Bacterial Production Research Articles

A Brief Review on the Emerging Role of Bacterial Pigments: From Industrial Uses to Novel Therapeutic Applications

Pigments produced by microorganisms are in high demand due to their safe, non-toxic, and biodegradable characteristics in both industrial and pharmaceutical fields. Using bacteria for pigment production offers several advantages, such as a short life cycle and ease of genetic modification. Numerous studies have highlighted that soil bacteria significantly contribute to the production of coloured pigments as secondary metabolites. Bacterial pigments are well-known for their antimicrobial, antioxidant, and anticancer properties, offering new therapeutic opportunities for the development of novel drugs. However, compared to fungal pigments, most bacterial pigments are still in the research and development stage. Hence, efforts to intensify bacterial pigment production are essential to make them readily available on the market at a low cost for various applications. This review article sheds light on bacterial pigments and their various applications based on the data available in the literature.

How carbon sources drive cellulose synthesis in two Komagataeibacter xylinus strains

Bacterial cellulose synthesis from defined media and waste products has attracted increasing interest in the circular economy context for sustainable productions. In this study, a glucose dehydrogenase-deficient Δgdh K2G30 strain of Komagataeibacter xylinus was obtained from the parental wild type through homologous recombination. Both strains were grown in defined substrates and cheese whey as an agri-food waste to assess the effect of gene silencing on bacterial cellulose synthesis and carbon source metabolism. Wild type K2G30 boasted higher bacterial cellulose yields when grown in ethanol-based medium and cheese whey, although showing an overall higher d-gluconic acid synthesis. Conversely, the mutant Δgdh strain preferred d-fructose, d-mannitol, and glycerol to boost bacterial cellulose production, while displaying higher substrate consumption rates and a lower d-gluconic acid synthesis. This study provides an in-depth investigation of two K. xylinus strains, unravelling their suitability for scale-up BC production.

Calcium Rescues Streptococcus pneumoniae D39 ΔmntE Manganese-Sensitive Growth Phenotype.

Calcium (Ca2+) functions as a universal signal messenger in eukaryotes but in bacteria, the physiological roles for Ca2+ are limited. Here, we examine the role of Ca2+ in Streptococcus pneumoniae during manganese (Mn2+) intoxication. S. pneumoniae mntE mutants, lacking the Mn2+ efflux transporter, exhibit impaired growth due to accumulation of Mn2+ when exposed to elevated exogenous Mn2+. This Mn2+-sensitive growth defect is restored to wild-type growth level by exogenous Ca2+, in a Ca2+-dependent manner. Despite growth restoration of the mntE mutant to wild-type levels, cellular Mn2+ remains elevated in this strain. Bacterial capsule production is also increased for the mntE mutant, resulting in reduced adherence capacity to surfaces and poor biofilm formation, which is consistent with it experiencing Mn2+ intoxication. Ca2+ presence did not significantly impact bacterial capsule production or biofilm formation. Further analysis of the cell morphology demonstrates that Ca2+ contributes to cell division and reduces cell chain lengths. Together, these data describe the first role of Ca in S. pneumoniae that has potential implications in bacterial virulence since Ca affects cell division and likely Mn2+-associated cellular processes.

Negative feedback of cyclic di-GMP levels optimizes switching between sessile and motile lifestyles in Vibrio cholerae.

