Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism

The genome of the filamentous fungus Aspergillus niger is rich in genes encoding pectinases, a broad class of enzymes that have been extensively studied due to their use in industrial applications. The sequencing of the A. niger genome provided more knowledge concerning the individual pectinolytic genes, but little is known about the regulatory...

Identifying inhibitory compounds in lignocellulosic biomass hydrolysates using an exometabolomics approach

Background: Inhibitors are formed that reduce the fermentation performance of fermenting yeast during the pretreatment process of lignocellulosic biomass. An exometabolomics approach was applied to systematically identify inhibitors in lignocellulosic biomass hydrolysates.Results: We studied the composition and fermentability of 24 different...

The intracellular galactoglycome in Trichoderma reesei during growth on lactose

Lactose (1,4-0-β-d-galactopyranosyl-d-glucose) is used as a soluble carbon source for the production of cellulases and hemicellulases for - among other purposes - use in biofuel and biorefinery industries. The mechanism how lactose induces cellulase formation in T. reesei is enigmatic, however. Previous results from our laboratory raised the...

A proper metabolomics strategy supports efficient food quality improvement: A case study on tomato sensory properties

In agricultural and food products, typical quality parameters are sensory properties, shelf-life, safety, health, nutritional value, crop yield per area and disease resistance. It is known that these parameters are importantly determined by the metabolites in the crops and food products. Metabolomics is the state-of-the-art routine technique...

Probiotic derived non-viable material for allergy prevention and treatment

Microbial renewable feedstock utilization: A substrate-oriented approach

Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates consist of complex mixtures of different fermentable sugars, but also contain inhibitors and salts that affect the performance of the productgenerating microbes. The performance of six industrially relevant...

Analyzing longitudinal microbial metabolomics data

A longitudinal experimental design in combination with metabolomics and multiway data analysis is a powerful approach in the identification of metabolites whose correlation with bioproduct formation shows a shift in time. In this paper, a strategy is presented for the analysis of longitudinal microbial metabolomics data, which was performed in...

Microbial production host selection for converting second-generation feedstocks into bioproducts

Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates are complex mixtures of different fermentable sugars, but also inhibitors and salts that affect the performance of the microbial production host. The performance of six industrially relevant microorganisms, i.e....

Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources

Metabolomics is an emerging, powerful, functional genomics technology that involves the comparative non-targeted analysis of the complete set of metabolites in an organism. We have set-up a robust quantitative metabolomics platform that allows the analysis of 'snapshot' metabolomes. In this study, we have applied this platform for the...

Microbial metabolomics: Toward a platform with full metabolome coverage

Achieving metabolome data with satisfactory coverage is a formidable challenge in metabolomics because metabolites are a chemically highly diverse group of compounds. Here we present a strategy for the development of an advanced analytical platform that allows the comprehensive analysis of microbial metabolomes. Our approach started with in...