Journal: bioRxiv

Article Title: Expanding the scope of redox-balance growth coupling techniques with a carbon cofeeding strategy

doi: 10.64898/2026.04.01.713023

Figure Lengend Snippet: Schematic depicting the genetic modifications to enable the overaccumulation of NADPH (Δ pgi , Δ edd , Δ qor , Δ sthA ) and the deletion of aceA to prohibit growth on acetate as a carbon source. Pathways enabling growth on a mixture of acetate and glucose are shown below and highlighted (red: acetaldehyde (strain APEQS_PduP), yellow: 3-HB (strain APEQS_3-HB), blue: mevalonate (strain APEQS_MEV_sa)). b, Simplified metabolic stoichiometries showing only bioavailable carbon and relevant reducing equivalents and assuming all carbon flows to acetyl-CoA (our pathways’ precursor molecule). Simplified stoichiometry of E. coli fermentative metabolism and APEQS metabolism when grown on glucose, showing redox-balanced fermentative or rescue pathways below. Ethanol fermentation requires less acetyl-CoA (green) than is produced from one glucose when redox balanced, reflecting its suitability as a fermentation pathway. Partially reducing pathways consume more acetyl-CoA (red) than is made available per unit glucose when redox balanced, indicating their inability to resolve redox balance in APEQS without acetate co-feeding. c, Unsuccessful growth coupling of strain APEQS_PduP in the absence of acetate (n=3). d, Unsuccessful growth coupling of strain APEQS_3-HB in the absence of acetate (n=3). e, Unsuccessful growth coupling of strain APEQS_MEV_sa in the absence of acetate (n=3). f, Successful growth coupling of strain APEQS_PduP when the strain is grown with additional 100 mM sodium acetate to satisfy stoichiometric constraints (n=3). g, Successful growth coupling of strain APEQS_3-HB when the strain is grown with additional 100 mM sodium acetate to satisfy stoichiometric constraints (n=3). h, Successful growth coupling of strain APEQS_MEV_sa when the strain is grown with additional 100 mM sodium acetate to satisfy stoichiometric constraints (n=3). All experiments were conducted in a MOPS medium containing 2% glucose with or without 100 mM acetate. Various concentrations of IPTG were added to modulate the induction of the three partially reducing pathways (high [IPTG]: blue (0.5 mM for p15A-based A5c backbone; 0.05 mM for ColE1-based pQE backbone), medium [IPTG]: purple (0.05 mM for p15A-based A5c backbone; 0.005 mM for ColE1-based pQE backbone), no IPTG: red). An empty vector control was included to demonstrate growth without leaky expression (orange). All growth experiments were repeated a minimum of 3 times and showed identical results.

Article Snippet: For growth coupling experiments and strain evolution, bacterial strains were grown in a minimal MOPS medium (Teknova M2106) containing 2% glucose (w/v) supplemented with the appropriate antibiotic based on the plasmid(s) present in the strain.

Techniques: Produced, Plasmid Preparation, Control, Expressing

Journal: mBio

Article Title: Shear flow promotes bacterial growth and shapes spatial gradients by rapidly replenishing scarce nutrients

doi: 10.1128/mbio.03446-25

Figure Lengend Snippet: Bacteria require high nutrient concentrations for batch culture growth. ( A ) Growth curves of P. aeruginosa cells in M9 minimal medium with varying glucose concentrations. Cell density measured by optical density at 600 nm. While increasing glucose impacted maximal culture density, it did not impact growth rate. ( B ) Maximum culture density of P. aeruginosa cells grown in varying glucose concentrations. Lines and shading show the average and standard deviation of three biological replicates. ( C ) Growth curves of P. aeruginosa cells in M9 minimal medium with varying ammonium chloride concentrations. Cell density measured by optical density at 600 nm. While increasing ammonium chloride impacted maximal culture density, it did not impact growth rate. ( D ) Maximum culture density of P. aeruginosa cells grown in varying ammonium chloride concentrations. Lines and shading show the average and standard deviation of three biological replicates. ( E ) Growth curves of V. cholerae cells in M9 minimal medium with varying glucose concentrations. Cell density measured by optical density at 600 nm. While increasing glucose impacted maximal culture density, it did not impact growth rate. ( F ) Maximum culture density of V. cholerae cells grown in varying glucose concentrations. Lines and shading show the average and standard deviation of three biological replicates. All shaded error bars are gray, semi-transparent overlays. Due to very small standard deviations, some of the shading is difficult to notice.

Article Snippet: M9 minimal medium was prepared using the Cold Spring Harbor protocol for M9 minimal medium preparation , freely available from their website.

Techniques: Bacteria, Standard Deviation

Journal: mBio

Article Title: Shear flow promotes bacterial growth and shapes spatial gradients by rapidly replenishing scarce nutrients

doi: 10.1128/mbio.03446-25

Figure Lengend Snippet: Flow is required for growth with extremely low nutrient concentrations. Quantification of cell division per hour under variable flow ( A ) or constant flow ( B ) carbon-limited P. aeruginosa , variable flow ( C ) or constant flow ( D ) nitrogen-limited P. aeruginosa , and variable flow ( E ) or constant flow ( F ) carbon-limited V. cholerae experiments. Carbon-limited indicates M9 minimal medium without an added carbon source, and nitrogen-limited indicates M9 minimal medium without an added nitrogen source. When flow was on, cells could grow in both carbon- and nitrogen-limited regimes. When flow stopped, cells were quickly unable to grow. Quantification shows the average and standard deviation of three biological replicates. For each biological replicate, 50 cells were chosen at random for quantification.

Article Snippet: M9 minimal medium was prepared using the Cold Spring Harbor protocol for M9 minimal medium preparation , freely available from their website.

Techniques: Standard Deviation

Journal: mBio

Article Title: Shear flow promotes bacterial growth and shapes spatial gradients by rapidly replenishing scarce nutrients

doi: 10.1128/mbio.03446-25

Figure Lengend Snippet: Bacteria grow with 1,000 times lower glucose concentrations in flow. ( A ) Representation of glucose concentrations required for growth in flow and in no flow. For comparison, the glucose concentrations typically used in experiments and the affinity of bacterial glucose transporters were included ( , ). Cell divisions per hour under flow at a shear rate of 800 s −1 ( B ) or no flow ( C ) using conditioned M9 minimal medium with various concentrations of added glucose. M9 minimal medium was conditioned by cells to remove contaminant carbon sources. Quantification represents the average and standard deviation of three biological replicates. For each biological replicate, 30 cells were chosen at random for quantification. Experiments were conducted in microfluidic devices with or without flow for direct comparison of results.

Article Snippet: M9 minimal medium was prepared using the Cold Spring Harbor protocol for M9 minimal medium preparation , freely available from their website.

Techniques: Bacteria, Comparison, Shear, Standard Deviation