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1.
Microbiome and Metabolome Profiles Associated With Different Types of Short Bowel Syndrome: Implications for Treatment.
Budinska, E, Gojda, J, Heczkova, M, Bratova, M, Dankova, H, Wohl, P, Bastova, H, Lanska, V, Kostovcik, M, Dastych, M, et al
JPEN. Journal of parenteral and enteral nutrition. 2020;(1):105-118
Abstract
BACKGROUND The gut microbiome and metabolome may significantly influence clinical outcomes in patients with short bowel syndrome (SBS). The study aimed to describe specific metagenomic/metabolomics profiles of different SBS types and to identify possible therapeutic targets. METHODS Fecal microbiome (FM), volatile organic compounds (VOCs), and bile acid (BA) spectrum were analyzed in parenteral nutrition (PN)-dependent SBS I, SBS II, and PN-independent (non-PN) SBS patients. RESULTS FM in SBS I, SBS II, and non-PN SBS shared characteristic features (depletion of beneficial anaerobes, high abundance of Lactobacilaceae and Enterobacteriaceae). SBS I patients were characterized by the abundance of oxygen-tolerant microrganisms and depletion of strict anaerobes. Non-PN SBS subjects showed markers of partial FM normalization. FM dysbiosis was translated into VOC and BA profiles characteristic for each SBS cohort. A typical signature of all SBS patients comprised high saturated aldehydes and medium-chain fatty acids and reduced short-chain fatty acid (SCFA) content. Particularly, SBS I and II exhibited low protein metabolism intermediate (indole, p-cresol) content despite the hypothetical presence of relevant metabolism pathways. Distinctive non-PN SBS marker was high phenol content. SBS patients' BA fecal spectrum was enriched by chenodeoxycholic and deoxycholic acids and depleted of lithocholic acid. CONCLUSIONS Environmental conditions in SBS gut significantly affect FM composition and metabolic activity. The common feature of diverse SBS subjects is the altered VOC/BA profile and the lack of important products of microbial metabolism. Strategies oriented on the microbiome/metabolome reconstitution and targeted delivery of key compounds may represent a promising therapeutic strategy in SBS patients.
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Diverse Physiological Functions of Cation Proton Antiporters across Bacteria and Plant Cells.
Tsujii, M, Tanudjaja, E, Uozumi, N
International journal of molecular sciences. 2020;(12)
Abstract
Membrane intrinsic transport systems play an important role in maintaining ion and pH homeostasis and forming the proton motive force in the cytoplasm and cell organelles. In most organisms, cation/proton antiporters (CPAs) mediate the exchange of K+, Na+ and Ca2+ for H+ across the membrane in response to a variety of environmental stimuli. The tertiary structure of the ion selective filter and the regulatory domains of Escherichia coli CPAs have been determined and a molecular mechanism of cation exchange has been proposed. Due to symbiogenesis, CPAs localized in mitochondria and chloroplasts of eukaryotic cells resemble prokaryotic CPAs. CPAs primarily contribute to keeping cytoplasmic Na+ concentrations low and controlling pH, which promotes the detoxification of electrophiles and formation of proton motive force across the membrane. CPAs in cyanobacteria and chloroplasts are regulators of photosynthesis and are essential for adaptation to high light or osmotic stress. CPAs in organellar membranes and in the plasma membrane also participate in various intracellular signal transduction pathways. This review discusses recent advances in our understanding of the role of CPAs in cyanobacteria and plant cells.
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The Role of Rhizosphere Bacteriophages in Plant Health.
Pratama, AA, Terpstra, J, de Oliveria, ALM, Salles, JF
Trends in microbiology. 2020;(9):709-718
Abstract
Microbiomes and their hosts influence each other; for instance, the microbiome improves host fitness, whereas the host supports microbiome nutrition. Most studies on this topic have focused on the role of bacteria and fungi, although research on viruses that infect bacteria, known as 'bacteriophages' (phages), has gained importance due to the potential role bacteriophages play in the resilience and functionality of the gut microbiome. Like the gut microbiome, the rhizosphere harbors a complex microbiome, but little is known about the role of phages in this ecosystem. In this opinion, we extend the knowledge gained in human gut virus metagenomics (viromics) to disentangle the potential role of phages in driving the resilience and functionality of the rhizosphere microbiome. We propose that future comparative studies across environments are necessary to unravel the underlying mechanisms through which phages drive the composition and functionality of the rhizosphere microbiome and its interaction with the plant host. Importantly, such understanding might generate strategies to improve plant resistance and resilience in the context of climate change.
