79. Lieder S, Jahn M, Seifert J, von Bergen M, Müller S, Takors R (2014) Subpopulationproteomics reveal growth rate, but not cell cycling, as a major impact on protein composition
in Pseudomonas putida KT2440. AMB Express 4:1–10
80. Delvigne F, Zune Q, Lara AR, Al-Soud W, Sørensen SJ (2014) Metabolic variability in
bioprocessing: implications of microbial phenotypic heterogeneity. Trends Biotechnol
32:608–616
81. Van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJM, Planqué R, Hulshof J,
O’Toole TG, Wahl SA, Teusink B (2014) Lost in transition: start-up of glycolysis yields
subpopulations of nongrowing cells. Science 343:1245114
82. Brognaux A, Han S, Sørensen SJ, Lebeau F, Thonart P, Delvigne F (2013) A low-cost,
multiplexable, automated flow cytometry procedure for the characterization of microbial stress
dynamics in bioreactors. Microb Cell Fact 12
83. Lieder S, Jahn M, Koepff J, Muller S, Takors R (2016) Environmental stress speeds up DNA
replication in Pseudomonas putida in chemostat cultivations. Biotechnol J 11:155–163
84. Hewitt CJ, von Caron GN, Axelsson B, McFarlane CM, Nienow AW (2000) Studies related to
the scale-up of high-cell-density E. coli fed-batch fermentations using multiparameter flow
cytometry: effect of a changing microenvironment with respect to glucose and dissolved
oxygen concentration. Biotechnol Bioeng 70:381–390
85. Patel A, Antonopoulou I, Enman J, Rova U, Christakopoulos P, Matsakas L (2019) Lipids
detection and quantification in oleaginous microorganisms: an overview of the current state of
the art. BMC Chem Eng 1
86. Marbà-Ardébol AM, Emmerich J, Neubauer P, Junne S (2017) Single-cell-based monitoring
of fatty acid accumulation in Crypthecodinium cohnii with three-dimensional holographic and
in situ microscopy. Process Biochem 52:223–232
87. Marbà-Ardébol AM, Bockisch A, Neubauer P, Junne S (2018) Sterol synthesis and cell size
distribution under oscillatory growth conditions in Saccharomyces cerevisiae scale-down
cultivations. Yeast 35:213–223
88. Lemoine A, Limberg MHMH, Kästner S, Oldiges M, Neubauer P, Junne S (2016) Performance loss of Corynebacterium glutamicum cultivations under scale-down conditions using
complex media. Eng Life Sci 16:620–632
89. Nachin L, Nannmark U, Nyström T (2005) Differential roles of the universal stress proteins of
Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol
187:6265–6272
90. Trivedi A, Mavi PS, Bhatt D, Kumar A (2016) Thiol reductive stress induces celluloseanchored biofilm formation in Mycobacterium tuberculosis. Nat Commun 7
91. Kurt T, Marbà-Ardébol AM, Turan Z, Neubauer P, Junne S, Meyer V (2018) Rocking
Aspergillus: morphology-controlled cultivation of Aspergillus niger in a wave-mixed bioreactor for the production of secondary metabolites. Microb Cell Factories 17:128
92. Lin PJ, Scholz A, Krull R (2010) Effect of volumetric power input by aeration and agitation on
pellet morphology and product formation of Aspergillus niger. Biochem Eng J 49:213–220
93. Gómez-Ríos D, Junne S, Neubauer P, Ochoa S, Ríos-Estepa R, Ramírez-Malule H (2019)
Characterization of the metabolic response of Streptomyces clavuligerus to shear stress in
stirred tanks and single-use 2D rocking motion bioreactors for clavulanic acid production.
Antibiotics 8
94. Hardy N, Moreaud M, Guillaume D, Augier F, Nienow A, Béal C, Chaabane FB (2017)
Advanced digital image analysis method dedicated to the characterization of the morphology
of filamentous fungus. J Microsc 266:126–140
95. Kuschel M, Siebler F, Takors R (2017) Lagrangian trajectories to predict the formation of
population heterogeneity in large-scale bioreactors. Bioengineering 4:27
96. Ladner T, Grünberger A, Probst C, Kohlheyer D, Büchs J, Delvigne F (2017) Application of
mini- and micro-bioreactors for microbial bioprocesses. In: Current developments in biotechnology and bioengineering: bioprocesses, bioreactors and controls. Elsevier, Amsterdam, pp
433–461
Potential of Integrating Model-Based Design of Experiments Approaches and. . .
