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Dodia H, Sunder AV, Borkar Y, Wangikar PP. Precision fermentation with mass spectrometry-based spent media analysis. Biotechnol Bioeng 2023; 120:2809-2826. [PMID: 37272489 DOI: 10.1002/bit.28450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023]
Abstract
Optimization and monitoring of bioprocesses requires the measurement of several process parameters and quality attributes. Mass spectrometry (MS)-based techniques such as those coupled to gas chromatography (GCMS) and liquid Chromatography (LCMS) enable the simultaneous measurement of hundreds of metabolites with high sensitivity. When applied to spent media, such metabolome analysis can help determine the sequence of substrate uptake and metabolite secretion, consequently facilitating better design of initial media and feeding strategy. Furthermore, the analysis of metabolite diversity and abundance from spent media will aid the determination of metabolic phases of the culture and the identification of metabolites as surrogate markers for product titer and quality. This review covers the recent advances in metabolomics analysis applied to the development and monitoring of bioprocesses. In this regard, we recommend a stepwise workflow and guidelines that a bioprocesses engineer can adopt to develop and optimize a fermentation process using spent media analysis. Finally, we show examples of how the use of MS can revolutionize the design and monitoring of bioprocesses.
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Affiliation(s)
- Hardik Dodia
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | | | - Yogen Borkar
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- Clarity Bio Systems India Pvt. Ltd., Pune, India
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Gaudana SB, Krishnakumar S, Alagesan S, Digmurti MG, Viswanathan GA, Chetty M, Wangikar PP. Rhythmic and sustained oscillations in metabolism and gene expression of Cyanothece sp. ATCC 51142 under constant light. Front Microbiol 2013; 4:374. [PMID: 24367360 PMCID: PMC3854555 DOI: 10.3389/fmicb.2013.00374] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/21/2013] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria, a group of photosynthetic prokaryotes, oscillate between day and night time metabolisms with concomitant oscillations in gene expression in response to light/dark cycles (LD). The oscillations in gene expression have been shown to sustain in constant light (LL) with a free running period of 24 h in a model cyanobacterium Synechococcus elongatus PCC 7942. However, equivalent oscillations in metabolism are not reported under LL in this non-nitrogen fixing cyanobacterium. Here we focus on Cyanothece sp. ATCC 51142, a unicellular, nitrogen-fixing cyanobacterium known to temporally separate the processes of oxygenic photosynthesis and oxygen-sensitive nitrogen fixation. In a recent report, metabolism of Cyanothece 51142 has been shown to oscillate between photosynthetic and respiratory phases under LL with free running periods that are temperature dependent but significantly shorter than the circadian period. Further, the oscillations shift to circadian pattern at moderate cell densities that are concomitant with slower growth rates. Here we take this understanding forward and demonstrate that the ultradian rhythm under LL sustains at much higher cell densities when grown under turbulent regimes that simulate flashing light effect. Our results suggest that the ultradian rhythm in metabolism may be needed to support higher carbon and nitrogen requirements of rapidly growing cells under LL. With a comprehensive Real time PCR based gene expression analysis we account for key regulatory interactions and demonstrate the interplay between clock genes and the genes of key metabolic pathways. Further, we observe that several genes that peak at dusk in Synechococcus peak at dawn in Cyanothece and vice versa. The circadian rhythm of this organism appears to be more robust with peaking of genes in anticipation of the ensuing photosynthetic and respiratory metabolic phases.
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Affiliation(s)
- Sandeep B Gaudana
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, India
| | - S Krishnakumar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, India
| | - Swathi Alagesan
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, India
| | - Madhuri G Digmurti
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, India
| | - Ganesh A Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, India
| | - Madhu Chetty
- Gippsland School of Information Technology, Monash University VIC, Australia
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, India
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Krishnakumar S, Gaudana SB, Viswanathan GA, Pakrasi HB, Wangikar PP. Rhythm of carbon and nitrogen fixation in unicellular cyanobacteria under turbulent and highly aerobic conditions. Biotechnol Bioeng 2013; 110:2371-9. [PMID: 23456695 DOI: 10.1002/bit.24882] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/24/2013] [Accepted: 02/20/2013] [Indexed: 11/07/2022]
Abstract
Nitrogen fixing cyanobacteria are being increasingly explored for nitrogenase-dependent hydrogen production. Commercial success however will depend on the ability to grow these cultures at high cell densities. Photo-limitation at high cell densities leads to hindered photoautotrophic growth while turbulent conditions, which simulate flashing light effect, can lead to oxygen toxicity to the nitrogenase enzyme. Cyanothece sp. strain ATCC 51142, a known hydrogen producer, is reported to grow and fix nitrogen under moderately oxic conditions in shake flasks. In this study, we explore the growth and nitrogen fixing potential of this organism under turbulent conditions with volumetric oxygen mass transfer coefficient (KL a) values that are up to 20-times greater than in shake flasks. In a stirred vessel, the organism grows well in turbulent regime possibly due to a simulated flashing light effect with optimal growth at Reynolds number of approximately 35,000. A respiratory burst lasting for about 4 h creates anoxic conditions intracellularly with near saturating levels of dissolved oxygen in the extracellular medium. This is concomitant with complete exhaustion of intracellular glycogen storage and upregulation of nifH and nifX, the genes encoding proteins of the nitrogenase complex. Further, the rhythmic oscillations in exhaust gas CO2 and O2 profiles synchronize faithfully with those in biochemical parameters and gene expression thereby serving as an effective online monitoring tool. These results will have important implications in potential commercial success of nitrogenase-dependent hydrogen production by cyanobacteria.
