Effect of elevated oxygen concentration on bacteria, yeasts, and cells propagated for production of biological compounds

Relevance of the Adjuvant Effect between Cellular Homeostasis and Resistance to Antibiotics in Gram-Negative Bacteria with Pathogenic Capacity: A Study of Klebsiella pneumoniae

Antibiotic resistance has become a global issue. The most significant risk is the acquisition of these mechanisms by pathogenic bacteria, which can have a severe clinical impact and pose a public health risk. This problem assumes that bacterial fitness is a constant phenomenon and should be approached from an evolutionary perspective to develop the most appropriate and effective strategies to contain the emergence of strains with pathogenic potential. Resistance mechanisms can be understood as adaptive processes to stressful conditions. This review examines the relevance of homeostatic regulatory mechanisms in antimicrobial resistance mechanisms. We focus on the interactions in the cellular physiology of pathogenic bacteria, particularly Gram-negative bacteria, and specifically Klebsiella pneumoniae. From a clinical research perspective, understanding these interactions is crucial for comprehensively understanding the phenomenon of resistance and developing more effective drugs and treatments to limit or attenuate bacterial sepsis, since the most conserved adjuvant phenomena in bacterial physiology has turned out to be more optimized and, therefore, more susceptible to alterations due to pharmacological action.

Elucidating the pivotal role of TSPO in porphyrin-related cellular processes, in Bacillus cereus

A structural homolog of the mammalian TSPO has been identified in the human pathogen Bacillus cereus. BcTSPO, in its recombinant form, has previously been shown to bind and degrade porphyrins. In this study, we generated a ΔtspO mutant strain in B. cereus ATCC 14579 and assessed the impact of the absence of BcTSPO on cellular proteomics and physiological characteristics. The proteomic analysis revealed correlations between the lack of BcTSPO and the observed growth defects, increased oxygen consumption, ATP deficiency, heightened tryptophan catabolism, reduced motility, and impaired biofilm formation in the ΔtspO mutant strain. Our results also suggested that BcTSPO plays a crucial role in regulating intracellular levels of metabolites from the coproporphyrin-dependent branch of the heme biosynthetic pathway. This regulation potentially underlies alterations in the metabolic landscape, emphasizing the pivotal role of BcTSPO in B. cereus aerobic metabolism. Notably, our study unveils, for the first time, the involvement of TSPO in tryptophan metabolism. These findings underscore the multifaceted role of TSPO, not only in metabolic pathways but also potentially in the microorganism's virulence mechanisms.

Oxygen-driven divergence of marine group II archaea reflected by transitions of superoxide dismutases

IMPORTANCE

Reactive oxygen species (ROS), including superoxide anion, is a series of substances that cause oxidative stress for all organisms. Marine group II (MGII) archaea are mainly live in the surface seawater and exposed to considerable ROS. Therefore, it is important to understand the antioxidant capacity of MGII. Our research found that Fe/Mn- superoxide dismutase (Fe/MnSOD) may be more suitable for MGII to resist oxidative damage, and the changes in oxygen concentrations and SOD metallic cofactors play an important role in the selection of SOD by the 17 clades of MGII, which in turn affects the species differentiation of MGII. Overall, this study provides insight into the co-evolutionary history of these uncultivated marine archaea with the earth system.

ABACO-2: a comprehensive model for microalgae-bacteria consortia validated outdoor at pilot-scale

Modelling microalgae-bacteria in wastewater treatment systems has gained significant attention in the last few years. In this study, we present an enhanced version of the ABACO model, named ABACO-2, which demonstrates improved accuracy through validation in outdoor pilot-scale systems. ABACO-2 enables the comprehensive characterization of microalgae-bacteria consortia dynamics, allowing to predict the biomass concentration (microalgae, heterotrophic bacteria, and nitrifying bacteria) and nutrient evolution. The updated version of the model incorporates new equations for nutrient coefficient yields, oxygen mass balance, and microorganism cellular decay, while significantly reducing the number of calibrated parameters, simplifying the parameter identification. Calibration and validation were performed using data from a 80 m2 raceway reactor operated in a semicontinuous mode over an extensive period (May to November, total of 206 days) at a fixed dilution rate of 0.2 day-1 (corresponding to 5 days of hydraulic retention time), where untreated urban wastewater was used as culture medium. ABACO-2 exhibited robustness, accurately forecasting biomass production, population dynamics, nutrient recovery, and prevailing culture conditions across a wide range of environmental and water composition conditions. Mathematical models are essential instruments for the industrial development and optimization of microalgae-related wastewater treatment processes, thereby contributing to the sustainability of the wastewater treatment industry.

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

BACKGROUND

Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS

Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS

Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS

The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.

The Effect of Plasma-Treated Water on Microbial Growth and Biosynthesis of Gamma-Decalactones by Yarrowia lipolytica Yeast

In recent years, the production of plasma-treated water (PTW) by low-temperature low-pressure glow plasma (LPGP) has been increasingly gaining in popularity. LPGP-treated water changes its physical and physiochemical properties compared to standard distilled water. In this study, a non-conventional lipolytic yeast species Yarrowia lipolytica was cultivated in culture media based on Nantes plasma water with heightened singlet oxygen content (Nantes PW) or in water treated with low-temperature, low-pressure glow plasma while in contact with air (PWTA) or nitrogen (PWTN). The research aimed to assess the influence of culture conditions on castor oil biotransformation to gamma-decalactone (GDL) and other secondary metabolites in media based on nanowater. The Nantes plasma water-based medium attained the highest concentration of gamma-decalactone (4.81 ± 0.51 g/L at 144 h of culture), maximum biomass concentration and biomass yield from the substrate. The amplified activity of lipases in the nanowater-based medium, in comparison to the control medium, is encouraging from the perspective of GDL biosynthesis, relying on the biotransformation of ricinoleic acid, which is the primary component of castor oil. Although lipid hydrolysis was enhanced, this step seemed not crucial for GDL concentration. Interestingly, the study validates the significance of oxygen in β-oxidation enzymes and its role in the bioconversion of ricinoleic acid to GDL and other lactones. Specifically, media with higher oxygen content (WPTA) and Nantes plasma water resulted in remarkably high concentrations of four lactones: gamma-decalactone, 3-hydroxy-gamma-decalactone, dec-2-en-4-olide and dec-3-en-4-olide.

