PhIP-Seq: methods, applications and challenges.

Phage-immunoprecipitation sequencing (PhIP-Seq) technology is an innovative, high-throughput antibody detection method. It enables comprehensive analysis of individual antibody profiles. This technology shows great potential, particularly in exploring disease mechanisms and immune responses. Currently, PhIP-Seq has been successfully applied in various fields, such as the exploration of biomarkers for autoimmune diseases, vaccine development, and allergen detection. A variety of bioinformatics tools have facilitated the development of this process. However, PhIP-Seq technology still faces many challenges and has room for improvement. Here, we review the methods, applications, and challenges of PhIP-Seq and discuss its future directions in immunological research and clinical applications. With continuous progress and optimization, PhIP-Seq is expected to play an even more important role in future biomedical research, providing new ideas and methods for disease prevention, diagnosis, and treatment.

Impact of NaCl stress on phytoconstituents and bioactivity of Matricaria chamomilla: a multi-analytical approach.

Matricaria chamomilla (Asteraceae), commonly known as chamomile can tolerate freezing temperatures and grows in many soil types. This plant is found on all continents and has significant medicinal value. There are more than 120 chemicals detected in chamomile flowers, with the majority found in the essential oil. In this study, M. chamomilla was given the NaCl stress of 0 mM, 1 mM, 100 mM, and 150 mM concentrations This study was the first to assess the efficacy of German chamomile upon exposure to salt stress hence plant particles that had been dried and powdered were analyzed using, phytochemical tests, Fourier Transform Infrared and UV-Vis spectroscopy, thin layer chromatography, fluorescence recovery after photobleaching assay, antibacterial and antioxidant activity. The characterization and results of these activities show amazing results which enhance their antibacterial property with an increased zone of inhibition when the samples of salt stress of the above-given concentrations were compared to the control samples. More graph analysis indicates an effective impact of salt stress on the phytoconstituents of M. chamomilla. Other than that, there was a clear flower induction upon salt stress, as a variety of compounds are regarded as essential to the biological functions of chamomile flowers according to the phytoconstituent screening which can be further used in the cosmetic industry, pharmaceutical industry, and all other fields as well for various application as a nano-drug or bio-drug. Due to this, this plant became essential for plant biotechnology research.

Harnessing bacterial endophytes for environmental resilience and agricultural sustainability.

In the current era of environmental disasters and the necessity of sustainable development, bacterial endophytes have gotten attention for their role in improving agricultural productivity and ecological sustainability. This review explores the multifaceted contributions of bacterial endophytes to plant health and ecosystem sustainability. Bacterial endophytes are invaluable sources of bioactive compounds, promising breakthroughs in medicine and biotechnology. They also serve as natural biocontrol agents, reducing the need for synthetic fertilizers and fostering environmentally friendly agricultural practices. It provides eco-friendly solutions that align with the necessity of sustainability since they can improve pest management, increase crop resilience, and facilitate agricultural production. This review also underscores bacterial endophytes' contribution to promoting sustainable and green industrial productions. It also presented how incorporating these microorganisms into diverse industrial sectors can harmonize humankind with ecological stability. The potential of bacterial endophytes has been largely untapped, presenting an opportunity for pioneering advancements in sustainable industrial applications. Their importance caught attention as they provided innovative solutions to the challenging problems of the new era. This review sheds light on the remarkable potential of bacterial endophytes in various industrial sectors. Further research is imperative to discover their multifaceted potential. It will be essential to delve deeper into their mechanisms, broaden their uses, and examine their long-term impacts.

The inorganic pyrophosphatases of microorganisms: a structural and functional review.

Pyrophosphatases (PPases) are enzymes that catalyze the hydrolysis of pyrophosphate (PPi), a byproduct of the synthesis and degradation of diverse biomolecules. The accumulation of PPi in the cell can result in cell death. Although the substrate is the same, there are variations in the catalysis and features of these enzymes. Two enzyme forms have been identified in bacteria: cytoplasmic or soluble pyrophosphatases and membrane-bound pyrophosphatases, which play major roles in cell bioenergetics. In eukaryotic cells, cytoplasmic enzymes are the predominant form of PPases (c-PPases), while membrane enzymes (m-PPases) are found only in protists and plants. The study of bacterial cytoplasmic and membrane-bound pyrophosphatases has slowed in recent years. These enzymes are central to cell metabolism and physiology since phospholipid and nucleic acid synthesis release important amounts of PPi that must be removed to allow biosynthesis to continue. In this review, two aims were pursued: first, to provide insight into the structural features of PPases known to date and that are well characterized, and to provide examples of enzymes with novel features. Second, the scientific community should continue studying these enzymes because they have many biotechnological applications. Additionally, in this review, we provide evidence that there are m-PPases present in fungi; to date, no examples have been characterized. Therefore, the diversity of PPase enzymes is still a fruitful field of research. Additionally, we focused on the roles of H+/Na+ pumps and m-PPases in cell bioenergetics. Finally, we provide some examples of the applications of these enzymes in molecular biology and biotechnology, especially in plants. This review is valuable for professionals in the biochemistry field of protein structure-function relationships and experts in other fields, such as chemistry, nanotechnology, and plant sciences.

