Segregated flux balance analysis constrained by population structure/function data: The case of PHA production by mixed microbial cultures

• Published in: Biotechnology and bioengineering 2013-08, Vol.110 (8), p.2267-2276
• Main Authors: Pardelha, F., Albuquerque, M.G.E., Carvalho, G., Reis, M.A.M., Dias, J.M.L., Oliveira, R.
• Format: Article
• Language: English
• Subjects: Azoarcus; Azoarcus - classification; Azoarcus - genetics; Azoarcus - metabolism; Bacteria; Bioreactors - microbiology; Biota; DNA, Bacterial - genetics; Fatty acids; Fermentation; Fluorescence in situ hybridization; flux balance analysis (FBA); In Situ Hybridization, Fluorescence; microautoradiography-fluorescent in situ hybridization (MAR-FISH); Microbial Consortia; mixed microbial cultures (MMCs); Molasses; Paracoccus; Paracoccus - classification; Paracoccus - genetics; Paracoccus - metabolism; polyhydroxyalkanoates (PHA); Polyhydroxyalkanoates - biosynthesis; Saccharum - metabolism; Thauera; Thauera - classification; Thauera - genetics; Thauera - metabolism
• ISSN: 0006-3592; 1097-0290
• DOI: 10.1002/bit.24894

In this study we developed a segregated flux balance analysis (FBA) method to calculate metabolic flux distributions of the individual populations present in a mixed microbial culture (MMC). Population specific flux data constraints were derived from the raw data typically obtained by the fluorescence in situ hybridization (FISH) and microautoradiography (MAR)‐FISH techniques. This method was applied to study the metabolic heterogeneity of a MMC that produces polyhydroxyalkanoates (PHA) from fermented sugar cane molasses. Three populations were identified by FISH, namely Paracoccus sp., Thauera sp., and Azoarcus sp. The segregated FBA method predicts a flux distribution for each of the identified populations. The method is shown to predict with high accuracy the average PHA storage flux and the respective monomeric composition for 16 independent experiments. Moreover, flux predictions by segregated FBA were slightly better than those obtained by nonsegregated FBA, and also highly concordant with metabolic flux analysis (MFA) estimated fluxes. The segregated FBA method can be of high value to assess metabolic heterogeneity in MMC systems and to derive more efficient eco‐engineering strategies. For the case of PHA‐producing MMC considered in this work, it becomes apparent that the PHA average monomeric composition might be controlled not only by the volatile fatty acids (VFA) feeding profile but also by the population composition present in the MMC. Biotechnol. Bioeng. 2013; 110: 2267–2276. © 2013 Wiley Periodicals, Inc. A segregated FBA method was developed and applied to a mixed microbial culture (MMC) that produces PHA from fermented sugar cane molasses. This method enables computation population specific flux vectors, therewith enabling profiling of the metabolic heterogeneity within a MMC. The segregated FBA is shown to accurately predict the average PHA storage flux and the respective monomeric composition for 16 independent experiments. Moreover, the predicted fluxes are shown to be highly concordant with MFA estimated fluxes.