Production Of Certain Metabolites Research Articles

More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities.

Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.

Increasing glycolysis by deletion of kcs1 and arg82 improved S-adenosyl-l-methionine production in Saccharomyces cerevisiae

Reprogramming glycolysis for directing glycolytic metabolites to a specific metabolic pathway is expected to be useful for increasing microbial production of certain metabolites, such as amino acids, lipids or considerable secondary metabolites. In this report, a strategy of increasing glycolysis by altering the metabolism of inositol pyrophosphates (IPs) for improving the production of S-adenosyl-l-methionine (SAM) for diverse pharmaceutical applications in yeast is presented. The genes associated with the metabolism of IPs, arg82, ipk1 and kcs1, were deleted, respectively, in the yeast strain Saccharomyces cerevisiae CGMCC 2842. It was observed that the deletions of kcs1 and arg82 increased SAM by 83.3 % and 31.8 %, respectively, compared to that of the control. In addition to the improved transcription levels of various glycolytic genes and activities of the relative enzymes, the levels of glycolytic intermediates and ATP were also enhanced. To further confirm the feasibility, the kcs1 was deleted in the high SAM-producing strain Ymls1ΔGAPmK which was deleted malate synthase gene mls1 and co-expressed the Acetyl-CoA synthase gene acs2 and the SAM synthase gene metK1 from Leishmania infantum, to obtain the recombinant strain Ymls1Δkcs1ΔGAPmK. The level of SAM in Ymls1Δkcs1ΔGAPmK reached 2.89 g L−1 in a 250-mL flask and 8.86 g L−1 in a 10-L fermentation tank, increasing 30.2 % and 46.2 %, respectively, compared to those levels in Ymls1ΔGAPmK. The strategy of increasing glycolysis by deletion of kcs1 and arg82 improved SAM production in yeast.

The Microbiome and Its Implications in Cancer Immunotherapy.

Cancer is responsible for ~18 million deaths globally each year, representing a major cause of death. Several types of therapy strategies such as radiotherapy, chemotherapy and more recently immunotherapy, have been implemented in treating various types of cancer. Microbes have recently been found to be both directly and indirectly involved in cancer progression and regulation, and studies have provided novel and clear insights into the microbiome-mediated emergence of cancers. Scientists around the globe are striving hard to identify and characterize these microbes and the underlying mechanisms by which they promote or suppress various kinds of cancer. Microbes may influence immunotherapy by blocking various cell cycle checkpoints and the production of certain metabolites. Hence, there is an urgent need to better understand the role of these microbes in the promotion and suppression of cancer. The identification of microbes may help in the development of future diagnostic tools to cure cancers possibly associated with the microbiome. This review mainly focuses on various microbes and their association with different types of cancer, responses to immunotherapeutic modulation, physiological responses, and prebiotic and postbiotic effects.

When do children need kidney replacement therapy?

Kidney replacement therapy (KRT) can provide lifesaving support for children with severely impaired kidney function. The decision about who needs KRT and when is often complex. Many acute kidney problems will resolve with conservative maanagemenent but some children with chronic or acute kidney impairment will find themselves in a position where KRT is required either as a bridge to recovery or kidney transplantation. Less commonly, children with metabolic disorders may find that the ability of their own kidneys is overwhelmed by excessive production of certain metabolites. These children may also benefit from short term KRT. This article aims to help paediatricians in training understand which children need kidney replacement therapy, the various types of treatment available, and when they are used.

In vitro production of some secondary metabolites from Cupressus sempervirens.

Cupressus sempervirens L. has known medicinal activities, which are related to the presence of miscellaneous secondary metabolites, involved in patents for pharmaceuticals and/or cosmetics in the market. The aim of this study is to perform a comparative investigation of the main metabolites in the wild, cultivated and callus cultures of C. sempervirens using different treatments and the in vitro production of certain metabolites from C. sempervirens callus cultures in concentrations adequate for use commercially and also to develop a convenient chromatographic method for both the qualitative and quantitative determination of the most beneficial flavonoids (rutin and quercitrin), along with other metabolites (ferruginol, 2-furancarboxaldehyde,5 methyl, pentadecanoic acid, totarol, quinic acid and hinokiol) using HPLC/DAD and GC/MS, respectively. Leaf extract of the wild plant induced reduction in cell viability of some tested cell lines as: human hepatocellular carcinoma cell (HEPG2), lung carcinoma cell (A549), human Caucasian breast adenocarcinoma (MCF7) and especially on human colon cancer cell (HCT116), which was higher than doxorubicin used as a standard. This study is a stepping stone for obtaining natural and renewable bioactive secondary metabolites from C. sempervirens through in vitro callus cultures.