Enhanced production of N-acetyl-glucosaminidase by marine Aeromonas caviae CHZ306 in bioreactor

N-Acetyl-glucosaminidases (GlcNAcases) are exoenzymes found in a wide range of living organisms, which have gained great attention in the treatment of disorders related to diabetes, Alzheimer's, Tay-Sachs', and Sandhoff's diseases; the control of phytopathogens; and the synthesis of bioactive GlcNAc-containing products. Aiming at future industrial applications, in this study, GlcNAcase production by marine Aeromonas caviae CHZ306 was enhanced first in shake flasks in terms of medium composition and then in bench-scale stirred-tank bioreactor in terms of physicochemical conditions. Stoichiometric balance between the bioavailability of carbon and nitrogen in the formulated culture medium, as well as the use of additional carbon and nitrogen sources, played a central role in improving the bioprocess, considerably increasing the enzyme productivity. The optimal cultivation medium was composed of colloidal α-chitin, corn steep liquor, peptone A, and mineral salts, in a 5.2 C:N ratio. Optimization of pH, temperature, colloidal α-chitin concentration, and kLa conditions further increased GlcNAcase productivity. Under optimized conditions in bioreactor (i.e., 34 °C, pH 8 and kLa 55.2 h-1), GlcNAcase activity achieved 173.4 U.L-1 after 12 h of cultivation, and productivity no less than 14.45 U.L-1.h-1 corresponding to a 370-fold enhancement compared to basal conditions.

Sustainable production and pharmaceutical applications of β-glucan from microbial sources

β-glucans are a large class of complex polysaccharides found in abundant sources. Our dietary sources of β-glucans are cereals that include oats and barley, and non-cereal sources can consist of mushrooms, microalgae, bacteria, and seaweeds. There is substantial clinical interest in β-glucans; as they can be used for a variety of diseases including cancer and cardiovascular conditions. Suitable sources of β-glucans for biopharmaceutical applications include bacteria, microalgae, mycelium, and yeast. Environmental factors including culture medium can influence the biomass and ultimately β-glucan content. Therefore, cultivation conditions for the above organisms can be controlled for sustainable enhanced production of β-glucans. This review discusses the various sources of β-glucans and their cultivation conditions that may be optimised to exploit sustainable production. Finally, this article discusses the immune-modulatory potential of β-glucans from these sources.

Remediation of metals and plastic from e-waste by iron mine indigenous acidophilic bacteria

The growing consumption of electrical and electronic equipment leads to high amounts of electronic waste (e-waste), which is now considered the fastest-growing waste stream at the national and international levels. As well as being a potential secondary resource due to its precious metals content, e-waste also contains strategic metals and plastics. For instance, mobile phones have about 25-55% plastic substances. A few studies have been performed to investigate the potential of indigenous bacteria in metals' bioleaching from the polluted environment. Heterotrophic bioleaching potential in acidic conditions had been preliminarily investigated. Two soil types of iron ore were considered the source of indigenous bacteria. Despite the acidophilic nature of the bacterial consortium, they continued their leaching activity regardless of alkaline conditions. Maximum biorecovery rate related to copper (4%) responding to the main soil, owing to the higher copper content of mobile phone waste. Chromium had the least recovery rate (⩽0.002%). Overall, the maximum metal recovery rate was 4.7%, achieved by tailing heterotrophs at an e-waste loading of 10 g l^-1. Statistical analysis had shown that there was no significant difference between the metal recovery rates and soil type or even the solid-liquid ratio (p > 0.05). Although acidophilic indigenous heterotrophs could not be an appropriate alternative for a large amount of metal recovery process, they might have considerable potential in the bioremediation of e-waste plastic fractions and metals in low concentrations simultaneously.

Introducing heterotrophic iron ore bacteria as new candidates in promoting the recovery of e-waste strategic metals

Electrical instruments are an integral part of human life resulting in a vast electronic waste generation (74.7 Mt by 2030), threatening human life and the environment due to its hazardous nature. Therefore, proper e-waste management is a necessity. Currently, bio-metallurgy is a sustainable process and an emerging research field. Simultaneous leaching of metals using two groups of indigenous heterotrophs and autotrophs was an exciting work done in this study. Bioleaching experiments using pre-adapted cultures were investigated at three e-waste densities: 5, 10, and 15 g/L. Statistical analysis was done using two-way ANOVA. Copper (93%), zinc (21.5%), and nickel (10.5%) had the highest recovery efficiencies. There was a significant difference between copper, nickel, tin, and zinc concentrations and the bacterial group (P < 0.05); Iron-oxidizing bacteria showed the most weight decrease and recovered 46-47% of total metals, mainly copper and nickel, while sulfur oxidizers were more capable of zinc leaching. The heterotrophs solubilized tin preferably and substantially decreased e-waste weight. Using heterotrophs alongside autotrophs is proposed to promote metal recovery.

The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies

Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO₃, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.

Formation, application, and storage-reactivation of aerobic granular sludge: A review

It was an important discovery in wastewater treatment that the microorganisms in the traditional activated sludge can form aerobic granular sludge (AGS) by self-aggregation under appropriate water quality and operation conditions. With a typical three-dimensional spherical structure, AGS has high sludge-water separation efficiency, great treatment capacity, and strong tolerance to toxic and harmful substances, so it has been considered to be one of the most promising wastewater treatment technologies. This paper comprehensively reviewed AGS from multiple perspectives over the past two decades, including the culture conditions, granulation mechanisms, metabolic and structural stability, storage, and its diverse applications. Some important issues, such as the reproducibility of culture conditions and the structural and functional stability during application and storage, were also summarized, and the research prospects were put forward. The aggregation behavior of microorganisms in AGS was explained from the perspectives of physiology and ecology of complex populations. The storage of AGS is considered to have large commercial potential value with the increase of large-scale applications. The purpose of this paper is to provide a reference for the systematic and in-depth study on the sludge aerobic granulation process.

Iron availability enhances the cellular energetics of aerobic Escherichia coli cultures while upregulating anaerobic respiratory chains

Aerobic Escherichia coli growth at restricted iron concentrations (≤ 1.75 ± 0.04 μM) is characterized by lower biomass yield, higher acetate accumulation and higher activation of the siderophore iron-acquisition systems. Although iron homeostasis in E. coli has been studied intensively, previous studies focused only on understanding the regulation of the iron import systems and the iron-requiring enzymes. Here, the effect of iron availability on the energy metabolism of E. coli has been investigated. It was established that aerobic cultures growing under limiting iron conditions showed lower ATP yield per glucose, lower growth rate and lower TCA cycle activity and respiration, at the same time as increased glucose consumption, acetate and pyruvate accumulation, practically mimicking microaerobic growth. However, at excess iron, independent of oxygen availability, the cultures showed high cellular energetics (5.8 ATP/mol of glucose) by using pathways requiring iron-rich complex proteins found in the TCA cycle and respiratory chain. In conditions of iron excess, some iron-requiring terminal reductases of the respiratory chain, that were thought to function only under anaerobiosis, were used by the E. coli, when in aerobic conditions, to maintain high respiratory activity. This allowed it to produce more biomass and more reactive oxygen species that were controlled by the higher activity of the antioxidant defenses (SOD, peroxidase and catalase) and the iron-sulfur cluster repair systems.