27
in Pseudomonas putida KT2440. AMB Express 4:1–10
80. Delvigne F, Zune Q, Lara AR, Al-Soud W, Sørensen SJ (2014) Metabolic variability in
bioprocessing: implications of microbial phenotypic heterogeneity. Trends Biotechnol
32:608–616
81. Van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJM, Planqué R, Hulshof J,
O’Toole TG, Wahl SA, Teusink B (2014) Lost in transition: start-up of glycolysis yields
subpopulations of nongrowing cells. Science 343:1245114
82. Brognaux A, Han S, Sørensen SJ, Lebeau F, Thonart P, Delvigne F (2013) A low-cost,
multiplexable, automated flow cytometry procedure for the characterization of microbial stress
dynamics in bioreactors. Microb Cell Fact 12
83. Lieder S, Jahn M, Koepff J, Muller S, Takors R (2016) Environmental stress speeds up DNA
replication in Pseudomonas putida in chemostat cultivations. Biotechnol J 11:155–163
84. Hewitt CJ, von Caron GN, Axelsson B, McFarlane CM, Nienow AW (2000) Studies related to
the scale-up of high-cell-density E. coli fed-batch fermentations using multiparameter flow
cytometry: effect of a changing microenvironment with respect to glucose and dissolved
oxygen concentration. Biotechnol Bioeng 70:381–390
85. Patel A, Antonopoulou I, Enman J, Rova U, Christakopoulos P, Matsakas L (2019) Lipids
detection and quantification in oleaginous microorganisms: an overview of the current state of
the art. BMC Chem Eng 1
86. Marbà-Ardébol AM, Emmerich J, Neubauer P, Junne S (2017) Single-cell-based monitoring
of fatty acid accumulation in Crypthecodinium cohnii with three-dimensional holographic and
in situ microscopy. Process Biochem 52:223–232
87. Marbà-Ardébol AM, Bockisch A, Neubauer P, Junne S (2018) Sterol synthesis and cell size
distribution under oscillatory growth conditions in Saccharomyces cerevisiae scale-down
cultivations. Yeast 35:213–223
88. Lemoine A, Limberg MHMH, Kästner S, Oldiges M, Neubauer P, Junne S (2016) Performance loss of Corynebacterium glutamicum cultivations under scale-down conditions using
complex media. Eng Life Sci 16:620–632
89. Nachin L, Nannmark U, Nyström T (2005) Differential roles of the universal stress proteins of
Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol
187:6265–6272
90. Trivedi A, Mavi PS, Bhatt D, Kumar A (2016) Thiol reductive stress induces celluloseanchored biofilm formation in Mycobacterium tuberculosis. Nat Commun 7
91. Kurt T, Marbà-Ardébol AM, Turan Z, Neubauer P, Junne S, Meyer V (2018) Rocking
Aspergillus: morphology-controlled cultivation of Aspergillus niger in a wave-mixed bioreactor for the production of secondary metabolites. Microb Cell Factories 17:128
92. Lin PJ, Scholz A, Krull R (2010) Effect of volumetric power input by aeration and agitation on
pellet morphology and product formation of Aspergillus niger. Biochem Eng J 49:213–220
93. Gómez-Ríos D, Junne S, Neubauer P, Ochoa S, Ríos-Estepa R, Ramírez-Malule H (2019)
Characterization of the metabolic response of Streptomyces clavuligerus to shear stress in
stirred tanks and single-use 2D rocking motion bioreactors for clavulanic acid production.
Antibiotics 8
94. Hardy N, Moreaud M, Guillaume D, Augier F, Nienow A, Béal C, Chaabane FB (2017)
Advanced digital image analysis method dedicated to the characterization of the morphology
of filamentous fungus. J Microsc 266:126–140
95. Kuschel M, Siebler F, Takors R (2017) Lagrangian trajectories to predict the formation of
population heterogeneity in large-scale bioreactors. Bioengineering 4:27
96. Ladner T, Grünberger A, Probst C, Kohlheyer D, Büchs J, Delvigne F (2017) Application of
mini- and micro-bioreactors for microbial bioprocesses. In: Current developments in biotechnology and bioengineering: bioprocesses, bioreactors and controls. Elsevier, Amsterdam, pp
433–461
Potential of Integrating Model-Based Design of Experiments Approaches and. . .
27