Current Trends of Rice Milling Byproducts for Agricultural Applications and Alternative Food Production Systems

Rice is one of the most economically important foods in the world today. The FAO has reported that managing rice processing and the resulting byproducts into more sustainable applications would be attractive for a variety of reasons. Rice processing involves several milling stages to produce edible final products. The milling process is the most important step in rice production because it sets the nutritional, cooking, and sensory qualities of crude rice. As crude rice goes through the milling process, it generates byproducts, such as bran, that have been shown to exhibit beneficial impacts on human and animal nutrition. While several rice byproducts have applications in agriculture, rice bran has probably received the most attention for its functional properties. Rice bran is a mixture of protein, fat, ash, and crude fiber. However, rice bran’s composition is largely dependent on the type of rice and the efficiency of the milling system. Based on studies with mice, rice bran has been shown to elicit prebiotic-like properties by preventing colonization of Salmonella in the gastrointestinal tract. More recently, in vitro incubation studies with chicken cecal contents have demonstrated that certain rice varieties are more inhibitory to Salmonella than others. Some of this may be related to impacts on cecal microbiome and production of certain metabolites. In this review, the byproducts of the milling process, how they are utilized, and potential application for conventional and alternative poultry production systems are discussed.

Introducing an Anti-Terminator Paralog Gene to Induce Production of Natural Products in Clostridium Species

Author(s): Leung, Alexander | Abstract: LoaP is a class of proteins that has the potential to induce bacterial species into creating natural products such as antibiotics. LoaP can be placed as an insert into bacterial genomes, where it can potentially drive gene expressions and subsequently activate secondary biosynthetic pathways. Here, a construct was cloned by placing LoaP as an insert into the plasmid of Clostridium beijerinckii. However, this LoaP overexpression strain failed to produce a compound that its wild-type creates. LoaP appeared to decrease production rather than increase production of certain metabolites, as the wild-type strain gave rise to more natural products than the transformant LoaP strain.

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential

BackgroundBlack Aspergilli represent one of the most important fungal resources of primary and secondary metabolites for biotechnological industry. Having several black Aspergilli sequenced genomes should allow targeting the production of certain metabolites with bioactive properties.ResultsIn this study, we report the draft genome of a black Aspergilli, A. tubingensis G131, isolated from a French Mediterranean vineyard. This 35 Mb genome includes 10,994 predicted genes. A genomic-based discovery identifies 80 secondary metabolites biosynthetic gene clusters. Genomic sequences of these clusters were blasted on 3 chosen black Aspergilli genomes: A. tubingensis CBS 134.48, A. niger CBS 513.88 and A. kawachii IFO 4308. This comparison highlights different levels of clusters conservation between the four strains. It also allows identifying seven unique clusters in A. tubingensis G131. Moreover, the putative secondary metabolites clusters for asperazine and naphtho-gamma-pyrones production were proposed based on this genomic analysis. Key biosynthetic genes required for the production of 2 mycotoxins, ochratoxin A and fumonisin, are absent from this draft genome. Even if intergenic sequences of these mycotoxins biosynthetic pathways are present, this could not lead to the production of those mycotoxins by A. tubingensis G131.ConclusionsFunctional and bioinformatics analyses of A. tubingensis G131 genome highlight its potential for metabolites production in particular for TAN-1612, asperazine and naphtho-gamma-pyrones presenting antioxidant, anticancer or antibiotic properties.

Exogenous N-acyl-homoserine lactones enhance the expression of flagella of Pseudomonas syringae and activate defence responses in plants.

In order to cope with pathogens, plants have evolved sophisticated mechanisms to sense pathogenic attacks and to induce defence responses. The N-acyl-homoserine lactone (AHL)-mediated quorum sensing in bacteria regulates diverse physiological processes, including those involved in pathogenicity. In this work, we study the interactions between AHL-producing transgenic tobacco plants and Pseudomonas syringae pv. tabaci 11528 (P. syringae 11528). Both a reduced incidence of disease and decrease in the growth of P. syringae 11528 were observed in AHL-producing plants compared with wild-type plants. The present data indicate that plant-produced AHLs enhance disease resistance against this pathogen. Subsequent RNA-sequencing analysis showed that the exogenous addition of AHLs up-regulated the expression of P. syringae 11528 genes for flagella production. Expression levels of plant defence genes in AHL-producing and wild-type plants were determined by quantitative real-time polymerase chain reaction. These data showed that plant-produced AHLs activated a wide spectrum of defence responses in plants following inoculation, including the oxidative burst, hypersensitive response, cell wall strengthening, and the production of certain metabolites. These results demonstrate that exogenous AHLs alter the gene expression patterns of pathogens, and plant-produced AHLs either directly or indirectly enhance plant local immunity during the early stage of plant infection.