The signaling molecule cyclic di-GMP (cdG) controls the switch between bacterial motility and biofilm production, and fluctuations in cellular levels of cdG have been implicated in Vibrio cholerae pathogenesis. Intracellular concentrations of cdG are controlled by the interplay of diguanylate cyclase (DGC) enzymes, which synthesize cdG to promote biofilms, and phosphodiesterase (PDE) enzymes, which hydrolyse cdG to drive motility. To track the complete regulatory logic of how V. cholerae responds to changing cdG levels, we followed a timecourse of overexpression of either the V. harveyi diguanylate cyclase QrgB or a variant of QrgB lacking catalytic activity (QrgB*). We find that QrgB increases cdG levels relative to QrgB* for 30 minutes after overexpression, but the effect of QrgB on cdG levels plateaus at 30 minutes, indicating tight adaptive control of cdG levels. In contrast, loss of VpsR, a master regulator activating biofilm formation upon binding to cdG, leads to higher baseline levels of cdG and continuously increasing cdG through 60 minutes after QrgB induction, revealing the existence of a negative feedback loop on cdG levels operating through VpsR. Through a combination of RNA polymerase ChIP-seq, RNA-seq, and genetic approaches, we show that transcription of a gene encoding a PDE, cdgC, is activated by VpsR at high cdG concentrations, mediating this negative feedback on cdG levels. We further identify a transcript encoded within, and antisense to, the cdgC open reading frame which we name sRNA negative regulator of CdgC (SnrC). RNA polymerase ChIP-seq and RNA-seq demonstrate SnrC to be expressed specifically under conditions of high cdG in the absence of VpsR. Ectopic SnrC expression increases cdG levels in a manner dependent on CdgC, demonstrating that its effect on cdG levels is likely through interference with CdgC production. Further, although cells lacking cdgC exhibit enhanced biofilm formation, these mutants are outcompeted by wild type V. cholerae in colonization assays that reward a combination of attachment, dispersal, and motility behaviors. These results underscore the importance of negative feedback regulation of cdG to maintain appropriate homeostatic levels for efficient transitioning between biofilm formation and motility, both of which are necessary over the course of the V. cholerae infection cycle.

In Silico Screening of Sulfonamide Derivatives against Glycolytic Enzymes Reveals Mutation‐Independent Interactions of Sulfisoxazole and Sulfamethazine

AbstractGlycolysis is a highly conserved biochemical process that involves the sequential conversion of glucose to pyruvate and the generation of adenosine triphosphate (ATP), generating energy for cellular functions. This is carried out by several enzymes that play an important role in glucose metabolism. The sulfonamide group of drugs is commonly used as an antibiotic that inhibits the bacterial folic acid production pathway, although its effects on glycolytic enzymes are unclear. Since altered glycolytic enzyme expression is linked to a variety of metabolic disorders as well as cancer, the quest for new ligands against glycolytic enzymes is never over. We revealed that different sulfonamide derivatives interact with glycolytic enzymes with varying binding affinities. Among the selected sulfonamides, sulfisoxazole and sulfamethazine had greater binding scores to certain glycolytic enzymes than others. In silico point mutation analysis predicts that sulfisoxazole and sulfamethazine interact with certain glycolytic enzymes in a residue‐independent manner. This research generates a repository of the 2D interactions of sulfonamide derivatives with glycolytic enzymes, binding energies, impacts of induced point mutations on the local environment, and changes in protein structural flexibility. In the future, sulfisoxazole and sulfamethazine may be repurposed as specific glycolytic enzyme inhibitors to combat a variety of glycolysis‐related metabolic disorders.

Bacterial production of ProTx-I, a gating modifier toxin that inhibits voltage-gated sodium (NaV) and TRPA1 channels

Bacterial production of ProTx-I, a gating modifier toxin that inhibits voltage-gated sodium (NaV) and TRPA1 channels

Staphylococcus aureus lipid factors modulate melanoma cell clustering and invasion.

The microbiome can influence cancer development and progression. However, less is known about the role of the skin microbiota in melanoma. Here, we took advantage of a zebrafish melanoma model to probe the effects of Staphylococcus aureus on melanoma invasion. We found that S. aureus produces factors that enhance melanoma invasion and dissemination in zebrafish larvae. We used a published in vitro 3D cluster formation assay that correlates increased clustering with tumor invasion. S. aureus supernatant increased clustering of melanoma cells and was abrogated by a Rho-Kinase inhibitor, implicating a role for Rho-GTPases. The melanoma clustering response was specific to S. aureus but not to other staphylococcal species, including S. epidermidis. Our findings suggest that S. aureus promotes melanoma clustering and invasion via lipids generated by the lipase Sal2 (officially known as GehB). Taken together, these findings suggest that specific bacterial products mediate melanoma invasive migration in zebrafish.

