The Effect of Feeding Strategy on Butanol Production by Clostridium beijerinckii NCIMB 8052 Using Glucose and Xylose

We performed fed-batch fermentations of glucose and xylose mixtures producing butanol. Our aim was to develop a feeding strategy for coping with carbon catabolite repression (CCR) and sequential utilization problems as well as understanding the effect of feeding strategy on fermentation kinetics. Experimental results showed that fermenter 1 with only xylose as the initial carbon source could co-utilize sugars for all mixed sugar feeds. On the other hand, fermenter 2 with only glucose as the initial sugar showed sequential utilization. Xylose in fermenter 2 accumulated while glucose was present; it was only utilized after the glucose was completely exhausted. Besides the sugar utilization profile, the feeding strategy had an impact on the fermentation kinetics. Maximum specific growth rates were 0.68 h-1 and 0.94 h-1, for fermenter 1 and 2,respectively. Fermenter 1 produced 4.98 g/l butanol and yield was 0.28 g/g, while fermenter 2 produced 0.5 g/l butanol with a yield value of 0.05 g/g. Total sugar utilization was also higher for fermenter 1, 81 % and 46 % for fermenter 2. The feeding strategy we proposed showed that wild type Clostridium beijerinckii NCIMB 8052 can co-utilize glucose and xylose, and produce butanol. Our observation suggests that we can tackle sequential utilization problem and enhance fermentation process with the proposed feeding strategy without having to manipulate the strain.publishedVersio

Response Surface Methodology for Understanding Glucose and Xylose Utilization by Clostridium beijerinckii NCIMB 8052

We applied response surface methodology to understand the effect and extend of carbon catabolite repression (CCR) on growth of Clostridium beijerinckii NCIMB 8052 using xylose and glucose as representative lignocellulosic sugars. We performed batch growth experiments based on the central composite design with different concentrations of glucose and xylose, and estimated the respective growth rates as the response. Fitting the quadratic model with interaction coefficient to experimental data gave a good quality of fit (R-squared=0.939). We found that glucose is the most significant factor affecting the growth rate. Interaction between glucose and xylose is another highly significant factor. Response surface illustrated that increasing or decreasing both sugar concentrations at the same time results in a decreasing growth rate, and increasing either sugar concentration while decreasing the other sugar increases the growth rate. It is an important finding as it suggests that CCR can be not only from glucose on xylose but also from xylose on glucose. A transcriptional study will be necessary to understand the repression mechanism and to improve the utilization of sugars in mixed form, thus lignocellulosic fermentation processes.publishedVersio

Kinetic Study of Butanol Production from Mixtures of Glucose and Xylose and Investigation of Different Pre-growth Strategies

This study proposes a dynamic model that describes key characteristics of fermentative butanol production from glucose and xylose mixtures. The model has 12 parameters and incorporates noncompetitive inhibitory interaction between sugars as well as inhibitions due to high substrate and butanol concentrations. Different pre-growth strategies to achieve co-utilization of sugars were explored together with their effects on fermentation kinetics. Mixed sugar fermentation by the cultures pre-grown on a mixture of glucose and xylose showed a higher endurance to inhibition, a 2-fold increase in butanol production and a 1.5-fold increase in total sugar consumption compared to cultures pre-grown on xylose only. The average squared correlation coefficients (r2) between experimental observations and model predictions were 0.917 and 0.926 for fermentations done by the cultures pre-grown on xylose only, and pre-grown on a mixture of glucose and xylose, respectively. Sensitivity analysis on the model parameters revealed that the growth parameters were the most critical. The proposed model can serve as a basis for modeling of microbial butanol production from lignocellulosic biomass and be applied to other substrates and microorganisms. © 2019(32 refs)acceptedVersio

Modeling the Growth of Clostridium beijerinckii NCIMB 8052 on Lignocellulosic Sugars

To our knowledge, this is the first growth model of Clostridium beijerinckii NCIMB 8052 on glucose and xylose as representative lignocellulosic sugars, which considers the synergistic effects of sugars on the growth rate. We fitted models with different types of interactions between the substrates to the growth rate data obtained with varying sugar concentrations. Noncompetitive binary substrate growth model gave the best fit with the smallest mean standard errors (MSE), and sum of squares error (SSE), 0.0778 and 0.0071, respectively. Confidence intervals for the parameter estimates showed that the substrate affinity constant for xylose, KsX (g/l) had the largest uncertainty, while the maximum specific growth rate on xylose, µmaxX (h-1) had the smallest. The correlation matrix showed that the model parameters were highly correlated. Carbon cataboliterepression (CCR) effect on the growth rate was of the noncompetitive type. Validation with other sugar concentration values is necessary to evaluate the prediction capability of the proposed model. A transcriptional study will be beneficial to understand global gene regulation mechanisms as guidance for improving the efficiency of lignocellulosic fermentation processes.publishedVersio

Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2)