Identifying a gene knockout strategy using a hybrid of the bat algorithm and flux balance analysis to enhance the production of succinate and lactate in Escherichia coli

The current problem for metabolic engineering is how to identify a suitable set of genes for knockout that can improve the production of certain metabolites and sustain the growth rate from the thousands of metabolic networks which are complex and combinatorial. Some approaches, such as OptKnock and OptGene, are developed to enhance the production of desired metabolites. However, the performances of these approaches are suboptimal and the obtained results are unsatisfactory because of computational limitations such as local minima. In this paper, we propose a hybrid of Bat Algorithm and Flux Balance Analysis (BATFBA) to enhance succinate and lactate production by identifying a set of genes for knock out. The Bat Algorithm is an optimisation algorithm, whereas Flux Balance Analysis (FBA) is a mathematical approach to analyse the flow of metabolites through a metabolic network. The Escherichia coli iJR904 dataset was used to determine optimal knockout genes, production rate, and growth rate. By applying this hybrid method to the iJR904 dataset, we found that BATFBA yielded better results than existing methods, such as OptKnock and a hybrid of Artificial Bee Colony algorithms and Flux Balance Analysis (ABCFBA), at predicting succinate and lactate production.

Identification of gene knockout strategies using a hybrid of an ant colony optimization algorithm and flux balance analysis to optimize microbial strains

Reconstructions of genome-scale metabolic networks from different organisms have become popular in recent years. Metabolic engineering can simulate the reconstruction process to obtain desirable phenotypes. In previous studies, optimization algorithms have been implemented to identify the near-optimal sets of knockout genes for improving metabolite production. However, previous works contained premature convergence and the stop criteria were not clear for each case. Therefore, this study proposes an algorithm that is a hybrid of the ant colony optimization algorithm and flux balance analysis (ACOFBA) to predict near optimal sets of gene knockouts in an effort to maximize growth rates and the production of certain metabolites. Here, we present a case study that uses Baker’s yeast, also known as Saccharomyces cerevisiae, as the model organism and target the rate of vanillin production for optimization. The results of this study are the growth rate of the model organism after gene deletion and a list of knockout genes. The ACOFBA algorithm was found to improve the yield of vanillin in terms of growth rate and production compared with the previous algorithms.

Use of Response Surface Methodology to Study the Combined Effect of Salt, pH, and Temperature on the Growth of Food-Spoiling Halotolerant Yeast, Debaryomyces nepalensis NCYC 3413

This paper reports the interaction of salt (NaCl and KCl), initial pH, and temperature and their effects on the specific growth rate and lag phase of food spoiling halotolerant yeast, Debaryomyces nepalensis. The optimization of salt, initial pH, and temperature was carried out using response surface methodology based on central composite design. The mathematical model showed that salt has a significant effect on specific growth rate and lag phase of D. nepalensis. The optimal conditions of salt concentration, pH, and temperature of growth were found to be 0.3 M NaCl, 7.1, 26 °C and 0.6 M KCl, 5.6, 25°C, respectively. Under these conditions, a maximum specific growth rate of 0.41 and 0.5 h−1 was observed in medium containing NaCl and KCl, respectively. Lag phase can be increased most effectively either by increasing salt concentrations or both by decreasing (≤20°C) or increasing the temperature (≥40°C) with moderate (1.5 M) or low salt concentration (0.5 M), respectively. Results show that D. nepalensis need to generate weak acids to maintain the intracellular pH under pH and saline stress conditions. The results obtained in this study will be helpful in using optimal conditions for the maximum growth of the strain for the production of certain metabolites like organic acids and glycerol and designing food preservation procedures.

Characterization of Antagonistic Potential of Trichoderma Spp. against some Soil Borne Plant Pathogens

Ten isolates of Trichoderma spp. isolated from rhizosphere of different crops were evaluated for their antagonistic potential against five soil borne plant pathogens, viz., Rliizoctonia solani, Fusarium oxysporum f sp radicis-lycopersici, Macrophomina phaseolina and Sclerotium rolfsii using dual culture technique and production of volatile and non-volatile antibiotics. Sclerotial antagonism by the biocontrol strains was tested with R. solani and S. rolfsii . The isolate T 2 , T 4 and T 7 against Pythium sp., T 1 , T 7 and T 10 against F. oxysporum f. sp radicislycopersici, T 3 and T 9 against R. solani , T 7 against S. rolfsii and T 6 against M. phaseolina were the most efficient. The highest percentage inhibition of respective pathogen through the production of certain metabolites of Trichoderma isolates was recorded with T 7 against Pythium sp, and Fusarium oxysporum sp. radicis-lycopersici , T 1 against R. solani , T 5 and T 6 against S. rolfsii and T 9 isolate against M. phaseolina . Trichoderma isolate T 9 and T 2 were most effective in inhibition of sclerotia formation, production and germination of sclerotia of R. solani and S. rolfsii , respectively.

