Lene Lange

"BioEconomy Research & Advisory" & associated Technical University of Denmark · "BioEconomy Research & Advisory" & DTU BIO

WO2014169920A2 WIPO (PCT)

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial role...

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering meth...

Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome‐based technologies that provide added‐value solutions. Microbiome research has exp...

Background Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis. Results In this Commentary, we present our...

In addition to challenges like climate change and biodiversity loss, the sustainability and resilience of agrifood systems worldwide are currently challenged by new threats, such as the COVID-19 pandemic and the Ukraine war. Furthermore, the resilience and sustainability of our agrifood systems need to be enhanced in ways that simultaneously increa...

Novel selective enzymatic refining of sweet potato processing residues requires judicious enzyme selection and enzyme discovery. We prepared a pectinaceous cell wall polysaccharide fraction from sweet potato using an enzymatic a treatment to preserve the natural linkages and substitutions. Polysaccharide composition and linkage analysis data confir...

Europe is at the forefront of developing a circular biobased economy, having moved swiftly ahead in the period 2014-2021, backed by the industry-led public private partnership programme, EU BBI-JU (Biobased Industry Joint Undertaking; 3.7 billion Euro). In the EU, the success of BBI-JU provided the foundation for a new vision of a circular biobased...

The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rap...

Confiance, fiabilité, responsabilité, éthique, transparence, rigueur, confidentialité, disponibilité, intégrité : voici quelques mots clefs importants pour parler de la protection des données et de ses enjeux. Concevoir l’avenir de la protection des données dans une économie globalisée et dans un contexte international incertain de guerre et de cri...

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describ...

Enteric methane (CH4) emission from cattle is strongly linked to the feeding regime and the rumen microbial community structure. Here, we report that feed-induced CH4-reducing effects correlate with specific alterations in the profile of the microbiome-encoded carbohydrate-active enzymes predicted from the rumen fluid metagenome. Rumen microbiome s...

The biobased business model, which initiated the era of improved use of the biological resources, upgrading resources otherwise wasted or downgraded, started with the “biomass to biofuel” biorefinery: economy by scale, requiring large investments, and stable supply of high volume, low-cost feedstock. A high-profiled business model for pioneering bi...

The non-spore forming Gram-positive actinomycetes Amycolatopsis keratiniphila subsp. keratiniphila D2T (DSM 44,409) has a high potential for keratin valorization as demonstrated by a novel biotechnological microbial conversion process consisting of a bacterial growth phase and a keratinolytic phase, respectively. Compared to the most gifted keratin...

The efficient bioactivation of CO2provides an alternative new strategy for producing high value chemicals and fuels. Normally,in vitroactivation of CO2can be achieved by using formate dehydrogenase (FDH). However, the CO2solubility and the activity of commercial FDHCb remain a tough challenge for the efficient bioactivation of CO2. Here, we report...

Microbiomes are all around us in natural and cultivated ecosystems, for example, soils, plants, animals and our own body. Microbiomes are essential players of biotechnological applications, and their functions drive human, animal, plant and environmental health. The rapidly developing microbiome research landscape was studied by a global mapping ex...

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Gi...

Rapid transition towards circular, biobased economy includes upscaling current knowledge/technologies and at the same time investing in public/private collaboration for developing biobased technologies. What is ready to be done and where investment is urgently needed can be summarized as follows: Reduction of emissions through improved resource eff...

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of...

How would the European bio-based industrial landscape look now if the Bio-based Industries Joint Undertaking (BBI JU) had not been created? While we obviously cannot know this, today after almost seven years of operation following its creation in 2014, the BBI JU has certainly established a solid reputation for high impact delivery and is driving t...

This paper gives an overview of development of the EU-bioeconomy, 2014–2020. The Vision of the new Circular Bio-based Economy, CBE is presented: Unlocking the full potential of all types of sustainably sourced biomass, crop residues, industrial side-streams, and wastes by transforming it into value-added products. The resulting product portfolio co...

New lysine decarboxylases, combined with the simultaneous cell-treatment and bioconversion processes have great potential in the large-scale production of cadaverine.

Abstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbi...

Keratin is an insoluble fibrous protein from natural environments, which can be recycled to value-added products by keratinolytic microorganisms. A microbial consortium with efficient keratinolytic activity was previously enriched from soil, but the genetic basis behind its remarkable degradation properties was not investigated yet. To identify the...