A review of the fungal polysaccharides as natural biopolymers: Current applications and future perspective.

As a unique natural resource, fungi are a sustainable source of lipids, polysaccharides, vitamins, proteins, and other nutrients. As a result, they have beneficial medicinal and nutritional properties. Polysaccharides are among the most significant bioactive components found in fungi. Increasing research has revealed that fungal polysaccharides (FPS) contain a variety of bioactivities, including antitumor, antioxidant, immunomodulatory, anti-inflammatory, hepatoprotective, cardioprotective, and anti-aging properties. However, the exact knowledge about FPS and their applications related to their future possibilities must be thoroughly examined to enhance a better understanding of this sustainable biopolymer source. Therefore, FPS' biological applications and their role in the food and feed industry, agriculture, and cosmetics applications were all discussed in this work. In addition, this review highlighted the mode of action of FPS on human diseases by regulating gut microbiota and discussed the mechanism of FPS as antioxidants in the living cell. The structure-activity connections of FPS were also highlighted and explored. Moreover, future perspectives were listed to pave the way for future studies of FPS applications. Hence, this study can be a scientific foundation for future FPS research and industrial applications.

From freezing to functioning: cellular strategies of cold-adapted bacteria for surviving in extreme environments.

The ability of cold-adapted bacteria to survive in extreme cold and diverse temperatures is due to their unique attributes like cell membrane stability, up-regulation of peptidoglycan biosynthesis, increased production of extracellular polymeric substances, and expansion of membrane pigment. Various cold-adapted proteins, including ice-nucleating proteins (INPs), antifreeze proteins (AFPs), cold shock proteins (Csps), and cold-acclimated proteins (CAPs), help the bacteria to survive in these environments. To sustain cells from extreme cold conditions and maintain stability in temperature fluctuations, survival strategies at the molecular level and their mechanism play significant roles in adaptations in cryospheric conditions. Furthermore, cold shock domains present in the multifunctional cold shock proteins play crucial roles in their adaptation strategies. The considerable contribution of lipopeptides, osmolytes, and membrane pigments plays an integral part in their survival in extreme environments. This review summarizes the evolutionary history of cold-adapted bacteria and their molecular and cellular adaptation strategies to thrive in harsh cold environments. It also discusses the importance of carotenoids produced, lipid composition, cryoprotectants, proteins, and chaperones related to this adaptation. Furthermore, the functions and mechanisms of adaptations within the cell are discussed briefly. One can utilize and explore their potential in various biotechnology applications and their evolutionary journey by knowing the inherent mechanism of their molecular and cellular adaptation to cold climatic conditions. This review will help all branches of the life science community understand the basic microbiology of psychrophiles and their hidden prospect in life science research.

The biotechnological potential of the Chloroflexota phylum.

In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.

Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific.

Prescottella, a distinct genus separate from Rhodococcus, has garnered attention for its adaptability and ecological versatility. In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Pacific. On the basis of 16S rRNA gene sequence analysis, average nucleotide identity and phylogenomic analysis, strain R16 clearly represents a novel species within the genus Prescottella. Genomic analyses indicate Prescottella sp. R16 contains a circular chromosome of 4,531,251 bp with an average GC content of 68.9%, 4,208 protein-coding genes, 51 tRNA genes, and 12 rRNA operons. Additionally, four CRISPRs and 24 genomic islands are also identified. The presence of rich categories related to catalytic activity, membrane part and metabolic process highlights their involvement in cellular component, biological process, and molecular function. The genome sequence of strain R16 also revealed the presence of 13 putative biosynthetic gene clusters for secondary metabolites, including those for ε-Poly-L-lysine, ectoine, heterobactin, isorenieratene and corynecin, suggesting its potential for antibiotic production and warranting further exploration.

The agavins (Agave carbohydrates) story.

