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1.
Potential influence of the microbiome environment in patients with biliary tract cancer and implications for therapy.
Wheatley, RC, Kilgour, E, Jacobs, T, Lamarca, A, Hubner, RA, Valle, JW, McNamara, MG
British journal of cancer. 2022;(5):693-705
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Abstract
Biliary tract cancers, including intra- and extra-hepatic cholangiocarcinoma as well as gallbladder cancer, are associated with poor prognosis and the majority of patients present with advanced-stage, non-resectable disease at diagnosis. Biliary tract cancer may develop through an accumulation of genetic and epigenetic alterations and can be influenced by microbial exposure. Furthermore, the liver and biliary tract are exposed to the gastrointestinal microbiome through the gut-liver axis. The availability of next-generation sequencing technology has led to an increase in studies investigating the relationship between microbiota and human disease. In particular, the interplay between the microbiome, the tumour micro-environment and response to systemic therapy is a prospering area of interest. Given the poor outcomes for patients with biliary tract cancer, this emerging field of research, through which new biomarkers may be identified, offers potential as a tool for early diagnosis, prognostication or even as a future therapeutic target. This review summarises the available evidence on the microbiome environment in patients with biliary tract cancer, including a discussion around confounding factors, implications for therapy and proposed future directions.
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Multitalented Synthetic Antimicrobial Peptides and Their Antibacterial, Antifungal and Antiviral Mechanisms.
Vanzolini, T, Bruschi, M, Rinaldi, AC, Magnani, M, Fraternale, A
International journal of molecular sciences. 2022;(1)
Abstract
Despite the great strides in healthcare during the last century, some challenges still remained unanswered. The development of multi-drug resistant bacteria, the alarming growth of fungal infections, the emerging/re-emerging of viral diseases are yet a worldwide threat. Since the discovery of natural antimicrobial peptides able to broadly hit several pathogens, peptide-based therapeutics have been under the lenses of the researchers. This review aims to focus on synthetic peptides and elucidate their multifaceted mechanisms of action as antiviral, antibacterial and antifungal agents. Antimicrobial peptides generally affect highly preserved structures, e.g., the phospholipid membrane via pore formation or other constitutive targets like peptidoglycans in Gram-negative and Gram-positive bacteria, and glucan in the fungal cell wall. Additionally, some peptides are particularly active on biofilm destabilizing the microbial communities. They can also act intracellularly, e.g., on protein biosynthesis or DNA replication. Their intracellular properties are extended upon viral infection since peptides can influence several steps along the virus life cycle starting from viral receptor-cell interaction to the budding. Besides their mode of action, improvements in manufacturing to increase their half-life and performances are also taken into consideration together with advantages and impairments in the clinical usage. Thus far, the progress of new synthetic peptide-based approaches is making them a promising tool to counteract emerging infections.
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Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide.
Chen, J, Xie, P, Huang, Y, Gao, H
International journal of molecular sciences. 2022;(2)
Abstract
Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.
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Microbial Diversity in the Indian Ocean Sediments: An Insight into the Distribution and Associated Factors.
Ambati, M, Kumar, MS
Current microbiology. 2022;(4):115
Abstract
Indian Ocean is the third largest oceanic division of the world and shelter to a huge microbial diversity. These microbes play an important role in the metabolism of carbon, sulfur, nitrogen, and phosphorus in the ocean water. They are also major contributors of carbon fixing and sequestration, as much as terrestrial plants to achieve CO2 emissions reduction. The prokaryotic community in the East Indian Ocean primarily comprises of heterotrophic bacteria like Alphaproteobacteria and Gammaproteobacteria, followed by Firmicutes and Actinobacteria. The Arabian Sea and the Bay of Bengal are typically characterized by presence of vast areas of oxygen minimum zones (OMZs) and have been witnessing a shift in the microbial diversity due to the changing conditions in the ocean water. Several canonical correspondence analyses reveal temperature, salinity, and phosphate levels as crucial environmental factors in propelling the distribution of diazotrophs. The viral consortia are dominated by the Caudovirales, an order of tailed bacteriophages. Due to the rapid change in the environmental factors such as topography, temperature, and sunlight contributing toward climate change, their role in sustaining the chemical composition of the ocean can be drastically affected especially with the evidence of several bacterial and fungal communities responding to latitudinal and temperature change. Therefore, we aim to critically review the status of microbial diversity in Indian Ocean to predict their response toward climate change as they are the sentinels of change in marine life and to understand the dynamics of microbial communities in the various locations of Indian Ocean.
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Bioprospecting Plant Growth Promoting Rhizobacteria for Enhancing the Biological Properties and Phytochemical Composition of Medicinally Important Crops.
Rizvi, A, Ahmed, B, Khan, MS, El-Beltagi, HS, Umar, S, Lee, J
Molecules (Basel, Switzerland). 2022;(4)
Abstract
Traditionally, medicinal plants have long been used as a natural therapy. Plant-derived extracts or phytochemicals have been exploited as food additives and for curing many health-related ailments. The secondary metabolites produced by many plants have become an integral part of human health and have strengthened the value of plant extracts as herbal medicines. To fulfil the demand of health care systems, food and pharmaceutical industries, interest in the cultivation of precious medicinal plants to harvest bio-active compounds has increased considerably worldwide. To achieve maximum biomass and yield, growers generally apply chemical fertilizers which have detrimental impacts on the growth, development and phytoconstituents of such therapeutically important plants. Application of beneficial rhizosphere microbiota is an alternative strategy to enhance the production of valuable medicinal plants under both conventional and stressed conditions due to its low cost, environmentally friendly behaviour and non-destructive impact on fertility of soil, plants and human health. The microbiological approach improves plant growth by various direct and indirect mechanisms involving the abatement of various abiotic stresses. Given the negative impacts of fertilizers and multiple benefits of microbiological resources, the role of plant growth promoting rhizobacteria (PGPR) in the production of biomass and their impact on the quality of bio-active compounds (phytochemicals) and mitigation of abiotic stress to herbal plants have been described in this review. The PGPR based enhancement in the herbal products has potential for use as a low cost phytomedicine which can be used to improve health care systems.