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Anammox-based processes: How far have we come and what work remains? A review by bibliometric analysis.
Nsenga Kumwimba, M, Lotti, T, Şenel, E, Li, X, Suanon, F
Chemosphere. 2020;:124627
Abstract
Nitrogen contamination remains a severe environmental problem and a major threat to sustainable development worldwide. A systematic analysis of the literature indicates that the partial nitritation-anammox (PN/AMX) process is still actively studied as a viable option for energy-efficient and feasible technology for the sustainable treatment of N- rich wastewaters, since its initial discovery in 1990. Notably, the mainstream PN/AMX process application remains the most challenging bottleneck in AMX technology and fascinates the world's attention in AMX studies. This paper discusses the recent trends and developments of PN/AMX research and analyzes the results of recent years of research on the PN/AMX from lab-to full-scale applications. The findings would deeply improve our understanding of the major challenges under mainstream conditions and next-stage research on the PN/AMX process. A great deal of efforts has been made in the process engineering, PN/AMX bacteria populations, predictive modeling, and the full-scale implementations during the past 22 years. A series of new and excellent experimental findings at lab, pilot and full-scale levels including good nitrogen removal performance even under low temperature (15-10 °C) around the world were achieved. To date, pilot- and full-scale PN/AMX have been successfully used to treat different types of industrial sewage, including black wastewater, sludge digester liquids, landfill leachate, monosodium glutamate wastewater, etc. Supplementing the qualitative analysis, this review also provides a quantitative bibliometrics study and evaluates global perspectives on PN/AMX research published during the past 22 years. Finally, general trends in the development of PN/AMX research are summarized with the aim of conveying potential future trajectories. The current review offers a valuable orientation and global overview for scientists, engineers, readers and decision makers presently focusing on PN/AMX processes.
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5.
Scavenging Bacterial Siderophores with Engineered Lipocalin Proteins as an Alternative Antimicrobial Strategy.
Dauner, M, Skerra, A
Chembiochem : a European journal of chemical biology. 2020;(5):601-606
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Abstract
Iron acquisition mediated by siderophores, high-affinity chelators for which bacteria have evolved specific synthesis and uptake mechanisms, plays a crucial role in microbiology and in host-pathogen interactions. In the ongoing fight against bacterial infections, this area has attracted biomedical interest. Beyond several approaches to interfere with siderophore-mediated iron uptake from medicinal and immunochemistry, the development of high-affinity protein scavengers that tightly complex the siderophores produced by pathogenic bacteria has appeared as a novel strategy. Such binding proteins have been engineered based on siderocalin-also known as lipocalin 2-an endogenous human scavenger of enterobactin and bacillibactin that controls the systemic spreading of commensal bacteria such as Escherichia coli. By using combinatorial protein design, siderocalin was reshaped to bind several siderophores from Pseudomonas aeruginosa and, in particular, petrobactin from Bacillus anthracis, none of which is recognized by the natural protein. Such engineered versions of siderocalin effectively suppress the growth of corresponding pathogenic bacteria by depriving them of their iron supply and offer the potential to complement antibiotic therapy in situations of acute or persistent infection.
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Recent Advances in Metabolic Pathways of Sulfate Reduction in Intestinal Bacteria.