Fructans, are carbohydrates defined as fructose-based polymers with countable degree of polymerization (DP) ranging so far from DP3 to DP60. There are different types of fructans depending on their molecular arrangement. They are categorized as linear inulins and levans, neoseries of inulin and levan, branched graminans, and highly branched neofructans, so called agavins (Agave carbohydrates). It is worth to note that agavins are the most recently described type of fructans and they are also the most complex ones. The complexity of these carbohydrates is correlated to their various isomers and degree of polymerization range, which is correlated to their multifunctional application in industry and human health. Here, we narrate the story of the agavins' discovery. This included their chemical characterization, their benefits, biotechnological applications, and drawbacks over human health. Finally, a perspective of the study of agavins and their interactions with other metabolites through metabolomics is proposed.

Synthesis and analysis of silica nanocarriers for pectinase immobilization: Enhancing enzymatic stability for continuous industrial applications.

Pectinolytic enzymes are among the important group of industrial enzymes that have wide applications in different food industries. In this study, pectinase-based silica nanocarriers were synthesized using co-precipitation and cross-linking techniques. The resulting silica nanoparticles were investigated using scanning electron microscopy (SEM), energy-dispersive electron microscopy (EDEX), and X-ray diffraction (XRD) for determination of its morphology, elemental composition, and crystalline pattern. Under the optimal immobilization conditions like 1.5 % glutaraldehyde, 3000 IU/mg pectinase concentration, 90 min immobilization time and 40 °C immobilization temperature, pectinase showed maximum immobilization yield. The immobilization of pectinase onto the silica nanocarriers led to enhanced catalytic characteristics, displaying higher enzymatic activity across various temperature and pH levels compared to soluble pectinase. Moreover, the immobilization substantially improved the temperature stability of pectinase, exhibiting 100 % of its initial activity even after 120 h of pre-incubation at 50 °C. Additionally, the silica nanocarrier pectinase retained 100 % of its original activity even after being reused 10 times in a single batch of reactions. These findings indicate that the immobilization of silica nanocarriers effectively enhances pectinase's industrial capabilities, making it economically feasible for industrial use and an efficient system for various biotechnological applications.

A review of the principles and biotechnological applications of glycoside hydrolases from extreme environments.

It is apparent that Biocatalysts are shaping the future by providing a more sustainable approach to established chemical processes. Industrial processes rely heavily on the use of toxic compounds and high energy or pH reactions, factors that both contributes to the worsening climate crisis. Enzymes found in bacterial systems and other microorganisms, from the glaciers of the Arctic to the sandy deserts of Abu Dhabi, provide key tools and understanding as to how we can progress in the biotechnology sector. These extremophilic bacteria harness the adaptive enzymes capable of withstanding harsh reaction conditions in terms of stability and reactivity. Carbohydrate-active enzymes, including glycoside hydrolases or carbohydrate esterases, are extremely beneficial for the presence and future of biocatalysis. Their involvement in the industry spans from laundry detergents to paper and pulp treatment by degrading oligo/polysaccharides into their monomeric products in almost all detrimental environments. This includes exceedingly high temperatures, pHs or even in the absence of water. In this review, we discuss the structure and function of different glycoside hydrolases from extremophiles, and how they can be applied to industrial-scale reactions to replace the use of harsh chemicals, reduce waste, or decrease energy consumption.

Molecular modification and biotechnological applications of microbial aspartic proteases.

The growing preference for incorporating microbial aspartic proteases in industries is due to their high catalytic function and high degree of substrate selectivity. These properties, however, are attributable to molecular alterations in their structure and a variety of other characteristics. Molecular tools, functional genomics, and genome editing technologies coupled with other biotechnological approaches have aided in improving the potential of industrially important microbial proteases by addressing some of their major limitations, such as: low catalytic efficiency, low conversion rates, low thermostability, and less enzyme yield. However, the native folding within their full domain is dependent on a surrounding structure which challenges their functionality in substrate conversion, mainly due to their mutual interactions in the context of complex systems. Hence, manipulating their structure and controlling their expression systems could potentially produce enzymes with high selectivity and catalytic functions. The proteins produced by microbial aspartic proteases are industrially capable and far-reaching in regulating certain harmful distinctive industrial processes and the benefits of being eco-friendly. This review provides: an update on current trends and gaps in microbial protease biotechnology, exploring the relevant recombinant strategies and molecular technologies widely used in expression platforms for engineering microbial aspartic proteases, as well as their potential industrial and biotechnological applications.

Halophilic filamentous fungi and their enzymes: Potential biotechnological applications.

