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Topic Review
Gut-Skin Microbiota Axis in Diabetic Wound Healing
Diabetic foot ulcers (DFU) are a growing concern worldwide as they pose complications in routine clinical practices such as diagnosis and management. Bacterial interactions on the skin surface are vital to the pathophysiology of DFU and may control delayed wound healing. 
  • 999
  • 16 Mar 2022
Topic Review
Microbial Communities of Peat in the Aapa-Type Mire
Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks. 
  • 998
  • 06 Feb 2022
Topic Review
Microbial Biofilms
Biofilms are complex communities of microorganisms that grow on surfaces and are embedded in a matrix of extracellular polymeric substances. These are prevalent in various natural and man-made environments, ranging from industrial settings to medical devices, where they can have both positive and negative impacts.
  • 998
  • 02 Aug 2023
Topic Review
Loop-Mediated Isothermal Amplification (LAMP)
Loop-mediated isothermal amplification (LAMP) is a sensitive molecular tool suitable for use as a near point-of-care test for the diagnosis of malaria.
  • 996
  • 23 Jun 2021
Topic Review
Alt a 1 Protein Family in Phylogenetic-Related Alternaria
Alternaria is a genus of worldwide fungi found in different habitats such as soil, the atmosphere, plants or indoor environments. Alternaria species are saprobic—largely involved in the decomposition of organic material—but they can also act as animal pathogens, causing disease in humans and animals, developing infections, toxicosis and allergic diseases. A. alternata is considered one of the most important sources of fungal allergens worldwide and it is associated with severe asthma and respiratory status. In fact,  Alt a 1, the main allergen of A. alternata, is an important marker for assessing the risk factor and severity of allergic respiratory disease. Another role of Alt a 1, from a evolutionary point of view, would be to define a family of proteins that would allow establishing taxonomic relationships between different fungal divisions. Finally, Alt a 1 has been shown to be a very useful marker for the identification of pathogenic molds contaminating plants and fruits.
  • 992
  • 28 Apr 2022
Topic Review
Seagrass Rhizosphere Sediment Bacteria
Seagrasses are an important part of the coral reef ecosystem, and their rhizosphere microbes are of great ecological importance. However, variations in diversity, composition, and potential functions of bacterial communities in the seagrass rhizosphere of coral reef ecosystems remain unclear. This study employed the high-throughput sequencing based on 16S rDNA gene sequences and functional annotation of prokaryotic taxa (FAPROTAX) analysis to investigate these variations based on seagrass species and sampling locations, respectively. Results demonstrated that the seagrass rhizosphere microbial community was mainly dominated by phylum Proteobacteria (33.47%), Bacteroidetes (23.33%), and Planctomycetes (12.47%), while functional groups were mainly composed of sulfate respiration (14.09%), respiration of sulfur compounds (14.24%), aerobic chemoheterotrophy (20.87%), and chemoheterotrophy (26.85%). Significant differences were evident in alpha diversity, taxonomical composition and putative functional groups based on seagrass species and sampling locations. Moreover, the core microbial community of all investigated samples was identified, accounting for 63.22% of all obtained sequences. Network analysis indicated that most microbes had a positive correlation (82.41%), and two module hubs (phylum Proteobacteria) were investigated. Furthermore, a significant positive correlation was found between the OTUs numbers obtained and the functional groups assigned for seagrass rhizosphere microbial communities (p < 0.01). Our result would facilitate future investigation of the function of seagrass rhizosphere microbes. 
  • 989
  • 27 Aug 2021
Topic Review
Microbiome in UC and pouchitis
The human gut microbiome represents the collective genomes of a vast range of microorganisms, also referred to as the microbiota, which include bacteria, virus, archaea and protozoa, that together form an extremely complex ecosystem capable of communicating with the immune system and determining an individual’s predisposition to develop disease states. Manipulating the gut microbiome through dietary interventions, prebiotic and probiotic compounds and faecal microbiota transplantation may expand the therapeutic landscape in ulcerative colitis (UC). Specific diets, such as the Mediterranean diet or diet rich in omega-3 fatty acids, may reduce intestinal inflammation or potentially reduce the risk of incident UC.
  • 987
  • 23 Jun 2021
Topic Review
Medicinal Plants against Candida spp.
The use of natural products to promote health is as old as human civilization. In recent years, the perception of natural products derived from plants as abundant sources of biologically active compounds has driven their exploitation towards the search for new chemical products that can lead to further pharmaceutical formulations. Candida fungi, being opportunistic pathogens, increase their virulence by acquiring resistance to conventional antimicrobials, triggering diseases, especially in immunosuppressed hosts. They are also pointed to as the main pathogens responsible for most fungal infections of the oral cavity. This increased resistance to conventional synthetic antimicrobials has driven the search for new molecules present in plant extracts, which have been widely explored as alternative agents in the prevention and treatment of infections.