Evaluation of the Growth-Inhibitory Spectrum of Three Types of Cyanoacrylate Nanoparticles on Gram-Positive and Gram-Negative Bacteria

The development of novel effective antibacterial agents is crucial due to increasing antibiotic resistance in various bacteria. Poly (alkyl cyanoacrylate) nanoparticles (PACA-NPs) are promising novel antibacterial agents as they have shown antibacterial activity against several Gram-positive and Gram-negative bacteria. However, the antibacterial mechanism remains unclear. Here, we compared the antibacterial efficacy of ethyl cyanoacrylate nanoparticles (ECA-NPs), isobutyl cyanoacrylate NPs (ⁱBCA-NPs), and ethoxyethyl cyanoacrylate NPs (EECA-NPs) using five Gram-positive and five Gram-negative bacteria. Among these resin nanoparticles, ECA-NPs showed the highest growth inhibitory effect against all the examined bacterial species, and this effect was higher against Gram-positive bacteria than Gram-negative. While ⁱBCA-NP could inhibit the cell growth only in two Gram-positive bacteria, i.e., Bacillus subtilis and Staphylococcus aureus, it had negligible inhibitory effect against all five Gram-negative bacteria examined. Irrespective of the differences in growth inhibition induced by these three NPs, N-acetyl-L-cysteine (NAC), a well-known reactive oxygen species (ROS) scavenger, efficiently restored growth in all the bacterial strains to that similar to untreated cells. This strongly suggests that the exposure to NPs generates ROS, which mainly induces cell growth inhibition irrespective of the difference in bacterial species and cyanoacrylate NPs used.

Hyperglycemia and steroid use increase the risk of rhino-orbito-cerebral mucormycosis regardless of COVID-19 hospitalization: Case-control study, India

Background

In the ongoing COVID-19 pandemic, an increased incidence of ROCM was noted in India among those infected with COVID. We determined risk factors for rhino-orbito-cerebral mucormycosis (ROCM) post Coronavirus disease 2019 (COVID-19) among those never and ever hospitalized for COVID-19 separately through a multicentric, hospital-based, unmatched case-control study across India.

Methods

We defined cases and controls as those with and without post-COVID ROCM, respectively. We compared their socio-demographics, co-morbidities, steroid use, glycaemic status, and practices. We calculated crude and adjusted odds ratio (AOR) with 95% confidence intervals (CI) through logistic regression. The covariates with a p-value for crude OR of less than 0·20 were considered for the regression model.

Results

Among hospitalised, we recruited 267 cases and 256 controls and 116 cases and 231 controls among never hospitalised. Risk factors (AOR; 95% CI) for post-COVID ROCM among the hospitalised were age 45–59 years (2·1; 1·4 to 3·1), having diabetes mellitus (4·9; 3·4 to 7·1), elevated plasma glucose (6·4; 2·4 to 17·2), steroid use (3·2; 2 to 5·2) and frequent nasal washing (4·8; 1·4 to 17). Among those never hospitalised, age ≥ 60 years (6·6; 3·3 to 13·3), having diabetes mellitus (6·7; 3·8 to 11·6), elevated plasma glucose (13·7; 2·2 to 84), steroid use (9·8; 5·8 to 16·6), and cloth facemask use (2·6; 1·5 to 4·5) were associated with increased risk of post-COVID ROCM.

Conclusions

Hyperglycemia, irrespective of having diabetes mellitus and steroid use, was associated with an increased risk of ROCM independent of COVID-19 hospitalisation. Rational steroid usage and glucose monitoring may reduce the risk of post-COVID.

High Cell Density Cultivation of Paracoccus sp. on Sugarcane Juice for Poly(3-hydroxybutyrate) Production

High cell density cultivation is a promising approach to reduce capital and operating costs of poly (3-hydroxybutyrate) (PHB) production. To achieve high cell concentration, it is necessary that the cultivation conditions are adjusted and controlled to support the best growth of the PHB producer. In the present study, carbon to nitrogen (C/N) ratio of a sugarcane juice (SJ)-based medium, initial sugar concentration, and dissolved oxygen (DO) set point, were optimized for batch cultivation of Paracoccus sp. KKU01. A maximum biomass concentration of 55.5 g/L was attained using the C/N ratio of 10, initial sugar concentration of 100 g/L, and 20% DO set point. Fed-batch cultivation conducted under these optimum conditions, with two feedings of SJ-based medium, gave the final cell concentration of 87.9 g/L, with a PHB content, concentration, and yield of 36.2%, 32.1 g/L, and 0.13 g/g-sugar, respectively. A medium-based economic analysis showed that the economic yield of PHB on nutrients was 0.14. These results reveal the possibility of using SJ for high cell density cultivation of Paracoccus sp. KKU01 for PHB production. However, further optimization of the process is necessary to make it more efficient and cost-effective.

Respirometric assessment of bacterial kinetics in algae-bacteria and activated sludge processes

Algae-bacteria (AB) consortia can be exploited for effective wastewater treatment, based on photosynthetic oxygenation to reduce energy requirements for aeration. While algal kinetics have been extensively evaluated, bacterial kinetics in AB systems are still based on parameters taken from the activated sludge models, lacking an experimental validation for AB consortia. A respirometric procedure was therefore proposed, to estimate bacterial kinetics in both activated sludge and AB, under different conditions of temperature, pH, dissolved oxygen, and substrate availability. Bacterial activities were differently influenced by operational/environmental conditions, suggesting that the adoption of typical activated sludge parameters could be inadequate for AB modelling. Indeed, respirometric results show that bacteria in AB consortia were adapted to a wider range of conditions, compared to activated sludge, confirming that a dedicated calibration of bacterial kinetics is essential for effectively modelling AB systems, and respirometry was proven to be a powerful and reliable tool to this purpose.

Effect of Processing Treatment and Modified Atmosphere Packing on Carrot's Microbial Community Structure by Illumina MiSeq Sequencing

The aim of this study was to analyze the microbiome of carrot (Daucus carota subsp. sativus) subjected to minimal pre-treatment (rinsing in organic acid solution) and packaging in a high-oxygen modified atmosphere, and then stored for 17 days under refrigeration conditions (4 °C). The highest levels of bacteria in the carrot microbiome were characterized, at almost 78%, by bacteria belonging to the Enterobacteriaceae and Pseudomonadaceae families. Rinsing in a solution of ascorbic and citric acids resulted in the improvement of microbiological quality in the first day of storage. However, the use of a high-oxygen modified atmosphere extended the shelf life of the minimally processed product. Compared to carrots stored in air, those stored in high oxygen concentration were characterized by a greater ratio of bacteria belonging to the Serratia and Enterobacter genera, and a lower ratio belonging to the Pseudomonas and Pantoea genera. Moreover, the β-biodiversity analysis confirmed that the oxygen concentration was the main factor influencing the differentiation of the metabiomes of the stored carrots. The bacterial strains isolated from carrots identified by molecular methods were mostly pathogenic or potentially pathogenic microorganisms. Neither the minimal pre-treatment nor packaging in high-oxygen atmosphere was able to eliminate the threat of pathogenic bacteria emerging in the product.