Microbiome research has consistently been placed in the spotlight over the past two decades, and has shown tremendous promise in the fields of medicine, environmental science, food production, and agriculture. Life on Earth does not exist without microbes, and we may benefit from learning more about them. Yet, there is no common understanding among...

Forward Osmosis (FO) is a promising technology that can offer sustainable solutions in the biorefinery wastewater and desalination fields, via low energy water recovery. However, microbial biomass and organic matter accumulation on membrane surfaces can hinder the water recovery and potentially lead to total membrane blockage. Biofouling developmen...

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula virulence and ecology. Given t...

An amendment to this paper has been published and can be accessed via the original article.

Aspergillus burnettii is a new species belonging to the A. alliaceus clade in Aspergillus subgenus Circumdati section Flavi isolated from peanut-growing properties in southern Queensland, Australia. A. burnettii is a fast-growing, floccose fungus with distinctive brown conidia and is a talented producer of biomass-degrading enzymes and secondary me...

Huge quantities of keratinaceous waste are a substantial and almost totally unexploited protein resource which could be upgraded for use as high value-added products by efficient keratinolytic enzymes. In this study, we found that Bacillus sp. 8A6 can efficiently degrade chicken feather after 24 h growth. According to phylogenetic analysis, the str...

The CUPP platform includes a web server for functional annotation and sub-grouping of carbohydrate active enzymes (CAZymes) based on a novel peptide-based similarity assessment algorithm, i.e. protein grouping according to Conserved Unique Peptide Patterns (CUPP). This online platform is open to all users and there is no login requirement. The web...

Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitat-related substrate utilization. Despite its importance for fitness, enzyme secretome composition is not used in fungal classification, since an overarching relationship between CAZyme profiles and fungal phylogeny/taxonomy has not been established....

In the future bio-based society, leaving the fossil-based era, a wide range of challenges will have to be solved by new biological solutions. Among the core technologies for this transformation are fungal (and bacterial) production of proteins, metabolites and chemicals and biological processing (using microbial enzymes, substituting for chemical p...

This introductory chapter provides an overview of seaweed biorefinery opportunities, providing basis for multiple value chains, contributing to nutrition and health of a growing global population, to local job generation and development, to ecosystem services, and not the least to climate change mitigation and adaptation. A unique and rich diversit...

The New Zealand government has set ambitious goals for primary sector growth and of zero net carbon emissions by 2050. This presents an opportunity and obligation to develop new ideas for grassland production systems to increase export value and generate new job opportunities, while reducing environmental impacts. The aim of this paper is to draw o...

A three catalytic domain multi-enzyme; a CE1 ferulic acid esterase, a GH62 α-L-arabinofuranosidase and a GH10 β-D-1,4-xylanase was identified in a metagenome obtained from wastewater treatment sludge. The capability of the CE1-GH62-GH10 multi-enzyme to degrade arabinoxylan was investigated to examine the hypothesis that CE1-GH62-GH10 would degrade...

Feruloyl esterases (EC 3.1.1.73), belonging to carbohydrate esterase family 1 (CE1), hydrolyze ester bonds between ferulic acid (FA) and arabinose moieties in arabinoxylans. Recently, some CE1 enzymes identified in metagenomics studies have been predicted to contain a family 48 carbohydrate-binding module (CBM48), a CBM family associated with starc...

The secretome, the complement of extracellular proteins, is a reflection of the interaction of an organism with its host or substrate, thus a determining factor for the organism’s fitness and competitiveness. Hence, the secretome impacts speciation and organismal evolution. The zoosporic Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, a...

We set out to investigate the genetic adaptations of the marine fungus Paradendryphiella salina CBS112865 for degradation of brown macroalgae. We performed whole genome and transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina grown on three species of brown algae and under carbon limitation. Genome comparison with c...

ABSTRACT Rhizophlyctis rosea is a ubiquitous, aerobic, zoosporic fungus, typically growing in agricultural soils. Overview is here given on the effects of major abiotic and biotic environmental factors on the growth, development, distribution and survival of R. rosea; and of the diversity, stability and activity of plant cell wall degrading enzyme...

The reversible interconversion of formate (HCOO-) and carbon dioxide (CO2) is catalyzed by formate dehydrogenase (FDH, EC 1.17.1.9). This enzyme can be used as a first step in the utilization of CO2 as carbon substrate for production of high-in-demand chemicals. However, comparison and categorization of the very diverse group of FDH enzymes has rec...

