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Topic Review
Verrucomicrobia
Verrucomicrobia is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes. Verrucomicrobia are abundant within the environment, though relatively inactive. This phylum is considered to have two sister phyla: Chlamydiae and Lentisphaerae within the PVC group. The Verrucomicrobia phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs). These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobia and an independent lineage amidst other bacteria. CSIs have also been found that are shared by Verrucomicrobia and Chlamydiae exclusively of all other bacteria. These CSIs provide evidence that Chlamydiae is the closest relative to Verrucomicrobia, and that they are more closely related to one another than to the Planctomycetales. Verrucomicrobia might belong in the clade Planctobacteria in the larger clade Gracilicutes. In 2008, the whole genome of Methylacidiphilum infernorum (2.3 Mbp) was published. On the single circular chromosome, 2473 predicted proteins were found, 731 of which had no detectable homologs. These analyses also revealed many possible homologies with Proteobacteria.
  • 1.2K
  • 21 Oct 2022
Topic Review
Genetic Engineering of Actinomycetes
The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the “actinomycetes era”, in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review  (Antibiotics 2020, 9(8), 494; https://doi.org/10.3390/antibiotics9080494), we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015–2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.
  • 1.2K
  • 28 Dec 2020
Topic Review
Mycobacterium avium Complex
Slow-growing mycobacteria, Mycobacterium avium, and rapid-growing mycobacteria, Mycobacterium abscessus, are important emerging human pathogens causing disease in vulnerable populations such as severelyimmunocompromised patients, patients with chronic lung diseases, and others with underlying health conditions. Their incidence is increasing worldwide in industrialized countries and they cause substantial yet underacknowledged burden of disease. An overview of the general characteristics, vulnerable populations most at risk, pathogenesis, treatment, and prevention for infections caused by Mycobacterium avium, in the context of MAC, and M. abscessus are presented in this review.
  • 1.2K
  • 14 Aug 2020
Topic Review
Organic winemaking and its subsets
The wine industry has evolved over time, and more so recently, to encompass many different subsets, one of which is the organic wine market. The organic wine industry has grown in recent years, especially in California. This rapid gain in interest has resulted in the evolution of several subsets, including biodynamic, natural, and clean wine. While biody-namic and natural wine, function more as a fulfillment of niche markets, clean wine may provide benefits for consumers that otherwise suffer from side effects of wine consumption. Low sulfite levels and lack of histamines in clean wine plausibly decrease headaches and adverse effects some consumers experience when drinking wine.
  • 1.2K
  • 21 Jan 2021
Topic Review
Tetrahydrofuran Biodegradation
Tetrahydrofuran (THF) is widely used as a precursor for polymer syntheses and a versatile solvent in industries. THF is an environmental hazard and carcinogenic to humans. We characterized the THF degradation potential of a number of THF-degrading bacteria reported before and a new isolated filamentous fungus Pseudallescheria boydii ZM01. Two different microbial THF degradation pathways have been proposed here. In addition, The initial key metabolic intermediate 2-hydroxytetrahydrofuran was detected and identified by gas chromatography (GC) analyses for the first time during the THF degradation process.
  • 1.2K
  • 10 Nov 2020
Topic Review
Mechanisms of Phase Variation
Bacteria live in environments that are in constant flux, and therefore have developed numerous methods to adapt to their ever-changing surroundings. One of these methods of adaptation is called Phase Variation (PV) which is a mechanism of -high-frequency reversible gene expression switching that enables bacteria to generate heterogeneity to successfully compete in uncertain conditions. This entry details the mechanisms of PV and takes a look at them in the context of examples from different bacterial species, with a focus on S. aureus. 
  • 1.2K
  • 02 Mar 2021
Topic Review
Computational Modeling of Human Microbiome
The human microbiome has been identified as a potentially significant contributor to human health, but the composition and role that the microbiome plays varies across body sites.  Technological improvements have enabled large-scale studies of the human microbiome and this review focuses on the data and health impacts that have been analyzed to date associated with the skin, oral, gut, and vaginal microbiomes.  One major challenge in this area that remains is to gain a better mechanistic understanding of the microbial consortium function and dynamics and how it impacts the human host.  Computational approaches can help analyze some of the interactions and complexity of the microbiome-host interactions and thus, discussion on relevant computational studies associated with the human microbiome are also presented.