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Microbial 5'-nucleotidases: their characteristics, roles in cellular metabolism, and possible practical applications.
Zakataeva, NP
Applied microbiology and biotechnology. 2021;(20):7661-7681
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Abstract
5'-Nucleotidases (EC 3.1.3.5) are enzymes that catalyze the hydrolytic dephosphorylation of 5'-ribonucleotides and 5'-deoxyribonucleotides to their respective nucleosides and phosphate. Most 5'-nucleotidases have broad substrate specificity and are multifunctional enzymes capable of cleaving phosphorus from not only mononucleotide phosphate molecules but also a variety of other phosphorylated metabolites. 5'-Nucleotidases are widely distributed throughout all kingdoms of life and found in different cellular locations. The well-studied vertebrate 5'-nucleotidases play an important role in cellular metabolism. These enzymes are involved in purine and pyrimidine salvage pathways, nucleic acid repair, cell-to-cell communication, signal transduction, control of the ribo- and deoxyribonucleotide pools, etc. Although the first evidence of microbial 5'-nucleotidases was obtained almost 60 years ago, active studies of genetic control and the functions of microbial 5'-nucleotidases started relatively recently. The present review summarizes the current knowledge about microbial 5'-nucleotidases with a focus on their diversity, cellular localizations, molecular structures, mechanisms of catalysis, physiological roles, and activity regulation and approaches to identify new 5'-nucleotidases. The possible applications of these enzymes in biotechnology are also discussed.Key points• Microbial 5'-nucleotidases differ in molecular structure, hydrolytic mechanism, and cellular localization.• 5'-Nucleotidases play important and multifaceted roles in microbial cells.• Microbial 5'-nucleotidases have wide range of practical applications.
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Waste-derived volatile fatty acids as carbon source for added-value fermentation approaches.
Chalima, A, de Castro, LF, Burgstaller, L, Sampaio, P, Carolas, AL, Gildemyn, S, Velghe, F, Ferreira, BS, Pais, C, Neureiter, M, et al
FEMS microbiology letters. 2021;(9)
Abstract
The establishment of a sustainable circular bioeconomy requires the effective material recycling from biomass and biowaste beyond composting/fertilizer or anaerobic digestion/bioenergy. Recently, volatile fatty acids attracted much attention due to their potential application as carbon source for the microbial production of high added-value products. Their low-cost production from different types of wastes through dark fermentation is a key aspect, which will potentially lead to the sustainable production of fuels, materials or chemicals, while diminishing the waste volume. This article reviews the utilization of a volatile fatty acid platform for the microbial production of polyhydroxyalkanoates, single cell oil and omega-3 fatty acids, giving emphasis on the fermentation challenges for the efficient implementation of the bioprocess and how they were addressed. These challenges were addressed through a research project funded by the European Commission under the Horizon 2020 programme entitled 'VOLATILE-Biowaste derived volatile fatty acid platform for biopolymers, bioactive compounds and chemical building blocks'.
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Microbiologically influenced corrosion inhibition mechanisms in corrosion protection: A review.
Lou, Y, Chang, W, Cui, T, Wang, J, Qian, H, Ma, L, Hao, X, Zhang, D
Bioelectrochemistry (Amsterdam, Netherlands). 2021;:107883
Abstract
Microbial activities can change the properties of biofilm/metal interfaces to accelerate or decelerate the corrosion of metals in a given environment. Microbiologically influenced corrosion inhibition (MICI) is the inhibition of corrosion that is directly or indirectly induced by microbial action. Compared with conventional methods for protection from corrosion, MICI is environmentally friendly and an emerging approach for the prevention and treatment of (bio)corrosion. However, due to the diversity of microorganisms and the fact that their metabolic processes are greatly complicated by environmental factors, MICI is still facing challenges for practical application. This review provides a comprehensive overview of the mechanisms of MICI under different conditions and their advantages and disadvantages for potential applications in corrosion protection.
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Application of bacterial tyrosinases in organic synthesis.
Agunbiade, M, Le Roes-Hill, M
World journal of microbiology & biotechnology. 2021;(1):2
Abstract
Bacterial tyrosinases, as in the case of other bacterial oxidative enzymes, have been found to possess biochemical characteristics that typically make them more suited to applications requiring special operational conditions such as alkaline pH, high or low temperature, the presence of organic solvents, and the presence of inhibitors. Even though a great deal is known about fungal tyrosinases, bacterial tyrosinases still vastly remain underexplored for their potential application in organic synthesis. A literature survey in particular highlights the gaps in our knowledge pertaining to their biochemical properties. Bacterial tyrosinases have not only shown promise in the synthesis of medically important compounds such as L-3,4-dihydroxyphenylalanine (L-DOPA) and melanin but have also seen application in cross-linking reactions of proteins and the polymerization of environmental pollutants. Their ability to catalyse o-hydroxylation reactions have shown some degree of promise in the biocatalytic conversion of resveratrol to piceatannol, tyrosol to hydroxytyrosol, and many more. In this review, we will explore the world of bacterial tyrosinases, their current applications, and future perspectives for the application of these enzymes in organic synthesis.
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Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.
Fritts, RK, McCully, AL, McKinlay, JB
Microbiology and molecular biology reviews : MMBR. 2021;(1)
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Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.