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Affiliation(s)
- S Krishnakumar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Zhang CY, Dong YS, Li YL, Fu CH, Zhao CF, Yu LJ. Unstructured models for suspension cultures of Taxus media cells in a bioreactor under substrate-sufficient conditions. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2012.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Role of extracellular protease in nitrogen substrate management during antibiotic fermentation: a process model and experimental validation. Appl Microbiol Biotechnol 2011; 91:1019-28. [DOI: 10.1007/s00253-011-3318-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 04/06/2011] [Accepted: 04/07/2011] [Indexed: 11/25/2022]
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Ödman P, Johansen CL, Olsson L, Gernaey KV, Lantz AE. On-line estimation of biomass, glucose and ethanol in Saccharomyces cerevisiae cultivations using in-situ multi-wavelength fluorescence and software sensors. J Biotechnol 2009; 144:102-12. [DOI: 10.1016/j.jbiotec.2009.08.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 08/27/2009] [Accepted: 08/31/2009] [Indexed: 10/20/2022]
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Maiti SK, Srivastava RK, Bhushan M, Wangikar PP. Real time phase detection based online monitoring of batch fermentation processes. Process Biochem 2009. [DOI: 10.1016/j.procbio.2009.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Srivastava RK, Jaiswal R, Panda D, Wangikar PP. Megacell phenotype and its relation to metabolic alterations in transketolase deficient strain ofBacillus pumilus. Biotechnol Bioeng 2009; 102:1387-97. [DOI: 10.1002/bit.22184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Actinomycetes scale-up for the production of the antibacterial, nocathiacin. Biotechnol Prog 2009; 25:176-88. [DOI: 10.1002/btpr.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Basu A, Das D, Bapat P, Wangikar PP, Phale PS. Sequential utilization of substrates by Pseudomonas putida CSV86: Signatures of intermediate metabolites and online measurements. Microbiol Res 2009; 164:429-37. [PMID: 17467253 DOI: 10.1016/j.micres.2007.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 12/12/2006] [Accepted: 02/16/2007] [Indexed: 11/23/2022]
Abstract
Pseudomonas putida CSV86 preferentially utilizes aromatics over glucose and co-metabolizes them with organic acids. On aromatics plus glucose, CSV86 utilized aromatics first with concomitant appearance of transient metabolites such as salicylate, benzaldehyde and benzoate. Citrate was the main extracellular metabolite observed during glucose uptake. The strain showed simultaneous utilization of organic acids and aromatic compounds. Based on the metabolite analysis and growth profiles, we hypothesize that the repression of glucose utilization could be due to organic acid intermediates generated from aromatic compound metabolism. The online measurements indicate the instantaneous metabolic state of the culture. For example, the CO(2) evolution and agitation speed show peak values during the two growth phases in the diauxic growth while dissolved oxygen values show decrease at the corresponding durations. These measurements correlated well with the offline measurements but provided a better time resolution of the process.
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Affiliation(s)
- Aditya Basu
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
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Medium optimization for enhanced production of Rifamycin B by Amycolatopsis mediterranei S699: Combining a full factorial design and a statistical approach. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bapat PM, Das D, Sohoni SV, Wangikar PP. Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterranei S699, a case study. Microb Cell Fact 2006; 5:32. [PMID: 17081297 PMCID: PMC1665455 DOI: 10.1186/1475-2859-5-32] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 11/02/2006] [Indexed: 01/08/2023] Open
Abstract
Background Industrial fermentation typically uses complex nitrogen substrates which consist of mixture of amino acids. The uptake of amino acids is known to be mediated by several amino acid transporters with certain preferences. However, models to predict this preferential uptake are not available. We present the stoichiometry for the utilization of amino acids as a sole carbon and nitrogen substrate or along with glucose as an additional carbon source. In the former case, the excess nitrogen provided by the amino acids is excreted by the organism in the form of ammonia. We have developed a cybernetic model to predict the sequence and kinetics of uptake of amino acids. The model is based on the assumption that the growth on a specific substrate is dependent on key enzyme(s) responsible for the uptake and assimilation of the substrates. These enzymes may be regulated by mechanisms of nitrogen catabolite repression. The model hypothesizes that the organism is an optimal strategist and invests resources for the uptake of a substrate that are proportional to the returns. Results Stoichiometric coefficients and kinetic parameters of the model were estimated experimentally for Amycolatopsis mediterranei S699, a rifamycin B overproducer. The model was then used to predict the uptake kinetics in a medium containing cas amino acids. In contrast to the other amino acids, the uptake of proline was not affected by the carbon or nitrogen catabolite repression in this strain. The model accurately predicted simultaneous uptake of amino acids at low cas concentrations and sequential uptake at high cas concentrations. The simulated profile of the key enzymes implies the presence of specific transporters for small groups of amino acids. Conclusion The work demonstrates utility of the cybernetic model in predicting the sequence and kinetics of amino acid uptake in a case study involving Amycolatopsis mediterranei, an industrially important organism. This work also throws some light on amino acid transporters and their regulation in A. mediterranei .Further, cybernetic model based experimental strategy unravels formation and utilization of ammonia as well as its inhibitory role during amino acid uptake. Our results have implications for model based optimization and monitoring of other industrial fermentation processes involving complex nitrogen substrate.
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Affiliation(s)
- Prashant M Bapat
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
- Center for Mikrobiel Bioteknologi, BioCentrum-DTU, Danmarks Tekniske Universitet, Bygning 223, DK-2800 Kgs. Lyngby, Denmark
| | - Debasish Das
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
| | - Sujata V Sohoni
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
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