Universal Pipeline for the Extraction of Nucleic Acids, Polysaccharides, and Proteins from Spent Microbial Biomass

NextGenRnD® Solution No. 17


Current Solution is applicable to precision fermentation used for production of some specific product. This product might be either a speciality product (e.g., an antibody, a protein, a vitamin, an antibiotic) or a bulk product like amino acids, alcohols, organic acids, and polymers. The amounts of spent microbial biomass (SMB) remaining after speciality product fermentation range from 10 to 1000 kg per 1 kg of product, whereas for bulk product, the SMB to bulk product ratio varies from 0.01 to 1.51. Thus, vast amounts of SMB remain after fermentation process and the valorization of SMB is a pressing problem from many perspectives. Vast amounts of energy and nutrients are contained within SMB, more precisely within the polymers of SMB, i.e., proteins, polysaccharides, and nucleic acids.

Even though there are different fermentation processes, after which various amounts of SMB remain there is one common characteristic for most precision fermentation processes. The products generated by fermentation process are typically secreted out of the microorganism (e.g., yeast, fungi, bacteria, mammalian cells, etc.). Thus, fermentation is designed in such a way that, at large, there are always three discrete entities: (1) the secreted fermentation product and other excreted metabolism products; (2) the growth medium; and (3) the microorganisms. After the completion of fermentation process, the secreted fermentation product is separated from excreted microorganisms’ metabolic products to near homogeneity through multiple purification stages. The growth medium is typically discarded, and the microorganisms become the SMB with some remaining growth medium – the starting SMB material, which enters the pipeline specified in NextGenRnD's Solution.

To get access to the valuable polymers/nutrients of SMB the following procedures are required. First, it is required to efficiently disrupt/lyse the microorganisms of SMB. Second, it is required to clear the disrupted/lysed SMB from large particulates by applying centrifugal force. Third, it is required to sequentially purify the nucleic acids, the polysaccharides, and the proteins from the cleared SMB lysate. All these stages should be robust, highly efficient, scalable, simple, and require minimum investment possible.

The current Solution specifies highly efficient and robust methods for the disruption and the processing of SMB as well as the high-level pipeline enabling to valorize up to 85% (P. pastoris) of yeast and up to 78% (E. coli) of bacteria in a large-scale format. The pipeline should also be applicable to mammalian cells.


In this Solution, NextGenRnD presents a universal pipeline for the extraction of nucleic acids, polysaccharides, and proteins from spent microbial biomass (SMB). At large, the Solution consists of three principles. First, ultra-efficient disruption of the microorganisms of which SMB is constituted. Second, extraction and purification of polymers (nucleic acids, polysaccharides, and proteins) retaining their structure and function. Third, the separation of the liquids and the solids created as the result of first and second principles application. The application of these principles results in the following products: (1) crude lipids + peptidoglycan; (2) nucleic acids; (3) proteins + polysaccharides. The process is large-scale-ready, efficient, original, and attractive not only for food applications (both for humans and aquaculture) but also for biotechnology companies and pharmaceutical industry.

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