way to investigate the structure of the community is to screen for crossfeeding patterns where certain groups of microorganisms are
Strategies for Shaping the Reactor Microbiome
To extend our knowledge about structure–function relationship in microbiomes, it is necessary to use omics approaches to elucidate interspecies interactions and their responses to the environment. Metaomics techniques (i.e., metagenomics, metatranscriptomics, metaproteomics, and metabolomics) can help to discover the function of microbiome members [4]. Metaomics allow us to study phylogenetic composition and functional potential without the need for culture enrichment. This is the key advantage
Concluding Remarks
How microbial communities become defined during the biological process, and which external and internal factors govern the reactor microbiome, are still being debated. In order to find the most important microbes and the most crucial connections in mixed culture systems, it is necessary to search for highly connected microorganisms that benefit from being specifically involved with high connectivity.
Acknowledgments
The presented work is part of the Caprobiome project funded by the National Centre for Research and Development (Poland) under the LIDER programme (contract no.: LIDER/013/261/L-5/13/NCBR/2014).
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