In developing countries, local enzyme production can help decrease the dependency of imported enzymes for bioconversion of e.g. cellulosic feedstocks, but the use of conventional nitrogen sources contributes significantly to such enzyme production cost. Use of local resources is therefore important to consider. Green seaweeds are marine macroalgae...

Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to de...

Background: Insight into the function of carbohydrate-active enzymes is required to understand their biological role and industrial potential. There is a need for better use of the ample genomic data in order to enable selection of the most interesting proteins for further studies. The basis for elaborating a new approach to sequence analysis is t...

The early-lineage, aerobic, zoosporic fungi from the Chytridiomycota constitute less than 1% of the described fungi and can use diverse sources of nutrition from plant or animal products. One of the ancestral sources of fungal nutrition could be products following enzymatic degradation of plant material. However, carbohydrate-active enzymes from th...

Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterise bacterial community compositions and identify biomass-degrading enzymes and the bacterial...

The aim of this study was to elucidate the evolution of enzyme secretome of early lineage fungi to contribute to resolving the basal part of Fungal Kingdom and pave the way for industrial evaluation of their unique enzymes. By combining results of advanced sequence analysis with secretome mass spectrometry and phylogenetic trees, we provide evidenc...

This study examines enzymatic production of linear xylooligosaccharides (XOS) and branched arabinoxylooligosaccharides (AXOS) from monocotyledonous biomass, wheat straw and ryegrass, and compares the in vitro effects of these XOS and AXOS on pig gut microbiota. XOS and AXOS were obtained from the biomass by treatment with different endo-1,4-β-xylan...

Background: More than one third of all food produced globally goes to waste. New biorefining and bio-processing approaches can help make higher value products from many more components of large scale agro- and food processes than previously exploited. If we do not take advantage of such new bioprocessing opportunities we will soon be wasting even m...

Forward osmosis (FO) is a low energy-intensive process since the driving force for water transport is the osmotic pressure difference, Δπ, between the feed and draw solutions, separated by the FO membrane, where πdraw > πfeed. The potential of FO in wastewater treatment and desalination have been extensively studied; however, regeneration of the dr...

Background: The production of ethanol through the biochemical conversion of syngas, a mixture of H2, CO and CO2, has been typically studied using pure cultures. However, mixed microbial consortia may offer a series of benefits such as higher resilience and adaptive capacity, and non-sterile operation, all of which contribute to reducing the utilit...

White-rot basidiomycetous (WRB) fungi are a group of wood-decaying fungi that are known to be endowed with the ability to secrete enzymes that can catalyze decomposition of a range of plant cell wall polysaccharides, including cellulose and lignin. Expression of these enzymes is induced by the substrate and the enzyme yields obtained depend on the...

Many species of zoosporic heterotrophic parasites, saprotrophs and mutualists in the Phyla Perkinsozoa (dinoflagellates), Oomycota, Hyphochytriomycota, Labyrinthulomycota and Phyomyxea share morphological characteristics with zoosporic true fungi especially with some of the Chytridiomycota and with fungus-like organisms in the Phyla Mesomycetozoea,...

The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we...

Fungus-growing termites rely on the mutualistic fungus Termitomyces and gut microbes for plant biomass degradation. Due to a certain degree of symbiont complementarity, this tripartite symbiosis has evolved as a complex bioreactor, enabling decomposition of nearly any plant polymer, likely contributing to the success of the termites as the main pla...

Biocatalysis is important for addressing global challenges: climate change, substitution of fossils, feeding a growing population—basically because bioprocessing in food, feed, and nonfood industries improves resource efficiency, getting more out of the raw biomaterials. Microbial enzymes are the active elements in biocatalysis. Enzymes are specifi...

The "aquatic phycomycetes" constitute an ecologically and economically important assemblage of eukaryotic microorganisms, because they share many morphological traits and important ecological functions and they interact with each other in aquatic ecosystems. The last two decades of research have provided both molecular and structural evidence that...

Backgound: Improved carbohydrate active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs an unique niche to look for...

Globally, animal feed protein is a key factor for production of meat for human consumption. Protein for animal feed is in many parts of the world not available in sufficient amounts; demand is met only through import of feed protein. Such protein deficit can be minimized through optimized use of local protein resources based on upgrade from e.g. gr...

Background Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each family makes it a major task to identify new family members and to provide basis for prediction of enzyme function. A fast and reliabl...