Isolation and Screening of Tyrosinase Producing Bacteria from Ahmednagar Region

Isolation and Screening of Tyrosinase Producing Bacteria from Ahmednagar Region

Bioengineering Approaches and Novel Biomaterials to Enhance Sternal Wound Healing after Cardiac Surgery: A Crosstalk between Innovation and Surgical Practice.

Median sternotomy and steel wires for sternal closure are the standard approach for cardiac surgery. An incomplete repair associated with chest wall motion, especially in the presence of predisposing factors, can lead to life-threatening deep sternal wound infection, also known as mediastinitis, in 2-5% of cases. Despite current antibiotic and surgical treatments, mediastinitis is associated with a 10-40% mortality rate and a significant increase in morbidity and hospital stay. High mortality and difficult treatment appear to be due to bacterial biofilm, a self-produced extracellular polymeric product that incorporates host tissue and is responsible for the failure of immune defenses and standard antimicrobial therapies. Nanostructures are an effective strategy to enhance the healing process, as they establish a favorable environment for the neosynthesis of the extracellular matrix, supporting tissue development. Synthetic polymers have been proven to exhibit suitable biodegradable and mechanical properties, and their biofunctionalization to enhance cell attachment and interaction with the extracellular matrix is being widely investigated. The use of antibiotic treatments suspended in poly-D,L-lactide and polyethylene oxide and electrospun into nanofibers, or in sponges, has been shown to inhibit bacterial biofilm production. Additionally, growth factors can be incorporated into 3D bioresorbable scaffolds with the aim of constituting a structural and biological framework to organize and expedite the healing process. Therefore, these combined approaches may change the treatment of mediastinitis in the near future.

Infection, inflammation and hepatic encephalopathy from a clinical perspective.

Hepatic encephalopathy (HE) is a syndrome that is associated with both acute and chronic liver injury. It manifests as a wide spectrum of neuropsychological abnormalities, ranging from subtle impairments in executive higher functions observed in cirrhosis, through to coma in acute liver failure. In acute liver failure, the central role of ammonia in the development of brain oedema has remained undisputed for 130 years. It latterly became apparent that infection and inflammation were profound determinants for the development of severe hepatic encephalopathy, associated with the development of cerebral oedema and intracranial hypertension. The relationship of the development of hepatic encephalopathy with blood ammonia levels in cirrhosis is less clear cut and the synergistic interplay of inflammation and infection with ammonia has been identified as being fundamental in the development and progression of hepatic encephalopathy. A perturbed gut microbiome and the presence of an impaired gut epithelial barrier that facilitates translocation of bacteria and bacterial degradation products into the systemic circulation, inducing systemic inflammation and innate and adaptive immune dysfunction, has now become the focus of therapies that treat hepatic encephalopathy in cirrhosis, and may explain why the prebiotic lactulose and rifaximin are efficacious. This review summarises the current clinical perspective on the roles of inflammation and infection in hepatic encephalopathy and presents the evidence base for existing therapies and those in development in the setting of acute and chronic liver failure.

Metabolic-methane mitigation by combination of probiotic Escherichia coli strain Nissle 1917 and biochar in rumen fluid in vitro fermentation of dairy cow