  • 987
  • 24 Nov 2021
Topic Review
Allelochemicals from Microalgae
Allelochemicals are toxic secondary metabolites produced by plants, microalgae, bacteria, and fungi that influence other organisms. The bioactivity of allelochemicals and their toxic or beneficial effects have been the focus of research in medicine and agriculture, and for their anticancer and antimicrobial properties. Microalgae are the source of a remarkable diversity of biologically active compounds, which can be involved in allelopathic interactions. The main chemical classes of microalgal allelochemicals are alkaloids, fatty acids and derivatives, polyketides, peptides, phenolics, and terpenoids. In the environment, these molecules are secreted by microalgae for communication, defence, and adaptation purposes.
  • 983
  • 17 May 2023
Topic Review
Enteropathy-associated T-cell Lymphoma
Enteropathy-associated T-cell lymphoma (EATL), previously termed enteropathy-associated T-cell lymphoma, type I and at one time termed enteropathy-type T-cell lymphoma (ETTL), is a complication of coeliac disease in which a malignant T-cell lymphoma develops in areas of the small intestine affected by the disease's intense inflammation. While a relatively rare disease, it is the most common type of primary gastrointestinal T-cell lymphoma. EATL had been defined as a single type of small intestine lymphoma, but in 2008, the World Health Organization (WHO) divided the disease into two subtypes: 1) EATL type I, which occurs in individuals with coeliac disease, a chronic immune disorder causing inflammatory responses to dietary gluten primarily in the upper reaches (i.e. jejunum and duodenum) of the small intestine; and 2) EATL type II, a disorder similar to EATL type I that occurs without coeliac disease. While type I and II EATL share many similar features, post-2008 studies found some significant differences between the two types. In 2016, the WHO redefined the two diseases as separate entities, keeping the term enteropathy-associated T-cell lymphoma for the coeliac disease-associated lymphoma and terming type 2 disease as monomorphic epitheliotropic intestinal T cell lymphoma (MEITL). EATL is five to ten times more common than is MEITL. The WHO also defined a third type of intestinal T-cell lymphoma that cannot not be classified as EATL or MEITL as peripheral T-cell lymphoma not otherwise specified (ITCL-NOS). EATL arises from the malignant transformation of small-intestinal intraepithelial lymphocytes (IEL). IEL are a heterogeneous group of principally T-cell lymphocytes residing in epithelial tissues that interface the environment, such as the mucosa of the bronchi, reproductive tract and gastrointestinal tract. At these sites, IEL are exposed and regulate immune responses to non-dietary and dietary antigens, pathogenic and non-pathogenic organisms and injured self tissues. Gastrointestinal tract IEL appear in the epithelium of the small intestine, colon, stomach and esophagus, residing between the epithelial cells that line these organs' lumens. These IEL often exhibit natural killer and cytotoxic T-cell cell activation markers, contain various toxic agents (e.g. perforin, granzyme) and therefore are capable, if activated, of causing severe tissue injuries. With coeliac disease, the IEL react to the glutelins in dietary gluten by increasing their numbers, becoming pathologically active, producing chronic inflammation that injures intestinal cells, interfering with nutrient absorption and creating an environment conducive to their malignant transformation into EATL. Optimal treatment of EATL has used regimens consisting of intensive chemotherapy, hematopoietic stem cell transplantation and, in cases with bulky, obstructive and/or perforated bowel disease, surgical intervention. The disease has a five-year overall survival rate of only ~20%. However, recent studies focusing on the malignant IEL in EATL have increased understanding of the disease and suggested newer chemotherapy-based strategies and novel molecular targets that might be attacked therapeutically to improve the disease's prognosis.
  • 982
  • 17 Nov 2022
Topic Review
Bacterial Metabolites Correlating with Depression
This comprehensive entry examines the different bacterial metabolites that potentially have implications for mental health issues such as depression.
  • 981
  • 06 Jan 2021
Topic Review
Control of Greenhouse Gas Fluxes
Covering up to 25% of the land surface and acting as a rapid CH4 sink and alternately as a CO2 source or sink, karstic subterranean ecosystems play a decisive role in the carbon cycle in terms of their contribution to the global balance of greenhouse gases. Recent data indicate that microbiota must play a significant ecological role in the biogeochemical processes that control the composition of the subterranean atmosphere, as well as in the availability of nutrients for the ecosystem. Nevertheless, there are still essential gaps in our knowledge concerning the budgets of greenhouse gases at the ecosystem scale and the possible feedback mechanisms between environmental-microclimatic conditions and the rates and type of activity of microbial communities in subterranean ecosystems.
