Microbial growth on substitutable substrates: Characterizing the consumer-resource relationship

Ramakrishna, Ramprasad; Ramkrishna, Doraiswami; Konopka, Allan

doi:10.1002/(sici)1097-0290(19970405)54:1<77::aid-bit9>3.0.co;2-v

Cited by 23 publications

(4 citation statements)

References 19 publications

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“…It has been reported that substitutable carbon substrates that are taken up sequentially, are taken up simultaneously when other substrates become limiting (Ramakrishna et al, 1997). Thus, it was of interest to see if nitrogen substrate limitation results in an altered substrate uptake pattern of A. balhimycina.…”

Section: Carbon Substrate Uptake Under Nitrogen Limitationmentioning

confidence: 99%

Substrate uptake, phosphorus repression, and effect of seed culture on glycopeptide antibiotic production: Process model development and experimental validation

Maiti

Singh

Lantz

et al. 2009

Biotech & Bioengineering

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Actinomycetes, the soil borne bacteria which exhibit filamentous growth, are known for their ability to produce a variety of secondary metabolites including antibiotics. Industrial scale production of such antibiotics is typically carried out in a multi-substrate medium where the product formation may experience catabolite repression by one or more of the substrates. Availability of reliable process models is a key bottleneck in optimization of such processes. Here we present a structured kinetic model to describe the growth, substrate uptake and product formation for the glycopeptide antibiotic producer strain Amycolatopsis balhimycina DSM5908. The model is based on the premise that the organism is an optimal strategist and that the various metabolic pathways are regulated via key rate limiting enzymes. Further, the model accounts for substrate inhibition and catabolite repression. The model is also able to predict key phenomena such as simultaneous uptake of glucose and glycerol but with different specific uptake rates, and inhibition of glycopeptide production by high intracellular phosphate levels. The model is successfully applied to both production and seed medium with varying compositions and hence has good predictive ability over a variety of operating conditions. The model parameters are estimated via a well-designed experimental plan. Adequacy of the proposed model was established via checking the model sensitivity to its parameters and confidence interval calculations. The model may have applications in optimizing seed transfer, medium composition, and feeding strategy for maximizing production.

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Section: Carbon Substrate Uptake Under Nitrogen Limitationmentioning

confidence: 99%

Substrate uptake, phosphorus repression, and effect of seed culture on glycopeptide antibiotic production: Process model development and experimental validation

Maiti

Singh

Lantz

et al. 2009

Biotech & Bioengineering

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“…An alternative to the generalized Lotka–Volterra model is the consumer–resource model, which describes the dynamics of individual taxa as a function of the availability of resources. This model assumes that species interact only through competition for a few limiting resources 23 , 24 , which greatly reduces the number of required parameter from the square of the taxon number (pairwise species interactions) to the number of resources, and hence it is parsimonious for complex systems such as microbial communities 25 . Recently, resource‐related models have been successfully used for modeling microbial community diversity dynamics 26 , 27 .…”

Section: Introductionmentioning

confidence: 99%

Assessing mechanisms for microbial taxa and community dynamics using process models

Wu,

Yang,

Ning

et al. 2023

mLife

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Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations. Using time‐series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer–resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.

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“…Further, we have proposed a model that accounts for growth and product formation kinetics of rifamycin B fermentation in a multi-substrate complex medium (Bapat et al 2006). Here, we present a cybernetic model (Kompala et al 1984;Dhurjati et al 1985;Ramkrishna et al 1997) for rifamycin B fermentation which accounts for the effect of various organic nitrogen sources on rifamycin B productivity. Five different S ONS were chosen based on the form in which nitrogen is available to the organism.…”

Section: Introductionmentioning

confidence: 99%

A cybernetic model to predict the effect of freely available nitrogen substrate on rifamycin B production in complex media

Bapat

Sohoni

Moses

et al. 2006

Appl Microbiol Biotechnol

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A cybernetic model to predict the effect of freely available nitrogen substrate on rifamycin B production in complex media Abstract It is well-known that secondary metabolite production is repressed by excess nitrogen substrate available in the fermentation media. Although the nitrogen catabolite repression has been known, quantitative process models have not been reported to represent this phenomenon in complex medium. In this paper, we present a cybernetic model for rifamycin B production via Amycolatopsis mediterranei S699 in complex medium, which is typically used in industry. Nitrogen substrate is assumed to be present in two forms in the medium; available nitrogen (S ANS ) such as free amino acids and unavailable nitrogen (S UNS ) such as peptides and proteins. The model assumes that an inducible enzyme catalyzes the conversion of S UNS to S ANS . Although S ANS is required for growth and product formation, high concentrations were found to inhibit rifamycin production. To experimentally validate the model, five different organic nitrogen sources were used that differ in the ratio of S ANS / S UNS . The model successfully predicts higher rifamycin B productivity for nitrogen sources that contain lower initial S ANS . The higher productivity is attributed to the sustained availability of S ANS at low concentration via conversion of S UNS to S ANS , thereby minimizing the effects of nitrogen catabolite repression on rifamycin production. The model can have applications in model-based optimization of substrate feeding recipe and in monitoring and control of fed batch processes.

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Microbial growth on substitutable substrates: Characterizing the consumer-resource relationship

Cited by 23 publications

References 19 publications

Substrate uptake, phosphorus repression, and effect of seed culture on glycopeptide antibiotic production: Process model development and experimental validation

Substrate uptake, phosphorus repression, and effect of seed culture on glycopeptide antibiotic production: Process model development and experimental validation

Assessing mechanisms for microbial taxa and community dynamics using process models

A cybernetic model to predict the effect of freely available nitrogen substrate on rifamycin B production in complex media

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