In response to climate change, there have been various trials to reduce methane emissions from ruminant animals in the livestock industry, and one of the typical candidates is probiotics used as feed additives. We employed Escherichia coli Nissle 1917 (EcN) as a promising probiotic for the reduction of methane emissions and investigated the molecular mechanism of methane-reducing effects using CRISPR/Cas9. The anaerobic culture of EcN with biochar (BC) could significantly increase acetate and hydrogen production. Additionally, RNA-seq analysis revealed an upregulation in the expression of acetate synthesis genes, namely, pta, poxB, and ackA. Subsequently, treatment of rumen fluid with EcN significantly decreased methane and increased acetate and propionate production, as observed through the analysis of short-chain fatty acids, and these effects could accelerate with additional supplementation of BC. The observation of changes in the microbial composition of rumen fluid following treatment with EcN and BC was made through rumen metagenomic analysis and RT-qPCR. The results revealed an increase in acetogen and propionate producing bacteria abundance and a decrease in methanogen abundance. Based on these findings, the CRISPR/Cas9 system was employed to elucidate the molecular mechanism of the methane-reducing capability of EcN. Gene deletion was performed targeting the genes poxB, ackA, and pta as key factors in acetate pathway in E. coli. The knockout of poxB, ackA, and pta could lead to the elimination of the methane-reduction of EcN as well as acetate-producing abilities. Collectively, the methane reduction ability of EcN in rumen fluid is associated with its acetate production capability, and the addition of BC significantly enhances methane mitigation capability of EcN.

Microbial Metabolism and Environmental Controls of Acetate Cycling in the Northwest Pacific Ocean

AbstractMicrobial acetate metabolism is an important part of marine carbon cycling. We present a comprehensive study to constrain microbial acetate metabolism and its regulation in surface seawater of the northwest Pacific Ocean. We found that acetate oxidation (rate constant k: 0.016–0.506 day−1) accounted for 77.6%–99.4% of the total microbial acetate uptake, suggesting that acetate was predominantly used as a microbial energy source. Acetate also served as a significant biomass carbon source, as reflected by the elevated contribution of acetate assimilation to bacterial carbon production. Acetate turnover was largely influenced by water mass mixing and nutrient conditions. Atmospheric deposition was a source of acetate in surface water and this process can also impact the microbial acetate uptake. Microbial utilization of acetate could account for up to 25.9% of the bacterial carbon demand, suggesting the significant role of acetate metabolism in microbial carbon cycling in the open ocean.

Constant and fluctuating high temperatures interact with Saharan dust leading to contrasting effects on aquatic microbes over time

Mediterranean lakes are facing heightened exposure to multiple stressors, such as intensified Saharan dust deposition, temperature increases and fluctuations linked to heatwaves. However, the combined impact of dust and water temperature on the microbial community in freshwater ecosystems remains underexplored. To assess the interactive effect of dust deposition and temperature on aquatic microbes (heterotrophic bacteria and phytoplankton), a combination of field mesocosm experiments covering a dust gradient (five levels, 0–320 mg L−1), and paired laboratory microcosms with increased temperature at two levels (constant and fluctuating high temperature) were conducted in a high mountain lake in the Spanish Sierra Nevada, at three points in time throughout the ice-free period. Heterotrophic bacterial production (HBP) increased with dust load regardless of the temperature regime. However, temperature regime affected the magnitude and nature of the interactive Dust×T effect on HBP. Specifically, constant and fluctuating high temperature showed opposing interactive effects in the short term that became additive over time. The relationships between HBP and predictor variables (soluble reactive phosphorus (SRP), excreted organic carbon (EOC), and heterotrophic bacterial abundance (HBA)), coupled with an evaluation of the mechanistic variable photosynthetic carbon use efficiency by bacteria (%CUEb), revealed that bacteria depended on primary production in nearly all treatments when dust was added. The %CUEb increased with dust load in the control temperature treatment, but it was highest at intermediate dust loads under both constant and fluctuating high temperatures. Overall, our results suggest that while dust addition alone strengthens algae-bacteria coupling, high temperatures lead to decoupling in the long term at intermediate dust loads, potentially impacting ecosystem function.