  • 980
  • 07 Jan 2021
Topic Review
Gut Microbiota and NAFLD
The pathogenesis of NAFLD is complex and not fully understood, but there is increasing evidence that the gut microbiota is strongly implicated in the development of NAFLD.
  • 979
  • 04 Aug 2021
Topic Review
Diagnosing Staph Infections with VOC Biomarkers
Staphylococci are broadly adaptable and their ability to grow in unique environments has been widely established, but the most common and clinically relevant staphylococcal niche is the skin and mucous membranes of mammals and birds. S. aureus causes severe infections in mammalian tissues and organs, with high morbidities, mortalities, and treatment costs. S. epidermidis is an important human commensal but is also capable of deadly infections. The development of volatile organic compound (VOC) profiles for the detection and identification of pathogens is an area of intensive research, with significant efforts toward establishing breath tests for infections.
  • 978
  • 13 Mar 2023
Topic Review
Bacterial Adaptation to Nano-Titania
Microbes could have prolonged exposure to nanomaterials because of their deposition in the natural environment and wide use in several fields. This could be responsible for the emergence, prevalence, and spread of microbial adaption/resistance to nanoparticles. The emergence of resistance is due to the selective pressure exerted by nanomaterials together with the peculiar flexibility of the microbial genome. This is particularly relevant for nano-titania (TiO2 nanoparticles (NPs)) because of its wide use and release into the environment. TiO2 NPs have been also investigated for their antibacterial activity showing a good performance against bacteria, alone or in combination with antibiotics. However, bacteria are able to invoke multiple response mechanisms in an attempt to adapt to TiO2 NPs. Mechanisms of nanoparticle resistance are different from those of antibiotic resistance because of the peculiar features of nanomaterials. As the antimicrobial activity of nanoparticles depends on their size, shape, and surface properties, the modification of these features by interaction with environmental components influences antibacterial properties, and thereafter the possible development of resistance. Bacterial adaption arises from global changes in metabolic pathways via the modulation of regulatory networks and can be related to single-cell or multicellular communities. The impact of TiO2 NPs on bacteria leads to several changes in microorganisms, mainly during long-term exposure, that can evolve towards adaptation and/or increased virulence.
  • 977
  • 08 Nov 2022
Topic Review
Plasmodium vivax Malaria
Plasmodium vivax malaria is a neglected tropical disease, despite being more geographically widespread than any other form of malaria.
  • 975
  • 06 Jan 2021
Topic Review
Inhibition of Multidrug Efflux Pumps in Bacterial Pathogens
Of the various bacterial mechanisms for antimicrobial resistance, active efflux is a well-known system that extrudes clinically relevant antimicrobial agents, rendering specific pathogens recalcitrant to the growth-inhibitory effects of multiple drugs. In particular, multidrug efflux pump members of the major facilitator superfamily (MFS) constitute central resistance systems in bacterial pathogens. MFS efflux confer resistance to multiple antimicrobial agents and are thus excellent targets for inhibition. Several efflux pump inhibitors (EPIs) of natural origin have been shown to possess efflux pump inhibition activities and could potentially be used to restore the efficacy of antibacterial drugs. 
  • 974
  • 29 May 2023
Topic Review
Nanotechnological Applications of Fusarium oxysporum
Fusarium oxysporum is the most encountered and economically important species of this genus. It includes pathogenic (plant, human, and animal) and non-pathogenic strains that even possess bio-control activity against fungal pests and some insects. It is one of the soil-borne pathogens that causes vascular wilt on many plants, which is characterized by various symptoms, including leaf epinasty, vascular browning, progressive wilting, defoliation, stunting, and plant death. Its species complex consists of several formae speciales (f. sp.) that collectively infect more than one hundred hosts, leading to serious losses in crops such as tomato, melon, banana, and cotton.
  • 973
  • 29 Mar 2022
Topic Review
Binding of Various Aminopolycarboxylates
Synthetic aminopolycarboxylates like ethylenediaminetetraacetate (EDTA) are common chelating agents. EDTA-degrading bacterium Chelativorans sp. BNC1 uses an ABC-type transporter for the uptake of free EDTA into its cells for biodegradation. The key component of the transporter is a periplasmic EDTA-binding protein, EppA, and the structural and functional analyses indicate that EppA is a general binding protein for the uptake of free aminopolycarboxylates, suggesting that stable metal-chelate complexes are not transported into the cells for biodegradation and explaining the persistence of stable metal-EDTA complexes in the environment.
  • 972
  • 02 Nov 2020
Topic Review
Ascomycota genomics, phylogenomics and proteomics
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments.
  • 971
  • 29 Dec 2020
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