Systems and methods for producing bioproducts

1. A system for making a bioproduct comprising:

a vessel capable of providing an environment suitable for containing whole broth that can produce the bioproduct, wherein the whole broth contains media and at least one undissolved species, the undissolved species being selected from the group consisting of live cells, dead cells, cell fragments, solid substrates having cells adhered thereto, and mixtures thereof;

an automated sampling system operably connected to the vessel and capable of extracting a sample from the vessel at predetermined intervals, the automated sampling system comprising a variable volume reservoir that includes a reservoir inlet, a reservoir outlet that is different from the reservoir inlet, and a reservoir that has a volume that can change from a first volume to a second volume and from the second volume to the first volume;

a first analytical instrument operably connected to the vessel, the analytical instrument being configured to measure at least one cell-level property of the undissolved species in the whole broth in the sample and generating at least one first signal in response thereto;

a second analytical instrument operably connected to the vessel, the second analytical instrument being configured to measure at least one property of the whole broth in the sample and generating at least one second signal in response thereto;

a control system configured to generate at least one output signal that controls at least one device that is configured to alter at least one property of the whole broth within the vessel, the at least one output signal being generated in response to the at least one first signal and the at least one second signal,

wherein the second volume of the reservoir is smaller than the first volume of the reservoir, and the automated sampling system is configured to receive the sample into the reservoir via the reservoir inlet when the reservoir volume changes from the second volume to the first volume and the automated sampling system is configured to discharge the sample from the reservoir when the reservoir volume changes from the first volume to the second volume, and

wherein the variable volume reservoir comprises a flexible diaphragm member and a housing, the flexible diaphragm member being configured to move between a first position where the reservoir has the first volume to draw the sample into the reservoir through the reservoir inlet and a second position where the reservoir has the second volume to discharge the sample from the reservoir through the reservoir outlet.

2. The system of claim 1 , wherein the bioproduct is selected from foods, beverages, biofuels, bioenergy, bio-based ethanol, biodiesel, bio-based adhesives, biochemicals, biotherapeutics, biodegradable plastics, and mixtures thereof, and the control system is configured to alter at least one property of the whole broth within the vessel to produce the bioproduct.

3. The system of claim 1 , wherein said bioproduct is a biotherapeutic and the control system is configured to alter at least one property of the whole broth within the vessel to produce the biotherapeutic.

4. The system of claim 3 , wherein said biotherapeutic is selected from pharmaceuticals, therapeutic proteins, protein fragments, antibodies, vaccines, and mixtures thereof.

5. The system of claim 1 , wherein the vessel is selected from anaerobic fermenters, aerobic fermenters, stirred-tank reactors, adherent bioreactors, wave-type bioreactors, and disposable bioreactors.

6. The system of claim 1 , wherein the undissolved species comprises one or more selected from the group consisting of bacteria, yeast, mammalian cells, and e - coli cells.

7. The system of claim 1 , wherein the at least one property of the whole broth is selected from media-level properties and cell-level properties.

8. The system of claim 1 , wherein the at least one property of the whole broth is selected from pH, dissolved oxygen, osmolality, nutrient concentrations, ammonia/ammonium, lactate/lactic acid, pCO2, electrolytes (such as K+, Ca++, and/or Na+), amino acids, NAD/NADH, impurities, purity, phenotypes, metabolic states, cell health, cell cycle, cell state, cell number, and viable cell volume.

9. The system of claim 1 , wherein the second analytical instrument is selected from the group consisting of pH probes, dissolved oxygen meters, ion-selective electrodes, osmometry, high-performance liquid chromatography, ultra performance liquid chromatography, gas chromatography, ion chromatography, conductivity, Raman spectroscopy, near infrared spectroscopy, dielectric spectroscopy, fluorometry, ultraviolet/visible spectroscopy, capacitance probes, luminescence, redox probes, flow cytometry, hemacytometry, electro-rotation, electrophoresis, dielectrophoresis, and mixtures thereof.

10. The system of claim 1 , wherein the device that is configured to alter at least one property of the whole broth is selected from mixing/agitation systems, temperature-control systems, gas pumps, nutrient pumps, product removal systems, impurity removal systems, pH adjustment systems, and mixtures thereof.

11. The system of claim 1 , wherein the sampling system extracts a sample from the vessel at least once every 4 hours.

12. The system of claim 1 , wherein the sampling system extracts a sample from the vessel at least once every 2 hours.

13. The system of claim 1 , wherein the sampling system extracts a sample from the vessel at least once every 1 hour.

14. The system of claim 1 , wherein the sampling system extracts a sample from the vessel at least once every 0.5 hours.

15. The system of claim 1 , wherein the control system is configured to alter at least one property of the whole broth within the vessel results in an improvement in at least one of bioproduct yield, bioproduct quality, bioproduct purity, bioproduct production rate, reduced cost, reduced energy consumption, and reduced waste generation, relative to a system that is controlled manually.

16. The system of claim 1 , wherein the sampling system is operably connected to the control system.

17. The system of claim 1 wherein the sampling system comprises:

(a) a sanitizing fluid inlet valve operable between an open position and a closed position;

(b) a gas inlet valve operable between an open position and a closed position;

(c) a sample collection valve operable between an open position and a closed position;

(d) a first outlet valve operable between an open position and a closed position; and

(e) a fluid flow path interconnecting (a) (d),

wherein when (a), (b), and (d) are in the closed position, (c) can be in the open position to withdraw a sample from the enclosed container into the reservoir along a first portion of the fluid flow path,

wherein when (a), (b), and (c) are in the closed position, the sample can be discharged from the reservoir along a second portion of the fluid flow path through (d), and

wherein when (a) is in the open position and (b) and (c) are in the closed position, a sanitizing fluid can be introduced into the fluid flow path through (a) to sanitize at least the first portion of the fluid flow path.

18. The system of claim 1 , wherein the at least one cell-level property measured by the first analytical instrument comprises cellular properties of the undissolved species that are indicative of cell behaviors, phenotypes, metabolic states, health, and/or cell cycle.

19. The system of claim 1 , wherein the first analytical instrument analyzes the undissolved species by dielectric spectroscopy, flow cytometry, Raman/NIR spectroscopy, automated hemacytometer, electro-rotation, electrophoresis, and/or dielectrophoresis.

20. The system of claim 1 , wherein the control system is configured to apply a cell state trajectory model in response to the at least one first signal and the at least one second signal, the at least one output signal being generated based on a result of the application of the cell state trajectory model.