Comparison and characterization of the bacterial microbiota and SIgA production in different gastrointestinal segments in horses

In the gastrointestinal mucosa, there is a close cooperation between secretory immunoglobulin A (SIgA) and the composition of the microbiota, which aims to maintain homeostasis as well as act as a protective barrier. The purpose of this study was to determine the composition of microbiota and SIgA production in different parts of the digestive tract (small intestine, cecum, colon and rectum) of nine healthy horses and its reflection in the feces. For this purpose, we determined: the composition of the microbiome (by next-generation Sequencing of Hypervariable Regions V3-V4 and V7-V9 of the 16 S rRNA gene analysis), the amount of SIgA in the intestinal content samples (by ELISA), as well as the number of IgA-producing cells (IgA+) in the tissue samples (by immohistochemical analysis). Significant differences were observed between the small intestine and the large colon in the composition and diversity of the microbiome, as well as the number of IgA + cells in the mucosal lamina propria and the abundance of SIgA in the intestinal lumen. The small intestine in relation to the large colon is characterised by fewer IgA + cells, more SIgA in the intestinal contents and a less diverse microbiome. However, the cecum appears to be the third separate ecosystem, with a high number of IgA + cells and a diverse microbiome. The fecal sample reflects the current state of the large colon, both in terms of the microbiome and SIgA content; however, it is not known to what extent it may be influenced by dysbiosis in other parts of the digestive tract.

PID Controller Design for an E. coli Fed-Batch Fermentation Process System Using Chaotic Electromagnetic Field Optimization

This paper presents an optimal tuning of a proportional integral differential (PID) controller used to maintain glucose concentration at a desired set point. The PID controller synthesizes an appropriate feed rate profile for an E. coli fed-batch cultivation process. Mathematical models are developed based on dynamic mass balance equations for biomass, substrate, and product concentration of the E. coli BL21(DE3)pPhyt109 fed-batch cultivation for bacterial phytase extracellular production. For model parameter identification and PID tuning, a hybrid metaheuristic technique—chaotic electromagnetic field optimization (CEFO)—is proposed. In the hybridization, a chaotic map is used for the generation of a new electromagnetic particle instead of the electromagnetic field optimization (EFO) search strategy. The CEFO combines the exploitation capability of the EFO algorithm and the exploration power of ten different chaotic maps. The comparison of the results with classical EFO shows the superior behaviour of the designed CEFO. An improvement of 30% of the objective function is achieved by applying CEFO. Based on the obtained mathematical models, 10 PID controllers are tuned. The simulation experiments show that the designed controllers are robust, resulting in a good control system performance. The closed-loop transient responses for the corresponding controllers are similar to the estimated models. The settling time of the control system based on the third PID controller for all estimated models is approximately 9 min and the overshoot is approximately 15%. The proposed CEFO algorithm can be considered an effective methodology for mathematical modelling and achievement of high quality and better performance of the designed closed-loop system for cultivation processes.

Bacterial Porins and Their Procoagulant Role: Implication in the Pathophysiology of Several Thrombotic Complications during Sepsis.

The association between sepsis and thrombotic complications is still not well known. Different mechanisms have been shown to be involved in the sepsis-induced prothrombotic state, but clinical scenarios may differ. In this review, we have summarized the role that bacterial products such as porins and toxins can have in the induction of the prothrombotic state during sepsis and the interaction that they can have with each other. Furthermore, the above-mentioned mechanisms might be involved in the pattern of the clinical presentation of thrombotic events during bacterial sepsis, which would secondarily explain the association between sepsis and venous thromboembolism, the association between sepsis and disseminated intravascular coagulation, and the association between sepsis and microangiopathic venous thromboembolism.

Modulating the Release Kinetics of Natural Product Actinomycin from Bacterial Nanocellulose Films and Their Antimicrobial Activity.