  • 1.2K
  • 01 Nov 2020
Topic Review
Mycobacterium Chimaera
Mycobacterium Chimaera (MC) in recent years has shown a high infectious capacity via the aerosol by operating room equipment and represent a new frontier of medico legal aspect of nosocomila infections
  • 1.2K
  • 29 Oct 2020
Topic Review
Distribution of Sulfate-Reducing Bacteria in the Environment
Sulfate-reducing bacteria (SRB) are a heterogeneous group of anaerobic microorganisms that play an important role in producing hydrogen sulfide not only in the natural environment, but also in the gastrointestinal tract and oral cavity of animals and humans.
  • 1.2K
  • 25 Oct 2021
Topic Review
Locust Bacterial Symbionts
Locusts have been devastating vegetation and agriculture since ancient times. The formation of huge swarms that migrate long distances is a hallmark of the locust phenomenon. An important aspect of locusts’ natural history is that of their interaction with the bacteria they harbor in and on their body. These locust-associated bacteria have been shown to affect certain physiological traits (such as immunity and swarm cohesion), as well as possibly also being affected by differentfactors in the locust biology. This review summarizes our current understanding of the locust-bacterial interaction. We focus on identifying the relevant bacterial strains and their locations within the insects; the role of the bacteria and their importance to their host’s life; the mechanism of transmitting important bacteria across locust generations; and more. Finally, we offer some new perspectives and research directions that could broaden our understanding of the locust-associated bacteria and their tentative instrumental role in locust outbreaks.
  • 1.2K
  • 19 Oct 2020
Topic Review
Biofilm
A biofilm is a community of microorganisms, especially bacteria, that maintains an organized and structured strategy for growing and proliferating on any surface for their survival. The organization of the cells among the bacteria in the biofilm has primarily been revealed by examining single species. The survival of the bacteria present in the biofilm is feasible because of their orientation in the form of microcolonies, which are encapsulated in the extracellular polymeric substance of the matrix. These are separated by open water channels that serve as the primordial circulatory system for the transportation of nutrients and the disposal of metabolic waste products. All the specific bacteria maintain a microenvironment controlling the pH, nutrient availability, and temperature, which influence the biofilm growth. Biofilm maturation is a multi-stage developmental process with distinct characteristics that should be taken into account when developing antibiotic treatment regimens for biofilms. Biofilms have been extensively accepted as one of the main causes responsible for human diseases.
  • 1.2K
  • 25 May 2022
Topic Review
Actinobacteria and Environmental Adaptations
Actinobacteria are among the secondary metabolites producers and hold high pharmacological and commercial interest. It has great capability to produce secondary metabolites such as immunomodulators, antibiotics, anti-cancer drugs, growth factors, anthelminthic enzymes and herbicides.describes the historical isolation of bioactive compounds from Actinobacteria from the first isolation by Selman Waksman.
  • 1.1K
  • 05 Aug 2021
Topic Review
ESKAPE Bacteria in the Dog
ESKAPE bacteria (i.e., Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are a group of common opportunistic pathogens associated mainly with nosocomial infections.
  • 1.1K
  • 30 Oct 2020
Topic Review
The Gene Elongation Mechanism
Gene elongation is a molecular mechanism consisting of an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. Several examples of genes with internal sequence repetitions are reported in literature; thus, gene elongation might have shaped the structures of many genes during the first steps of molecular and cellular evolution.  
  • 1.1K
  • 28 Oct 2020
Topic Review
Attenuated Vaccine
An attenuated vaccine (or a live attenuated vaccine, LAV) is a vaccine created by reducing the virulence of a pathogen, but still keeping it viable (or "live"). Attenuation takes an infectious agent and alters it so that it becomes harmless or less virulent. These vaccines contrast to those produced by "killing" the virus (inactivated vaccine). Attenuated vaccines stimulate a strong and effective immune response that is long-lasting. In comparison to inactivated vaccines, attenuated vaccines produce a stronger and more durable immune response with a quick immunity onset. Attenuated vaccines function by encouraging the body to create antibodies and memory immune cells in response to the specific pathogen which the vaccine protects against. Common examples of live attenuated vaccines are measles, mumps, rubella, yellow fever, and some influenza vaccines.