Effect of sunlight and salinity on the survival of pathogenic and non-pathogenic strains of Vibrio parahaemolyticus in water microcosms

The effect of sunlight and salinities (10, 20, 39, and 60 psu) on the survival of Vibrio parahaemolyticus strains carrying either (thermostable direct hemolysin) tdh, the (thermostable related hemolysin) trh, and both or none of them were studied in water microcosms stabilized at 20°C using plate count agar and acridine orange direct viable count. All V. parahaemolyticus strains exposed to sunlight rapidly lose their culturability and evolve into a viable but non-culturable state (VBNC). However, the tdh positive strains remain more culturable than the non-virulent or trh positive strain but statically insignificant. At tested salinities, the survival time was higher at 10, 20, and 60 psu compared with that observed in seawater (39 psu). In seawater under dark condition, Vibrio strains remain culturable for up to 200 days with a significant difference between strains (p < 0.05). Furthermore, the non-pathogenic strain survives longer than the virulent ones. At different salinities, a better adaptation is observed at 10 and 20 psu compared with 39 and 60 psu. Resuscitations essays performed on VBNC bacteria in a nutrient broth at 20°C and 37°C does not show any revivification. PRACTITIONER POINTS: Effect of sunlight and salinities on the survival of V. parahaemolyticus in the marine environment. Resuscitation essay performed on viable but no cultivable bacteria. Microscope motility examines show that all strains exposed to sunlight remain motile after the loss of cultivability.

Epidemiology and Pathophysiology of COVID-19-Associated Mucormycosis: India Versus the Rest of the World

The coronavirus disease 2019 (COVID-19) pandemic has led to a concerning resurgence of mucormycosis. More than 47,000 cases of mucormycosis were reported in three months from India. We update our systematic review on COVID-19-associated mucormycosis (CAM) till June 21st, 2021, comparing cases reported from India and elsewhere. We included individual patient details of 275 cases of CAM, of which 233 were reported from India and 42 from the rest of the world. Diabetes mellitus was the most common underlying risk factor for CAM in India than in other countries. The fatality rate of cases reported from India (36.5%) was less than the globally reported cases (61.9%), probably due to the predominance of rhino-orbital mucormycosis. On a multivariate analysis, we found that pulmonary or disseminated mucormycosis cases and admission to the intensive care unit were associated with increased mortality, while combination medical therapy improved survival. The paucity of pulmonary and disseminated mucormycosis cases from India suggests that these cases were either not diagnosed or reported, further supported by a trend of search data from the Google search engine. In this review, we discuss the factors explaining the substantial rise in cases of CAM. We also propose a hypothetical model describing the epidemiologic triad of CAM.

Cell line development for continuous high cell density biomanufacturing: Exploiting hypoxia for improved productivity

Oxygen deficiency (hypoxia) induces adverse effects during biotherapeutic protein production leading to reduced productivity and cell growth. Hypoxic conditions occur during classical batch fermentations using high cell densities or perfusion processes. Here we present an effort to create novel engineered Chinese hamster ovary (CHO) cell lines by exploiting encountered hypoxic bioprocess conditions to reinforce cellular production capacities. After verifying the conservation of the hypoxia-responsive pathway in CHO cell lines by analyzing oxygen sensing proteins HIF1a, HIF1β and VDL, hypoxia-response-elements (HREs) were functionally analyzed and used to create hypoxia-responsive expression vectors. Subsequently engineered hypoxia sensitive CHO cell lines significantly induced protein expression (SEAP) during adverse oxygen limitation encountered during batch fermentations as well as high cell density perfusion processes (2.7 fold). We also exploited this novel cell system to establish a highly effective oxygen shift as innovative bioprocessing strategy using hypoxia induction to improve production titers. Thus, substantial improvements can be made to optimize CHO cell productivity for novel bioprocessing challenges as oxygen limitation, providing an avenue to establish better cell systems by exploiting adverse process conditions for optimized biotherapeutic production.

Advancements in the Pharmaceutical Applications of Probiotics: Dosage Forms and Formulation Technology

Probiotics have demonstrated their high potential to treat and/or prevent various diseases including neurodegenerative disorders, cancers, cardiovascular diseases, and inflammatory diseases. Probiotics are also effective against multidrug-resistant pathogens and help maintain a balanced gut microbiota ecosystem. Accordingly, the global market of probiotics is growing rapidly, and research efforts to develop probiotics into therapeutic adjuvants are gaining momentum. However, because probiotics are living microorganisms, many biological and biopharmaceutical barriers limit their clinical application. Probiotics may lose their activity in the harsh gastric conditions of the stomach or in the presence of bile salts. Moreover, they easily lose their viability under thermal or oxidative stress during their preparation and storage. Therefore, stable formulations of probiotics are required to overcome the various physicochemical, biopharmaceutical, and biological barriers and to maximize their therapeutic effectiveness and clinical applicability. This review provides an overview of the pharmaceutical applications of probiotics and covers recent formulation approaches to optimize the delivery of probiotics with particular emphasis on various dosage forms and formulation technologies.

Oxygenated Nanocellulose-A Material Platform for Antibacterial Wound Dressing Devices

Both carboxylated cellulose nanofibrils (CNF) and dissolved oxygen (DO) have been reported to possess antibacterial properties. However, the combination for use as wound dressings against biofilm infections in chronic wounds is less known. The present study reports the development of oxygenated CNF dispersions that exhibit strong antibacterial effect. Carboxylated CNF dispersions with different oxidation levels were oxygenated by the OXY BIO System and tested for antibacterial activity against Pseudomonas aeruginosa and Staphylococcus aureus. The results reveal that the higher oxidation level of the CNFs, the better antibacterial effect. Scanning electron microscopy of bacterial biofilms revealed that a potential mechanism of action of the CNFs is the formation of a network surrounding and entrapping the bacteria. This effect is further potentiated by the oxygenation process. A CNF sample (concentration 0.6 wt %) that was oxygenated to a DO level of 46.4 mg/L demonstrated a strong antibacterial effect against S. aureus in vivo using a mouse model of surgical site infection. The oxygenated CNF dispersion reduced the bacterial survival by 71%, after 24 h treatment. The potent antibacterial effect indicates that oxygenated nanocellulose is a promising material for antibacterial wound dressings.

Resolving the Rules of Robustness and Resilience in Biology Across Scales

Why do some biological systems and communities persist while others fail? Robustness, a system's stability, and resilience, the ability to return to a stable state, are key concepts that span multiple disciplines within and outside the biological sciences. Discovering and applying common rules that govern the robustness and resilience of biological systems is a critical step toward creating solutions for species survival in the face of climate change, as well as the for the ever-increasing need for food, health, and energy for human populations. We propose that network theory provides a framework for universal scalable mathematical models to describe robustness and resilience and the relationship between them, and hypothesize that resilience at lower organization levels contribute to robust systems. Insightful models of biological systems can be generated by quantifying the mechanisms of redundancy, diversity, and connectivity of networks, from biochemical processes to ecosystems. These models provide pathways towards understanding how evolvability can both contribute to and result from robustness and resilience under dynamic conditions. We now have an abundance of data from model and non-model systems and the technological and computational advances for studying complex systems. Several conceptual and policy advances will allow the research community to elucidate the rules of robustness and resilience. Conceptually, a common language and data structure that can be applied across levels of biological organization needs to be developed. Policy advances such as cross-disciplinary funding mechanisms, access to affordable computational capacity, and the integration of network theory and computer science within the standard biological science curriculum will provide the needed research environments. This new understanding of biological systems will allow us to derive ever more useful forecasts of biological behaviors and revolutionize the engineering of biological systems that can survive changing environments or disease, navigate the deepest oceans, or sustain life throughout the solar system.