The present study aimed to create a more sustainable and controlled delivery system based on natural biopolymer bacterial nanocellulose (BNC) and bacterial natural product actinomycin (Act), with the applicative potential in the biomedical field. In order to provide improved interaction between BNC and the active compound, and thus to modulate the release kinetics, the TEMPO oxidation of BNC support was carried out. A mix of actinomycins from bacterial fermentation (ActX) were used as natural antimicrobial agents with an established bioactivity profile and clinical use. BNC and TEMPO-oxidized BNC films with incorporated active compounds were obtained and analyzed by FTIR, SEM, XPS, and XRD. The ActX release profiles were determined in phosphate-buffer solution, PBS, at 37 °C over time. FTIR analysis confirmed the improved incorporation and efficiency of ActX adsorption on oxidized BNC due to the availability of more active sites provided by oxidation. SEM analysis indicated the incorporation of ActX into the less-dense morphology of the TEMPO-oxidized BNC in comparison to pure BNC. The release kinetics of ActX were significantly affected by the BNC structure, and the activated BNC sample indicated the sustained release of active compounds over time, corresponding to the Fickian diffusion mechanism. Antimicrobial tests using Staphylococcus aureus NCTC 6571 confirmed the potency of this BNC-based system for biomedical applications, taking advantage of the capacity of modified BNC to control and modulate the release of bioactive compounds.

Insights into Agitated Bacterial Cellulose Production with Microbial Consortia and Agro-Industrial Wastes

Insights into Agitated Bacterial Cellulose Production with Microbial Consortia and Agro-Industrial Wastes

Conditional Optimization of Single Cell Protein Production from Crude Oil by <i>Pseudomonas aeruginosa</i>

The study was carried out to investigate the possible biodegradation of crude oil as a carbon by the bacterium <i>Pseudomonas aeruginosa</i> isolated from marine environment (Ras El-Menkar- Benghazi- Libya) using basal yeast extract protease peptone-3 (BYP) enriched medium. The isolated bacterium was identified and characterized according to its cultural condition and microbial biochemical properties. Different experiments were developed throughout this study to stimulate bacterial growth and production of single cell protein (SCP). The results show that the optimal concentration of crude oil as a carbon source for the highest bacterial growth (1.14g/l), and production of SCP (0.65g/l; 57.02% of the biomass dry weight) was 1%. This was required to utilize up to 50.6% of oil as a carbon source. As to the nitrogen source, the optimal concentration of ammonium chloride was 0.1%, in which the bacterial growth and SCP production increased to 1.23 g/l and 0.67 g/l respectively. The stimulating effects of organic and inorganic factors on the bacterial growth and SCP production was also tested. Addition of inorganic nutrients such as potassium phosphate (0.05%), magnesium sulphate (0.01%), and organic nutrient in the form of yeast extract (0.1%) to the fermentation medium slightly promoted the bacterial growth which reflected positively on SCP production and the percentage of the consumed crude oil, (>57%) at final pH value of 8.0. The obtained results indicated that the isolated<i> Pseudomonas aeruginosa</i> posses the ability to utilize the crude oil and use it as a carbon for bacterial growth and production of SCP.

Bacterial Production of CDKL5 Catalytic Domain: Insights in Aggregation, Internal Translation and Phosphorylation Patterns.

Cyclin-dependent kinase-like 5 (CDKL5) is a serine/threonine protein kinase involved in human brain development and functioning. Mutations in CDKL5, especially in its catalytic domain, cause a severe developmental condition named CDKL5 deficiency disorder. Nevertheless, molecular studies investigating the structural consequences of such mutations are still missing. The CDKL5 catalytic domain harbors different sites of post-translational modification, such as phosphorylations, but their role in catalytic activity, protein folding, and stability has not been entirely investigated. With this work, we describe the expression pattern of the CDKL5 catalytic domain in Escherichia coli demonstrating that it predominantly aggregates. However, the use of solubility tags, the lowering of the expression temperature, the manual codon optimization to overcome an internal translational start, and the incubation of the protein with K+ and MgATP allow the collection of a soluble catalytically active kinase. Interestingly, the resulting protein exhibits hypophosphorylation compared to its eukaryotic counterpart, proving that bacteria are a useful tool to achieve almost unmodified CDKL5. Posing questions about the CDKL5 autoactivation mechanism and the determinants for its stability, this research provides a valuable platform for comparative biophysical studies between bacterial and eukaryotic-expressed proteins, contributing to our understanding of neurodevelopmental disorders associated with CDKL5 dysfunction.