Industrial systems biology

Otero, José M.; Nielsen, Jens

doi:10.1002/bit.22592

Cited by 134 publications

(61 citation statements)

References 134 publications

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“…Nowadays, this approach is very important since the application of systems biology to fermentation technology particularly for improving industrial strains, process optimization, and even scale-up will be facilitated if biological characteristics are strongly included in bioprocess development [18,19].…”

Section: Biofilm Vs Cell Immobilizationmentioning

confidence: 99%

Recent Advances on Filamentous Fungal Biofilms for Industrial Uses

Gutiérrez-Correa

Ludeña

Ramage

et al. 2012

Appl Biochem Biotechnol

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Industrial enzymes are produced by submerged fermentation (SF) and by solid-state fermentation (SSF) to a lesser extent. Although SSF has several advantages, its scale-up is difficult. The role of physiological and genetic properties of microorganisms growing attached to surfaces could explain the advantages of SSF. Filamentous fungi are naturally adapted to growth on surfaces and in these conditions they show a particular physiological behavior which is different from that in SF; thus, they also form biofilms. Fermentation by filamentous fungal biofilms (FFB) is a homogeneous production system within a liquid environment based on the infrastructure of the SF process with the productive efficiency of the SSF. Enzyme production levels of FFB are much higher than those obtained in SF and they are also amenable of mixed fungal cultivation. Transcriptomic and proteomic tools are used to uncover the fundamental biological issues behind FFB. Several genes encoding cellulolytic enzymes are either differentially expressed or overexpressed in FFB. Moreover, our proteomic studies of Aspergillus niger biofilms compared to SF indicate that many intracellular proteins are either differentially expressed or overexpressed. Clinically important fungi like A. fumigatus also form biofilms when they infect lungs and recent studies demonstrate same gene expression features. These results support our hypothesis of cell adhesion and its role in the new schemes for improved fermentative production of industrial enzymes.

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Section: Biofilm Vs Cell Immobilizationmentioning

confidence: 99%

Recent Advances on Filamentous Fungal Biofilms for Industrial Uses

Gutiérrez-Correa

Ludeña

Ramage

et al. 2012

Appl Biochem Biotechnol

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“…In addition FBAbased approaches can help to design synthetic metabolic pathways (Medema et al , 2012, Vieira et al , 2014 and microbial strains (Burgard et al , 2003, Stanford et al , 2015, Tepper and Shlomi, 2010. Finally, these models represent a major step in systems biology, because they allow the integration of different 'omics' data for obtaining detailed metabolic characterization (Otero and Nielsen, 2010).…”

Section: Fluxomicsmentioning

confidence: 99%

White biotechnology: State of the art strategies for the development of biocatalysts for biorefining

Heux

Meynial-Salles

O’Donohue

et al. 2015

Biotechnology Advances

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“…Compared to metabolome analysis such technologies are much more matured and hence easier applicable in the industrial context. Nevertheless, there are examples clearly showing how metabolomics and other omics technologies can successfully contribute [77][78][79][80].…”

Section: Application Of Microbial Metabolomicsmentioning

confidence: 99%

Metabolomics in Biotechnology (Microbial Metabolomics)

Oldiges

Noack

Paczia

2013

Metabolomics in Practice

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IntroductionThe first documentation of the term metabolomics goes back to two independent publications in 1998 and was used in the context of describing the metabolic behavior of microbial systems, showing a distinct phenotype regarding their physiology and extracellular metabolite spectrum [1,2]. For sure, these were not the first publications with such research activity, but these were the ones which obviously coined the term metabolomics. Later on, this term was picked up by the scientific community not only for the microbial field but also for many other scientific areas and paved its way to become one of the representatives of the omics era. In this sense, the suffix -ome is ''used to direct attention to holistic abstractions, an eventual goal, of which only a few parts may be initially in hand'' [3] and its origin goes back to the early twentieth century. Initially, the German botanist Hans Winkler is attributed to have coined the term genome by the combination of the terms gene and chromosome (Greek word soma = body) [4]. This keyword functioned as blueprint for the many other -omes that are currently investigated. Finally, they all go back to the Greek word soma and in opposite to the genome this term seems to be not precisely fitting for the metabolome, as the metabolites are not located or arranged in a body, but are distributed all over the system.Since 1998, the term metabolomics was increasingly used in the literature showing significant increase (Figure 15.1) and indicating the fast development of the field.The field of microbial metabolomics can be subdivided into the investigation of the endo-and exo-metabolome (intra-vs extracellular) as well as different approaches such as target analysis, metabolic profiling, and metabolic finger-/footprinting (Figure 15.2) [5,6]. On the one hand, the target analysis aims at the quantitative analysis of substrate and/or product metabolites of a given metabolic conversion, whereas metabolic profiling focuses on the quantitative analysis of a set of predefined metabolites belonging to a class of compounds or members of particular pathways or a linked group of metabolites (e.g., sugars, sugar phosphates, lipids, organic acids). On the other hand, metabolic Metabolomics in Practice: Successful Strategies to Generate and Analyze Metabolic Data, First Edition. Edited by Michael Lämmerhofer and Wolfram Weckwerth.

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Industrial systems biology

Cited by 134 publications

References 134 publications

Recent Advances on Filamentous Fungal Biofilms for Industrial Uses

Recent Advances on Filamentous Fungal Biofilms for Industrial Uses

White biotechnology: State of the art strategies for the development of biocatalysts for biorefining

Metabolomics in Biotechnology (Microbial Metabolomics)

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