Increasing the Production of β-Glucan from Saccharomyces carlsbergensis RU01 by Using Tannic Acid

In this study, we increased β-glucan production from brewer's yeast, Saccharomyces carlsbergensis RU01, by using tannic acid. High-pressure freezing and transmission electron microscopy (HPF-TEM) revealed that the yeast cell wall obtained from yeast malt (YM) medium supplemented with 0.1% w/v tannic acid was thicker than that of yeast cultured in YM medium alone. The production of β-glucan from S. carlsbergensis RU01 was optimized in 3% w/v molasses and 0.1% w/v diammonium sulfate (MDS) medium supplemented with 0.1% w/v tannic acid. The results showed that MDS medium supplemented with 0.1% w/v tannic acid significantly increased the dry cell weight (DCW), and the β-glucan production was 0.28±0.01% w/v and 11.99±0.04% w/w. Tannic acid enhanced the β-glucan content by up to 42.23%. β-Glucan production in the stirred tank reactor (STR) was 1.4-fold higher than that in the shake flask (SF) culture. Analysis of the β-glucan composition by Fourier transform infrared (FTIR) spectroscopy showed that the β-glucan of S. carlsbergensis RU01 cultured in MDS medium supplemented with 0.1% w/v tannic acid had a higher proportion of polysaccharide than that of the control. In addition, β-glucans from brewer's yeast can be used as prebiotic and functional foods for human health and in animal feed.

Production of polyhydroxyalkanoates (PHAs) by Bacillus megaterium using food waste acidogenic fermentation-derived volatile fatty acids

High production costs still hamper fast expansion of commercial production of polyhydroxyalkanoates (PHAs). This problem is greatly related to the cultivation medium which accounts for up to 50% of the whole process costs. The aim of this research work was to evaluate the potential of using volatile fatty acids (VFAs), derived from acidogenic fermentation of food waste, as inexpensive carbon sources for the production of PHAs through bacterial cultivation. Bacillus megaterium could assimilate glucose, acetic acid, butyric acid, and caproic acid as single carbon sources in synthetic medium with maximum PHAs production yields of 9-11%, on a cell dry weight basis. Single carbon sources were then replaced by a mixture of synthetic VFAs and by a VFAs-rich stream from the acidogenic fermentation of food waste. After 72 h of cultivation, the VFAs were almost fully consumed by the bacterium in both media and PHAs production yields of 9-10%, on cell dry weight basis, were obtained. The usage of VFAs mixture was found to be beneficial for the bacterial growth that tackled the inhibition of propionic acid, iso-butyric acid, and valeric acid when these volatile fatty acids were used as single carbon sources. The extracted PHAs were revealed to be polyhydroxybutyrate (PHB) by characterization methods of Fourier-transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC). The obtained results proved the possibility of using VFAs from acidogenic fermentation of food waste as a cheap substrate to reduce the cost of PHAs production.

Influence of the packaging atmosphere and presence of co-contaminants on the growth of photobacteria on chicken meat

Fresh meat is commonly packaged in modified atmosphere to decelerate spoilage processes. The applied gas mixture affects the growth of spoilage organisms and selectively shapes the spoilage community. In this study, we investigated the impact of O₂ and CO₂ on the growth of Photobacterium (P.) phosphoreum and P. carnosum strains in situ on chicken meat by packaging under different modified atmospheres (air, 70% O₂/30% CO₂, 70% N₂/30% CO₂, 100% N₂). Combination of 70% O₂ and 30% CO₂ resulted in significant growth reduction of the analyzed strains, suggesting inhibitory effects of both gases in combination. In contrast, 30% CO₂ alone had only a minor effect and photobacteria are supposed to have a growth advantage over other meat spoilers in this atmosphere. Additionally, single growth of the strains in the different atmospheres was compared when challenged with the presence of Pseudomonas (Ps.) fragi or Brochothrix (B.) thermosphacta as prominent co-contaminants in different ratios (10:1, 1:1, 1:10). Presence of co-contaminants resulted in increased cell numbers of P. carnosum TMW2.2149 but reduced or unchanged cell numbers of P. phosphoreum TMW2.2103 in most packaging atmospheres. The initial ratio of photobacteria and co-contaminants defined the relative abundance during storage but did not change the type of the interaction. Our results suggest either a commensalistic (P. carnosum) or competitive interaction (P. phosphoreum) of photobacteria and co-contaminants on modified atmosphere packaged chicken, respectively. Furthermore, in a mix comprising seven prominent spoilers, strains of both Photobacterium species prevailed as a constant part of the spoilage microbiome during 7 days of refrigerated storage on chicken meat packaged under O₂/CO₂ atmosphere.

Investigation of relationships between fecal contamination, cattle grazing, human recreation, and microbial source tracking markers in a mixed-land-use rangeland watershed

The United States National Forests are mixed-use lands that support human recreation and cattle grazing. Overuse by humans or cattle, however, can lead to the fecal contamination of local waterways. Until recently, the source of these contaminants was a subject of conjecture; however, microbial source tracking tools have become widely used and are proving to be a valid methodology to identify the contamination source. This study aims to analyze and model the quantity and sources of fecal contamination in the Mink Creek watershed in southeastern Idaho. The U.S. Forest Service Caribou-Targhee National Forest (USFS) manages this watershed. Previous research has indicated that some localities within the watershed exceed US EPA standards for coliform bacteria. In 2019, water samples were collected before livestock began grazing and throughout the spring, summer, and fall after livestock grazing had ended. Fourteen sites were sampled seven times during the field season, allowing the water to be analyzed for total coliforms and E. coli bacteria. Microbial source tracking techniques using Bacteroides bacteria, which are known to live in specific digestive tracks, were used to identify the source of E. coli at each sampling location. The analysis indicated that E. coli counts exceeded state regulatory limits 35% of the time. These exceedances were associated with DNA source tracking markers for humans (58.8%), cattle (5.9%), or both cattle and humans (5.9%). Unknown sources were responsible for the Bacteroides bacteria 29.4% of the time. A statistical model was developed to estimate E. coli using the datasets of microbial source tracking measures, the presence or absence of humans, cattle, the proximity of the sampling date to a holiday, and other seasonal factors. The resulting model showed good performance indices at all the 14 sites based on a K-fold cross-validation scheme (R² = 0.83 and NSE = 0.69). The results demonstrated that E. coli exceedances have a close association with human recreation and unknown sources and negatively influenced by dissolved oxygen.