Recently, interest in the study of microorganisms growing under extreme conditions, particularly halophiles, has increased due to their potential use in industrial processes. Halophiles are the class of microorganisms that grow optimally at high NaCl concentrations and are capable of producing halophilic enzymes capable of catalyzing reactions under harsh conditions. So far, fungi are the least studied halophilic microorganisms, even though they have been shown to counteract these extreme conditions by producing secondary metabolites with very interesting properties. This review highlights mechanisms that allow halophilic fungi to adapt high salinity and the specificity of their enzymes to a spectrum of action in industrial and environmental applications. The peculiarities of these enzymes justify the urgent need to apply green alternative compounds in industries.

Genomic Insights into the Microbial Agent Streptomyces albidoflavus MGMM6 for Various Biotechnology Applications.

Microbial biotechnology plays a crucial role in improving industrial processes, particularly in the production of compounds with diverse applications. In this study, we used bioinformatic approaches to analyze the genomic architecture of Streptomyces albidoflavus MGMM6 and identify genes involved in various metabolic pathways that have significant biotechnological potential. Genome mining revealed that MGMM6 consists of a linear chromosome of 6,932,303 bp, with a high G+C content of 73.5%, lacking any plasmid contigs. Among the annotated genes, several are predicted to encode enzymes such as dye peroxidase, aromatic ring-opening dioxygenase, multicopper oxidase, cytochrome P450 monooxygenase, and aromatic ring hydroxylating dioxygenases which are responsible for the biodegradation of numerous endogenous and xenobiotic pollutants. In addition, we identified genes associated with heavy metal resistance, such as arsenic, cadmium, mercury, chromium, tellurium, antimony, and bismuth, suggesting the potential of MGMM6 for environmental remediation purposes. The analysis of secondary metabolites revealed the presence of multiple biosynthesis gene clusters responsible for producing compounds with potent antimicrobial and metal-chelating activities. Furthermore, laboratory tests conducted under controlled conditions demonstrated the effectiveness of MGMM6 in inhibiting phytopathogenic microbes, decolorizing and degrading aromatic triphenylmethane dyes, particularly Blue Brilliant G250, from wastewater by up to 98 ± 0.15%. Overall, the results of our study highlight the promising biotechnological potential of S. albidoflavus MGMM6.

Diatom-Bacteria Interactions in the Marine Environment: Complexity, Heterogeneity, and Potential for Biotechnological Applications.

Diatom-bacteria interactions evolved during more than 200 million years of coexistence in the same environment. In this time frame, they established complex and heterogeneous cohorts and consortia, creating networks of multiple cell-to-cell mutualistic or antagonistic interactions for nutrient exchanges, communication, and defence. The most diffused type of interaction between diatoms and bacteria is based on a win-win relationship in which bacteria benefit from the organic matter and nutrients released by diatoms, while these last rely on bacteria for the supply of nutrients they are not able to produce, such as vitamins and nitrogen. Despite the importance of diatom-bacteria interactions in the evolutionary history of diatoms, especially in structuring the marine food web and controlling algal blooms, the molecular mechanisms underlying them remain poorly studied. This review aims to present a comprehensive report on diatom-bacteria interactions, illustrating the different interplays described until now and the chemical cues involved in the communication and exchange between the two groups of organisms. We also discuss the potential biotechnological applications of molecules and processes involved in those fascinating marine microbial networks and provide information on novel approaches to unveiling the molecular mechanisms underlying diatom-bacteria interactions.

Metabolomics Applied to Cyanobacterial Toxins and Natural Products.

The biological and chemical diversity of Cyanobacteria is remarkable. These ancient prokaryotes are widespread in nature and can be found in virtually every habitat on Earth where there is light and water. They are producers of an array of secondary metabolites with important ecological roles, toxic effects, and biotechnological applications. The investigation of cyanobacterial metabolites has benefited from advances in analytical tools and bioinformatics that are employed in metabolomic analyses. In this chapter, we review selected articles highlighting the use of targeted and untargeted metabolomics in the analyses of secondary metabolites produced by cyanobacteria. Here, cyanobacterial secondary metabolites have been didactically divided into toxins and natural products according to their relevance to toxicological studies and drug discovery, respectively. This review illustrates how metabolomics has improved the chemical analysis of cyanobacteria in terms of speed, sensitivity, selectivity, and/or coverage, allowing for broader and more complex scientific questions.

Structure and function relationship of formate dehydrogenases: an overview of recent progress.

Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.

Bacteria and microalgae associations in periphyton-mechanisms and biotechnological opportunities.

Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae-bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae-bacteria consortia, by drawing out knowledge from natural periphyton.