Background: Systems biology approaches to study metabolic switching in Streptomyces coelicolor A3(2) depend on cultivation conditions ensuring high reproducibility and distinct phases of culture growth and secondary metabolite production. In addition, biomass concentrations must be sufficiently high to allow for extensive time-series sampling before occurrence of a given nutrient depletion for transition triggering. The present study describes for the first time the development of a dedicated optimized submerged batch fermentation strategy as the basis for highly time-resolved systems biology studies of metabolic switching in S. coelicolor A3(2). Results: By a step-wise approach, cultivation conditions and two fully defined cultivation media were developed and evaluated using strain M145 of S. coelicolor A3(2), providing a high degree of cultivation reproducibility and enabling reliable studies of the effect of phosphate depletion and L-glutamate depletion on the metabolic transition to antibiotic production phase. Interestingly, both of the two carbon sources provided, D-glucose and L-glutamate, were found to be necessary in order to maintain high growth rates and prevent secondary metabolite production before nutrient depletion. Comparative analysis of batch cultivations with (i) both L-glutamate and D-glucose in excess, (ii) L-glutamate depletion and D-glucose in excess, (iii) L-glutamate as the sole source of carbon and (iv) D-glucose as the sole source of carbon, reveal a complex interplay of the two carbon sources in the bacterium's central carbon metabolism. Conclusions: The present study presents for the first time a dedicated cultivation strategy fulfilling the requirements for systems biology studies of metabolic switching in S. coelicolor A3(2). Key results from labelling and cultivation experiments on either or both of the two carbon sources provided indicate that in the presence of D-glucose, L-glutamate was the preferred carbon source, while D-glucose alone appeared incapable of maintaining culture growth, likely due to a metabolic bottleneck at the oxidation of pyruvate to acetyl-CoA

Health benefits of microalgae and their microbiomes

Microalgae comprise a phylogenetically very diverse group of photosynthetic unicellular pro- and eukaryotic organisms growing in marine and other aquatic environments. While they are well explored for the generation of biofuels, their potential as a source of antimicrobial and prebiotic substances have recently received increasing interest. Within this framework, microalgae may offer solutions to the societal challenge we face, concerning the lack of antibiotics treating the growing level of antimicrobial resistant bacteria and fungi in clinical settings. While the vast majority of microalgae and their associated microbiota remain unstudied, they may be a fascinating and rewarding source for novel and more sustainable antimicrobials and alternative molecules and compounds. In this review, we present an overview of the current knowledge on health benefits of microalgae and their associated microbiota. Finally, we describe remaining issues and limitation, and suggest several promising research potentials that should be given attention.publishedVersio

Rabies virus uniquely reprograms the transcriptome of human monocyte-derived macrophages

Macrophages are amongst the first immune cells that encounter rabies virus (RABV) at virus entry sites. Activation of macrophages is essential for the onset of a potent immune response, but insights into the effects of RABV on macrophage activation are scarce. In this study we performed high-throughput sequencing on RNA extracted from macrophages that were exposed to RABV for 48 hours, and compared their transcriptional profiles to that of non-polarized macrophages (M0), and macrophages polarized towards the canonical M1, M2a and M2c phenotypes. Our analysis revealed that RABV-stimulated macrophages show high expression of several M1, M2a and M2c signature genes. Apart from their partial resemblance to these phenotypes, unbiased clustering analysis revealed that RABV induces a unique and distinct polarization program. Closer examination revealed that RABV induced multiple pathways related to the interferon- and antiviral response, which were not induced under other classical polarization strategies. Surprisingly, our data show that RABV induces an activated rather than a fully suppressed macrophage phenotype, triggering virus-induced activation and polarization. This includes multiple genes with known antiviral (e.g. APOBEC3A, IFIT/OAS/TRIM genes), which may play a role in anti-RABV immunity.</p

Electrodynamics of balanced charges

In this work we modify the wave-corpuscle mechanics for elementary charges introduced by us recently. This modification is designed to better describe electromagnetic (EM) phenomena at atomic scales. It includes a modification of the concept of the classical EM field and a new model for the elementary charge which we call a balanced charge (b-charge). A b-charge does not interact with itself electromagnetically, and every b-charge possesses its own elementary EM field. The EM energy is naturally partitioned as the interaction energy between pairs of different b-charges. We construct EM theory of b-charges (BEM) based on a relativistic Lagrangian with the following properties: (i) b-charges interact only through their elementary EM potentials and fields; (ii) the field equations for the elementary EM fields are exactly the Maxwell equations with proper currents; (iii) a free charge moves uniformly preserving up to the Lorentz contraction its shape; (iv) the Newton equations with the Lorentz forces hold approximately when charges are well separated and move with non-relativistic velocities. The BEM theory can be characterized as neoclassical one which covers the macroscopic as well as the atomic spatial scales, it describes EM phenomena at atomic scale differently than the classical EM theory. It yields in macroscopic regimes the Newton equations with Lorentz forces for centers of well separated charges moving with nonrelativistic velocities. Applied to atomic scales it yields a hydrogen atom model with a frequency spectrum matching the same for the Schrodinger model with any desired accuracy.Comment: Manuscript was edited to improve the exposition and to remove noticed typo

Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity

Moghadam MS, Albersmeier A, Winkler A, et al. Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity. BMC Genomics. 2016;17(1): 117

Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord

Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01T , was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269T (98.3%). Predominant fatty acids were C16V0 iso, C16V0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, hosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G C C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01T D CCM 9049T D DSM 111582T ) is proposed.publishedVersio