TECHNOLOGY FOCUS - BIOLOGY - Preferred Components: The limited glucose concentration is less than 5 g/l. The first stage is aerobic. The fermentation medium in the second stage is glucose excess. The glucose excess concentration is 5-25 g/l. The second stage is microaerobic. The microorganism is a genus consisting of Clostridium, Zymomonas, Escherichia, Salmonella, Serratia, Erwinia, Klebsiella, Shigella, Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Alcaligenes, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Schizosaccharomyces, Kluyveromyces, Yarrowia, Pichia, Zygosaccharomyces, Debaryomyces, Candida, Brettanomyces, Pachysolen, Hansenula, Issatchenkia, Trichosporon, Yamadazyma, and Saccharomyces (preferred).    TECHNOLOGY FOCUS - ORGANIC CHEMISTRY - Preferred Process: The process comprises: providing the fermentation medium in a first fermenter comprising the recombinant microorganism; monitoring a controlled variable of the first fermenter; adjusting a manipulated variable of the first fermenter based on the set point of the monitored controlled variable; providing the fermentation medium in a second fermenter comprising the recombinant microorganism; monitoring the controlled variable of the second fermenter; and adjusting the manipulated variable of the second fermenter based on the adjustment made to the first fermenter, where the adjustment of the manipulated variable in the second fermenter increases the biomass of the recombinant microorganism in the second fermenter. The set point of the controlled variable is dynamically adjusted based on byproduct level. The process is carried out in two stages, where the first stage is a biomass growth phase, and the second stage is a transition phase from the growth phase to a butanol production phase for the recombinant microorganism. The fermentation medium in the first stage is glucose limited. The butanol biosynthetic pathway is a 1-butanol biosynthetic pathway, a 2-butanol biosynthetic pathway, and an isobutanol biosynthetic pathway. The 1-butanol biosynthetic pathway comprises at least one gene encoding a polypeptide that performs a conversion of substrate to product, such as: (1) acetyl-coenzyme A (CoA) to acetoacetyl-CoA, as catalyzed by acetyl-CoA acetyltransferase; (2) acetoacetyl-CoA to 3-hydroxybutyryl-CoA, as catalyzed by 3-hydroxybutyryl-CoA dehydrogenase; (3) 3-hydroxybutyryl-CoA to crotonyl-CoA, as catalyzed by crotonase; (4) crotonyl-CoA to butyryl-CoA, as catalyzed by butyryl-CoA dehydrogenase; (5) butyryl-CoA to butyraldehyde, as catalyzed by butyraldehyde dehydrogenase; and (6) butyraldehyde to 1-butanol, as catalyzed by 1-butanol dehydrogenase. The 2-butanol biosynthetic pathway comprises at least one gene encoding a polypeptide that performs a conversion of substrate to product, such as: (i) pyruvate to alpha-acetolactate, as catalyzed by acetolactate synthase; (ii) alpha-acetolactate to acetoin, as catalyzed by acetolactate decarboxylase; (iii) acetoin to 2,3-butanediol, as catalyzed by butanediol dehydrogenase; (iv) 2,3-butanediol to 2-butanone, as catalyzed by butanediol dehydratase; and (v) 2-butanone to 2-butanol, as catalyzed by 2-butanol dehydrogenase. The isobutanol biosynthetic pathway comprises at least one gene encoding a polypeptide that performs a conversion of substrate to product, such as: pyruvate to acetolactate, as catalyzed by acetolactate synthase; acetolactate to 2,3-dihydroxyisovalerate, as catalyzed by ketol-acid reductoisomerase; 2,3-dihydroxyisovalerate to alpha -ketoisovalerate, as catalyzed by dihydroxy-acid dehydratase; alpha -ketoisovalerate to isobutyraldehyde, as catalyzed by a branched chain keto acid decarboxylase; and isobutyraldehyde to isobutanol, as catalyzed by branched-chain alcohol dehydrogenase. Preferred Components: The controlled variable is respiratory quotient (RQ), specific oxygen uptake rate (Sp. OUR), specific carbon dioxide evolution rate (Sp. CER), pH, biomass level, specific growth rate, oxygen partial pressure (pO2), rate of heat generation, specific butanol production rate, and/or specific byproduct production rate. The respiratory quotient set point is 0.67-1.5, preferably 0.95-1.05, or 2-50, preferably 5-10. The specific oxygen uptake rate set point is 1.5 (preferably 0.05-0.5) mM/g of cells per hour, or 2-10 (preferably 3-5) mM/g of cells per hour. The specific carbon dioxide evolution rate set point is 1-10 (preferably 2.5-5.5) mM/g of cells pre hour. The pH set point is 3.5-7, preferably 5-6. The oxygen partial pressure set point is 0.1-5%, preferably 0.1-1%, or 5-30%, preferably 10-30%. The specific butanol production rate set point is 0-0.005 (preferably 0.00025-0.001) g/g of cells per hour. The controlled variable is temperature. The temperature set point is 30 degrees C. The byproduct is isobutyrate, isobutyric acid (preferred), dihydroxyisovalerate, ketoisovalerate, isobutyraldehyde, lactate, acetolactate, acetate, formate, and/or glycerol. The specific isobutyric acid production rate is 0.001-0.02 (preferably 0.0025-0.005) g/g of cells per hour. The manipulated variable is feed rate, feed composition, air flow rate, air composition, stirring rate, and/or pressure. The controlled variable is carbon dioxide to butanol production molar ratio. The carbon dioxide to butanol production molar ratio set point is 2-10, preferably 2-2.25. The controlled variable is specific butanol production rate. The specific butanol production rate set point is 0.1-1 (preferably 0.2-0.5) g/g of cells per hour.