Peptide signaling without feedback in signal production operates as a true quorum sensing communication system in Bacillus subtilis

Bacterial quorum sensing (QS) is based on signal molecules (SM), which increase in concentration with cell density. At critical SM concentration, a variety of adaptive genes sharply change their expression from basic level to maximum level. In general, this sharp transition, a hallmark of true QS, requires an SM dependent positive feedback loop, where SM enhances its own production. Some communication systems, like the peptide SM-based ComQXPA communication system of Bacillus subtilis, do not have this feedback loop and we do not understand how and if the sharp transition in gene expression is achieved. Based on experiments and mathematical modeling, we observed that the SM peptide ComX encodes the information about cell density, specific cell growth rate, and even oxygen concentration, which ensure power-law increase in SM production. This enables together with the cooperative response to SM (ComX) a sharp transition in gene expression level and this without the SM dependent feedback loop. Due to its ultra-sensitive nature, the ComQXPA can operate at SM concentrations that are 100-1000 times lower than typically found in other QS systems, thereby substantially reducing the total metabolic cost of otherwise expensive ComX peptide.

Integrated Stirred-Tank Bioreactor with Internal Adsorption for the Removal of Ammonium to Enhance the Cultivation Performance of gdhA Derivative Pasteurella multocida B:2

Growth of mutant gdhA Pasteurella multocida B:2 was inhibited by the accumulation of a by-product, namely ammonium in the culture medium during fermentation. The removal of this by-product during the cultivation of mutant gdhA P. multocida B:2 in a 2 L stirred-tank bioreactor integrated with an internal column using cation-exchange adsorption resin for the improvement of cell viability was studied. Different types of bioreactor system (dispersed and internal) with resins were successfully used for ammonium removal at different agitation speeds. The cultivation in a bioreactor integrated with an internal column demonstrated a significant improvement in growth performance of mutant gdhA P. multocida B:2 (1.05 × 1011 cfu/mL), which was 1.6-fold and 8.4-fold as compared to cultivation with dispersed resin (7.2 × 1010 cfu/mL) and cultivation without resin (1.25 × 1010 cfu/mL), respectively. The accumulation of ammonium in culture medium without resin (801 mg/L) was 1.24-fold and 1.37-fold higher than culture with dispersed resin (642.50 mg/L) and culture in the bioreactor integrated with internal adsorption (586.50 mg/L), respectively. Results from this study demonstrated that cultivation in a bioreactor integrated with the internal adsorption column in order to remove ammonium could reduce the inhibitory effect of this by-product and improve the growth performance of mutant gdhA P. multocida B:2.

Sulfide restrains the growth of Methylocapsa acidiphila converting renewable biogas to single cell protein

Methane-oxidizing bacteria (MOB) that can use biogas and recycled nitrogen from wastewater as a sustainable feedstock for single cell protein (SCP) synthesis are receiving increasing attention. Though promising, limited knowledge is available on the alternative strains especially the ones that can tolerant to strict environments such as acidic conditions. Furthermore, how would the hydrogen sulfide affect the MOB (especially the alternative strains) for SCP synthesis when crude biogas is used as feedstock is still unknown. In this study, the capability of an acidic-tolerant methanotrophic bacterium Methylocapsa acidiphila for SCP production using raw biogas and the associated inhibitory effect of sulfide on the bioconversion was for the first time investigated. Results showed that the inhibitory effect of sulfide on the growth of M. acidiphila was observed starting from 8.13 mg L^-1 Na₂S (equivalent to approximately 1000 ppm of H₂S in crude biogas). The total amino acid content in the dry biomass decreased more than two times due to sulfide inhibition compared with the control samples without the presence of sulfide (585.96 mg/g dry biomass), while the proportion of essential amino acids in the total amino acid was not affected when the concentration of Na₂S was lower than 5.73 mg L^-1. The performance of M. acidiphila in a sulfide-rich environment was further studied at different operational conditions. The feeding gas with a CH₄/O₂ ratio of 6:4 could help to alleviate the sulfide inhibition, compared with other ratios (4:6 and 8:2). Moreover, the sequential supply of the feed gas could also alleviate sulfide inhibition. In addition, the MOB's growth rate was higher when applying a higher mixing rate of 120 rpm, compared with 70 rpm and 0, due to a better gas-liquid mass transfer. The inoculum size of 20% and 10% resulted in a faster growth rate compared with the 5%. Furthermore, M. acidiphila could assimilate either NH₄⁺ or NO₃^- as nitrogen source with a similar growth rate, giving it the potential to recycle nitrogen from a wide range of wastewaters. The results will not only create new knowledge for better understanding the role of hydrogen sulfide in the assimilation of raw biogas by acid-tolerant M. acidiphila but also provide technical insights into the development of an efficient and robust process for the waste-to-protein conversion.

The unexplored bacterial lifestyle on leaf surface

Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface.

Metabolism, ATP production and biofilm generation by Staphylococcus epidermidis in either respiratory or fermentative conditions

Staphylococcus epidermidis is a Gram-positive saprophytic bacterium found in the microaerobic/anaerobic layers of the skin that becomes a health hazard when it is carried across the skin through punctures or wounds. Pathogenicity is enhanced by the ability of S. epidermidis to associate into biofilms, where it avoids attacks by the host and antibiotics. To test the effect of oxygen on metabolism and biofilm generation, cells were cultured at different oxygen concentrations ([O₂]). As [O₂] decreased, S. epidermidis metabolism went from respiratory to fermentative. Remarkably, the rate of growth decreased at low [O₂] while a high concentration of ATP ([ATP]) was kept. Under hypoxic conditions bacteria associated into biofilms. Aerobic activity sensitized the cell to hydrogen peroxide-mediated damage. In the presence of metabolic inhibitors, biofilm formation decreased. It is suggested that at low [O₂] S. epidermidis limits its growth and develops the ability to form biofilms.

Reduced culture temperature attenuates oxidative stress and inflammatory response facilitating expansion and differentiation of adipose-derived stem cells

Background

Adipose-derived stem cell (ASC) expansion under atmospheric oxygen levels (21%) was previously shown to cause increased reactive oxygen species (ROS) accumulation and genetic instability compared to cells cultured under physiological oxygen levels (2–8%). However, since culture under physiological oxygen levels is costly and complicated, a simpler method to reduce ROS accumulation is desirable. The current study aimed to determine whether lower culture temperature can reduce ROS production in ASCs without impairing their culture expansion.

Methods

Proliferation, differentiation, ROS accumulation, and gene expression were compared between ASC cultures at 35 °C and 37 °C. ASCs isolated either from rat fat depots or from human lipoaspirates were examined in the study.