  • 1.1K
  • 01 Dec 2022
Topic Review
Protein Glycosylation
Protein glycosylation is a highly conserved post-translational modification among organisms. It plays fundamental roles in many biological processes, ranging from protein trafficking and cell adhesion to host–pathogen interactions. According to the amino acid side chain atoms to which glycans are linked, protein glycosylation can be divided into two major categories: N-glycosylation and O-glycosylation. However, there are other types of modifications such as the addition of GPI to the C-terminal end of the protein. Besides the importance of glycoproteins in biological functions, they are a major component of the fungal cell wall and plasma membrane and contribute to pathogenicity, virulence, and recognition by the host immunity. Given that this structure is absent in host mammalian cells, it stands as an attractive target for developing selective compounds for the treatment of fungal infections.
  • 1.1K
  • 27 Oct 2021
Topic Review
The Biological Activities of Marine Exopolysaccharides
The unique living environment of marine microorganisms endows them with the potential to produce novel compounds with diverse biological activities. Exopolysaccharide (EPS) is a high molecular weight carbohydrate polymer secreted by microorganisms during growth and metabolism. The complex and diverse structures of EPS endow them with unique biological activities and functions. 
  • 1.1K
  • 23 Aug 2022
Topic Review
Spondyloarthritis
Spondyloarthritis (SpA) is a group of autoimmune inflammatory diseases that leads to inflammation of the spine or peripheral joints, namely axial SpA and peripheral SpA respectively. SpA is a painful and debilitating disease that affects mostly individuals aged 45 years old or younger. Trillions of microorganism reside in the human gut and interact with the immune system, and these reactions may trigger different autoimmune diseases including SpA. Dysbiosis, an imbalance of gut microbiota, may affect the mucosal barrier integrity, resulting in gut inflammation. In animal study, none of the germfree mice developed features of SpA. However, after introduction of gut commensal, over 80% of them developed features of SpA. Different gut microbiome compositions also affect the degree of gut inflammation in HLA-B27 transgenic rats. Moreover, nearly 50% of the SpA patients had subclinical gut inflammation. Chronic gut inflammation also correlated with increased bone marrow edema on MRI in SpA patients. These findings suggest there is a link between gut microorganisms and the occurrence of SpA.
  • 1.1K
  • 18 Nov 2020
Topic Review
Entomopathogen Isolation
Microbes that cause infections amongst insects leading to death or serious disabilities are known as entomopathogens. Entomopathogenic bacteria and fungi are quite frequently found in soils and insect cadavers. The first step in utilizing these microbes as biopesticides is to isolate them, and several culture media and insect baiting procedures have been tested in this direction. In this work, the authors review the current techniques that have been developed so far, in the last five decades, and display brief protocols which can be adopted for the isolations of these entomopathogens. Among bacteria, this study focuses on Serratia spp. and bacteria from the class Bacilli. Among fungi, the review focuses those from the order Hypocreales, for example, genera Beauveria, Clonostachys, Lecanicillium, Metarhizium, and Purpureocillium. The authors chose these groups of entomopathogenic bacteria and fungi based on their importance in the microbial biopesticide market.
  • 1.1K
  • 13 Jan 2021
Topic Review
Microbial L-asparaginase Application in Food
L-asparaginase (E.C.3.5.1.1) hydrolyzes L-asparagine to L-aspartic acid and ammonia, which has been widely applied in the pharmaceutical and food industries. Microbes have advantages for L-asparaginase production, and there are several commercially available forms of L-asparaginase, all of which are derived from microbes. Generally, L-asparaginase has an optimum pH range of 5.0–9.0 and an optimum temperature of between 30 and 60 °C. However, the optimum temperature of L-asparaginase from hyperthermophilic archaea is considerable higher (between 85 and 100 °C). The native properties of the enzymes can be enhanced by using immobilization techniques. The stability and recyclability of immobilized enzymes makes them more suitable for food applications. 
  • 1.1K
  • 20 Aug 2021
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