Genetic segregation of natural Saccharomyces cerevisiae strains derived from spontaneous fermentation of Aglianico wine.

Investigation of the meiotic segregation of karyotypes and physiological traits in indigenous Saccharomyces strains isolated from Aglianico (South Italy) red wine. Segregation was studied in F1 and F2 descendants. Tetrads were isolated from sporulating cultures by micromanipulation. The spore clones were subjected to karyotype analysis by pulse-field gel electrophoresis (Bio-Rad model CHEF-DR II) and to various physiological tests. Certain chromosomes of the isolates showed 2:2 segregation patterns in F1 but proved to be stable in F2. The ability of cells to utilize maltose also segregated in a 2 : 2 manner in F1 and did not segregate in F2. Resistance to CuSO4, SO2 tolerance, the fermentative power and the production of certain metabolites segregated in both F1 and F2 generations and showed patterns indicating the involvement of polygenic regulation. The analysis revealed a high degree of genetic instability and demonstrated that meiosis can improve chromosomal and genetic stability. Winemaking is critically dependent on the physiological properties and genetic stability of the fermenting Saccharomyces yeasts. Selection of clones from F2 or later generations can be a method of reduction of genetic instability.

Involvement of Soil Microorganisms in the Accelerated Degradation of Diphenamid

Degradation of diphenamid in soil with accelerated degradation and in nontreated control soil and the involvement of soil microorganisms in these processes were investigated. Soil with accelerated degradation and mixed bacterial cultures originating from the same soil degraded diphenamid and its monodemethylated metabolite (diphen M-1) much faster than the control. The bidemethylated derivative (diphen M-2) was degraded much more slowly than diphenamid or diphen M-1. The abundance of fungi capable of degrading diphenamid was similar in the soils with and without accelerated degradation. Degradation of diphenamid by mixed bacterial cultures from a soil with accelerated degradation was much faster than by a culture from nontreated soil and was suppressed by the fungicides thiram and fentin acetate. These two fungicides, as well as the bactericide chloramphenicol, suppressed diphenamid degradation in mixed bacterial cultures. The antifungal cycloheximide and the actinomycete suppressor PCNB did not affect the degradation of diphenamid. Metabolism of14C-diphenamid in a soil with accelerated degradation and in mixed bacterial cultures originating from the same soil showed similarities with regard to evolution of14CO2and production of certain metabolites, while the metabolism of diphenamid byFusarium, which rapidly degrades diphenamid in cultures, was different with regard to the above parameters. This study suggests that development of accelerated degradation in a soil involves a shift in population and/or in activity of microbial degraders in favor of bacteria. It appears that the accelerated degradation occurred by inducing oxidative reaction which involves demethylation of diphenamid.

The effect of intestinal microflora on the enterohepatic circulation of mercapturic acid pathway metabolites.

The metabolism of four xenobiotics, pentachloromethylthiobenzene, 2-chloro-n-iso-propylacetanilide, 2-acetamido-4-(chloromethyl) thiazole and 2,4',5-trichlorobiphenyl, which are known to be metabolized via the mercapturic acid pathway, was examined in germfree and conventional rats. An essential role for the intestinal flora in the metabolism of the above compounds and in the production of certain metabolites was established. Mechanisms for the formation of these latter metabolites from the mercapturates are proposed. These mechanisms involve enterohepatic circulation and metabolism by the intestinal flora. The significance of xenobiotic metabolism by the intestinal microflora is discussed.

Metabolism of progesterone by the term human placenta perfused in-situ

In situ perfusions using labelled progesterone as substrate were carried out in the human term placenta. Rapid metabolism was demonstrated. The major metabolites isolated in radiochemically pure form were 20α-hydroxypregn-4-en-3-one and 6β-hydroxypregn-4-ene-3,20-dione. Another metabolite was identified tentatively as 5β-pregnane-3,20-dione. No C-18 or C-19 steroids were found. Previous hypotheses have stressed the role of the fetus in the production of certain metabolites identified in umbilical cord blood. It is suggested that placenta I production be considered as well.