Results

Rat visceral ASCs (vASCs) cultured at 35 °C demonstrated reduced ROS production and apoptosis and enhanced expansion and adipogenic differentiation compared to vASCs cultured at 37 °C. Similarly, the culture of human ASCs (hASCs) at 35 °C led to reduced ROS accumulation and apoptosis, with no effect on the proliferation rate, compared to hASCs cultured at 37 °C. Comparison of gene expression profiles of 35 °C versus 37 °C vASCs uncovered the development of a pro-inflammatory phenotype in 37 °C vASCs in correlation with culture temperature and ROS overproduction. This correlation was reaffirmed in both hASCs and subcutaneous rat ASCs.

Conclusions

This is the first evidence of the effect of culture temperature on ASC growth and differentiation properties. Reduced temperatures may result in superior ASC cultures with enhanced expansion capacities in vitro and effectiveness in vivo.

Comparative genomics shows differences in the electron transport and carbon metabolic pathways of Mycobacterium africanum relative to Mycobacterium tuberculosis and suggests an adaptation to low oxygen tension

The geographically restricted Mycobacterium africanum lineages (MAF) are primarily found in West Africa, where they account for a significant proportion of tuberculosis. Despite this phenomenon, little is known about the co-evolution of these ancient lineages with West Africans. MAF and M. tuberculosis sensu stricto lineages (MTB) differ in their clinical, in vitro and in vivo characteristics for reasons not fully understood. Therefore, we compared genomes of 289 MAF and 205 MTB clinical isolates from the 6 main human-adapted M. tuberculosis complex lineages, for mutations in their Electron Transport Chain and Central Carbon Metabolic pathway in order to explain these metabolic differences. Furthermore, we determined, in silico, whether each mutation could affect the function of genes encoding enzymes in these pathways. We found more mutations with the potential to affect enzymes in these pathways in MAF lineages compared to MTB lineages. We also found that similar mutations occurred in these pathways between MAF and some MTB lineages. Generally, our findings show further differences between MAF and MTB lineages that may have contributed to the MAF clinical and growth phenotype and indicate potential adaptation of MAF lineages to a distinct ecological niche, which we suggest includes areas characterized by low oxygen tension.

Methane oxidising bacteria to upcycle effluent streams from anaerobic digestion of municipal biowaste

Conventional microbial protein production relies on the usage of pure chemicals and gases. Natural gas, which is a fossil resource, is the common input gas for bacterial protein production. Alternative sources for gas feedstock and nutrients can sufficiently decrease the operational cost and environmental impact of microbial protein production processes. In the present study, the effluents streams of municipal biowaste anaerobic digestion, were used to grow methane oxidising bacteria which can be used as protein source. Results demonstrated that a 40:60 CH₄:O₂ (v/v) gas feeding resulted in microbial biomass production of 0.95 g-DM/L by a Methylophilus dominated community. When raw biogas was used as input for methane corresponding to the same initial methane partial pressure as before, instead of pure methane, the growth was partially hindered (0.61 g-DM/L) due to the presence of H₂S (IC₅₀: 1376 ppm). Hence, desulfurization is suggested before using biogas for microbial protein production. At semi-continuous mode, results showed that the produced biomass had relatively high protein content (>40% of dry weight) and the essential amino acids lysine, valine, leucine and histidine were detected at high levels.

Investigation of the effects of oxidative stress-inducing factors on culturing and productivity of Bordetella pertussis

The stress response of Bordetella pertussis during fermentation was assessed by means of fluorescence-based techniques. During the manufacturing of vaccines, B. pertussis is subjected to stress during adaptation to a new environment and operating conditions in the bioreactor, which can have harmful consequences on growth and protein yield. In this study, stress was imposed by varying the percentage of dissolved oxygen (DO) and inoculum size, and by adding rotenone and hydrogen peroxide. In this study, fluorescence spectroscopy is used as a tool for measuring oxidative stress. High levels of DO during fed-batch operation had no detrimental effect on growth, but the specific productivity of pertactin (PRN) decreased. Cultures that were started with an inoculum size that was 10 times smaller than the control resulted in significantly less PRN as compared to controls where reduction was more significant in flasks as compared to bioreactors. A comparison of filtered to heat-sterilized media revealed that filtered media offered a protective effect against H₂ O₂ . Heat sterilization of the media might result in the destruction of components that offer protection against oxidative stress. Nonetheless, filter sterilization on its own would be insufficient for large-scale manufacturing. It should be emphasized that the effects of these stressors while investigating for other microorganisms have not been studied for B. pertussis.

In-depth analysis of swim bladder-associated microbiota in rainbow trout (Oncorhynchus mykiss)

Our knowledge regarding microbiota associated with the swim bladder of physostomous, fish with the swim bladder connected to the esophagus via the pneumatic duct, remains largely unknown. The goal of this study was to conduct the first in-depth characterization of the swim bladder-associated microbiota using high-throughput sequencing of the V4 region of the 16 S rRNA gene in rainbow trout (Oncorhynchus mykiss). We observed major differences in bacterial communities composition between swim bladder-associated microbiota and distal intestine digesta microbiota in fish. Whilst bacteria genera, such as Cohnella, Lactococcus and Mycoplasma were more abundant in swim bladder-associated microbiota, Citrobacter, Rhodobacter and Clavibacter were more abundant in distal intestine digesta microbiota. The presumptive metabolic function analysis (PICRUSt) revealed several metabolic pathways to be more abundant in the swim bladder-associated microbiota, including metabolism of carbohydrates, nucleotides and lipoic acid as well as oxidative phosphorylation, cell growth, translation, replication and repair. Distal intestine digesta microbiota showed greater abundance of nitrogen metabolism, amino acid metabolism, biosynthesis of unsaturated fatty acids and bacterial secretion system. We demonstrated swim bladder harbors a unique microbiota, which composition and metabolic function differ from microbiota associated with the gut in fish.

Selective proteolysis by matrix metalloproteinases of photo-oxidised dermal extracellular matrix proteins

Photodamage in chronically sun-exposed skin manifests clinically as deep wrinkles and histologically as extensive remodelling of the dermal extracellular matrix (ECM) and in particular, the elastic fibre system. We have shown previously that loss of fibrillin microfibrils, a key elastic fibre component, is a hallmark of early photodamage and that these ECM assemblies are susceptible in vitro to physiologically attainable doses of ultraviolet radiation (UVR). Here, we test the hypotheses that UVR-mediated photo-oxidation is the primary driver of fibrillin microfibril and fibronectin degradation and that prior UVR exposure will enhance the subsequent proteolytic activity of UVR-upregulated matrix metalloproteinases (MMPs). We confirmed that UVB (280-315 nm) irradiation in vitro induced structural changes to both fibrillin microfibrils and fibronectin and these changes were largely reactive oxygen species (ROS)-driven, with increased ROS lifetime (D₂O) enhancing protein damage and depleted O₂ conditions abrogating it. Furthermore, we show that although exposure to UVR alone increased microfibril structural heterogeneity, exposure to purified MMPs (1, -3, -7 and - 9) alone had minimal effect on microfibril bead-to-bead periodicity; however, microfibril suspensions exposed to UVR and then MMPs were more structurally homogenous. In contrast, the susceptibly of fibronectin to proteases was unaffected by prior UVR exposure. These observations suggest that both direct photon absorption and indirect production of ROS are important mediators of ECM remodelling in photodamage. We also show that fibrillin microfibrils are relatively resistant to proteolysis by MMPs -1, -3, -7 and - 9 but that these MMPs may selectively remove damaged microfibril assemblies. These latter observations have implications for predicting the mechanisms of tissue remodelling and targeted repair.

