BACKGROUND: Succinic acid production has been studied from a metabolic engineering or a downstream processing perspective, separately. The concentration of succinic acid and other by-products obtained after the strain design influences the production cost during the recovery and purification stage. A metabolic engineering-downstream coupling evaluation is important when selecting the metabolic targets for the strain design. In this in silico study, the metabolic engineering of an Escherichia coli strain to produce succinic acid using glycerol as a carbon source in the downstream process was evaluated in terms of operational cost and energy consumption. (0.3068, 0.0576, 0.1089 h -1 ) and succinate productivity (2.7534, 6.0772, 5.5661 mmol g -1 DW h -1 ), respectively. The results showed that the succinic acid productivity constituted a central parameter when selecting the appropriate gene targets for deletion, despite the presence of organic acids in the downstream process and the biomass growth rate. RESULTS: Three strain scenarios were selected using a bi-level linear optimization problem solved by Mixed Integer Linear Programing, and simulated in a transient fashion with dynamic flux balance analysis considering both biomass growth rate CONCLUSION: A metabolism-downstream coupled model shows that the bioproduct productivity and fermentation timeare key points when considering the operational cost and energy consumption involved in the engineering of strains for industrial-scale production.Metabolic engineering targets were obtained using OptKnock, which is a bi-level linear optimization problem solved by MILP. 33

Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes.

Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, a potentially serious threat to cotton production worldwide, including in sub-Saharan countries. Development of disease symptoms, such as water soaking, has been linked to the activity of a class of type 3 effectors, called TAL (transcription activator-like) effectors, which induce susceptibility genes in the host’s cells. To gain further insight into the global diversity of the pathogen, to elucidate their repertoires of TAL effector genes and to better understand the evolution of these genes in the cotton-pathogenic xanthomonads, we sequenced the genomes of three African strains of X. citri pv. malvacearum using nanopore technology. We show that the cotton-pathogenic pathovar of X. citri is a monophyletic lineage containing at least three distinct genetic subclades, which appear to be mirrored by their repertoires of TAL effectors. We observed an atypical level of TAL effector gene pseudogenization, which might be related to resistance genes that are deployed to control the disease. Our work thus contributes to a better understanding of the conservation and importance of TAL effectors in the interaction with the host plant, which can inform strategies for improving resistance against bacterial blight in cotton.