Exploring the genome of Arctic Psychrobacter sp. DAB_AL32B and construction of novel Psychrobacter-specific cloning vectors of an increased carrying capacity

Cold-active bacteria are currently of great interest in biotechnology, and their genomic and physiological features have been extensively studied. One of the model psychrotolerant bacteria are Psychrobacter spp. Analysis of Arctic psychrophilic Psychrobacter sp. DAB_AL32B genome content provided an insight into its overall stress response, and genes conferring protection against various life-limiting factors (i.e., low temperature, increased ultraviolet radiation, oxidative stress and osmotic pressure) were recognized and described. Moreover, it was revealed that the strain carries a large plasmid pP32BP2. Its replication system was used for the construction of two novel shuttle vectors (pPS-NR-Psychrobacter-Escherichia coli-specific plasmid and pPS-BR-Psychrobacter-various Proteobacteria-specific plasmid) of an increased carrying capacity, which may be used for genetic engineering of Psychrobacter spp.

High dissolved oxygen tension triggers outer membrane vesicle formation by Neisseria meningitidis

Background

Outer membrane vesicles (OMVs) are nanoparticles released by Gram-negative bacteria and can be used as vaccines. Often, detergents are used to promote release of OMVs and to remove the toxic lipopolysaccharides. Lipopolysaccharides can be detoxified by genetic modification such that vesicles spontaneously produced by bacteria can be directly used as vaccines. The use of spontaneous OMVs has the advantage that no separate extraction step is required in the purification process. However, the productivity of spontaneous OMVs by bacteria at optimal growth conditions is low. One of many methods for increasing OMV formation is to reduce the linkage of the outer membrane to the peptidoglycan layer by knocking out the rmpM gene. A previous study showed that for Neisseria meningitidis this resulted in release of more OMVs. Furthermore, cysteine depletion was found to trigger OMV release and at the same time cause reduced growth and oxidative stress responses. Here we study the effect of growth rate and oxidative stress on OMV release.

Results

First, we identified using chemostat and accelerostat cultures of N. meningitidis that increasing the growth rate from 0.03 to 0.18 h⁻¹ has a limited effect on OMV productivity. Thus, we hypothesized that oxidative stress is the trigger for OMV release and that oxidative stress can be introduced directly by increasing the dissolved oxygen tension of bacterial cultures. Slowly increasing oxygen concentrations in a N. meningitidis changestat showed that an increase from 30 to 150% air saturation improved OMV productivity four-fold. Batch cultures controlled at 100% air saturation increased OMV productivity three-fold over batch cultures controlled at 30% air saturation.

Conclusion

Increased dissolved oxygen tension induces the release of outer membrane vesicles in N. meningitidis cultures. Since oxygen concentration is a well-controlled process parameter of bacterial cultures, this trigger can be applied as a convenient process parameter to induce OMV release in bacterial cultures. Improved productivity of OMVs not only improves the production costs of OMVs as vaccines, it also facilitates the use of OMVs as adjuvants, enzyme carriers, or cell-specific drug delivery vehicles.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1007-7) contains supplementary material, which is available to authorized users.

Optimization of Fermentation Conditions and Media for Production of Glucose Isomerase from Bacillus megaterium Using Response Surface Methodology

Glucose isomerase is an enzyme widely used in food industry for producing high-fructose corn syrup. Many microbes, including Bacillus megaterium, have been found to be able to produce glucose isomerase. However, the number of studies of glucose isomerase production from Bacillus megaterium is limited. In this study, we establish the optimal medium components and culture conditions for Bacillus megaterium glucose isomerase production by evaluating the combined influence of multiple factors and different parameters via Plackett-Burman design and response surface methodology in Modde 5.0 software. The optimized conditions, which were experimentally confirmed as follows: D-xylose (1.116%), K₂HPO₄ (0.2%), MgSO₄·7H₂O (0.1%), yeast extract (1.161%), peptone (1%), pH 7.0, inoculum size 20% (w/v), shaking 120 rpm at 36.528°C for 48 hours, give rise to production of highest activity of glucose isomerase (0.274 ± 0.003 U/mg biomass). These results provide additional important information for future development of large-scale glucose isomerase production by Bacillus megaterium.

Karyotype variation of CHO host cell lines over time in culture characterized by chromosome counting and chromosome painting

Genomic rearrangements are a common phenomenon in rapidly growing cell lines such as Chinese hamster ovary (CHO) cells, a feature that in the context of production of biologics may lead to cell line and product instability. Few methods exist to assess such genome wide instability. Here, we use the population distribution of chromosome numbers per cell as well as chromosome painting to quantify the karyotypic variation in several CHO host cell lines. CHO-S, CHO-K1 8 mM glutamine, and CHO-K1 cells adapted to grow in media containing no glutamine were analyzed over up to 6 months in culture. All three cell lines were clearly distinguishable by their chromosome number distribution and by the specific chromosome rearrangements that were present in each population. Chromosome Painting revealed a predominant karyotype for each cell line at the start of the experiment, completed by a large number of variants present in each population. Over time in culture, the predominant karyotype changed for CHO-S and CHO-K1, with the diversity increasing and new variants appearing, while CHO-K1 0 mM Gln preferred chromosome pattern increased in percent of the population over time. As control, Chinese hamster lung fibroblasts were shown to also contain an increasing number of variants over time in culture.

Novel haloarchaeon Natrinema thermophila having the highest growth temperature among haloarchaea with a large genome size

Environmental temperature is one of the most important factors for the growth and survival of microorganisms. Here we describe a novel extremely halophilic archaeon (haloarchaea) designated as strain CBA1119^T isolated from solar salt. Strain CBA1119^T had the highest maximum and optimal growth temperatures (66 °C and 55 °C, respectively) and one of the largest genome sizes among haloarchaea (5.1 Mb). It also had the largest number of strain-specific pan-genome orthologous groups and unique pathways among members of the genus Natrinema in the class Halobacteria. A dendrogram based on the presence/absence of genes and a phylogenetic tree constructed based on OrthoANI values highlighted the particularities of strain CBA1119^T as compared to other Natrinema species and other haloarchaea members. The large genome of strain CBA1119^T may provide information on genes that confer tolerance to extreme environmental conditions, which may lead to the discovery of other thermophilic strains with potential applications in industrial biotechnology.