Kushkevych, I, Cejnar, J, Treml, J, Dordević, D, Kollar, P, Vítězová, M
Cells. 2020;(3)
Abstract
Sulfate is present in foods, beverages, and drinking water. Its reduction and concentration in the gut depend on the intestinal microbiome activity, especially sulfate-reducing bacteria (SRB), which can be involved in inflammatory bowel disease (IBD). Assimilatory sulfate reduction (ASR) is present in all living organisms. In this process, sulfate is reduced to hydrogen sulfide and then included in cysteine and methionine biosynthesis. In contrast to assimilatory sulfate reduction, the dissimilatory process is typical for SRB. A terminal product of this metabolism pathway is hydrogen sulfide, which can be involved in gut inflammation and also causes problems in industries (due to corrosion effects). The aim of the review was to compare assimilatory and dissimilatory sulfate reduction (DSR). These processes occur in some species of intestinal bacteria (e.g., Escherichia and Desulfovibrio genera). The main attention was focused on the description of genes and their location in selected strains. Their coding expression of the enzymes is associated with anabolic processes in various intestinal bacteria. These analyzed recent advances can be important factors for proposing possibilities of metabolic pathway extension from hydrogen sulfide to cysteine in intestinal SRB. The switch from the DSR metabolic pathway to the ASR metabolic pathway is important since toxic sulfide is not produced as a final product.
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CRISPR/Cas9: Nature's gift to prokaryotes and an auspicious tool in genome editing.
Khanzadi, MN, Khan, AA
Journal of basic microbiology. 2020;(2):91-102
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a family of DNA direct repeats found in many prokaryotic genomes. It was discovered in bacteria as their (adaptive) immune system against invading viruses. Cas9 is an endonuclease enzyme linked with the CRISPR system in bacteria. Bacteria use the Cas9 enzyme to chop viral DNA sequences by unwinding it and then finding the complementary base pairs to the guide RNA. CRISPR/Cas9 is a modern and powerful molecular biology approach that is widely used in genome engineering (to activate/repress gene expression). It can be used in vivo to cause targeted genome modifications with better efficiency as compared to meganucleases, zinc-finger nucleases and transcription activator-like effector nucleases. CRISPR/Cas9 is a simple, reliable, and rapid method for causing gene alterations that open new horizons of gene editing in a variety of living organisms, including humans, for the treatment of several diseases. In this short review, we explored the basic mechanisms underlying its working principles along with some of its current applications in a number of diverse fields.
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Multi-metal nutrient restriction and crosstalk in metallostasis systems in microbial pathogens.
Jordan, MR, Wang, J, Capdevila, DA, Giedroc, DP
Current opinion in microbiology. 2020;:17-25
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Abstract
Transition metals from manganese to zinc function as catalytic and structural cofactors for an amazing diversity of proteins and enzymes, and thus are essential for all forms of life. During infection, inflammatory host proteins limit the accessibility of multiple transition metals to invading pathogens in a process termed nutritional immunity. In order to respond to host-mediated metal starvation, bacteria employ both protein and RNA-based mechanisms to sense prevailing transition metal concentrations that collectively regulate systems-level strategies to maintain cellular metallostasis. In this review, we discuss a number of recent advances in our understanding of how bacteria orchestrate the adaptive response to host-mediated multi-metal restriction, highlighting crosstalk among these regulatory systems.
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Addressing the challenges in antisepsis: focus on povidone iodine.
Barreto, R, Barrois, B, Lambert, J, Malhotra-Kumar, S, Santos-Fernandes, V, Monstrey, S
International journal of antimicrobial agents. 2020;(3):106064
Abstract
OBJECTIVES Using antiseptics in wound care can promote healing by preventing and treating infection. However, using antiseptics can present many challenges, including issues with tolerability, inactivation by organic matter and the emergence of antimicrobial resistance/cross-resistance. This review discussed the key challenges in antisepsis, focusing on povidone-iodine (PVP-I) antiseptic. METHODS Literature searches were conducted in PubMed, in January 2019, with a filter for the previous 5 years. Searches were based on the antimicrobial efficacy, antiseptic resistance, wound healing properties, and skin tolerability for the commonly used antiseptics PVP-I, chlorhexidine gluconate (CHG), polyhexanide (PHMB), and octenidine (OCT). Additional papers were identified based on author expertise. RESULTS When compared with CHG, PHMB and OCT, PVP-I had a broader spectrum of antimicrobial activity against Gram-negative bacteria, actinobacteria, bacterial spores, fungi and viruses, and a similar and broad spectrum of activity against Gram-positive bacteria. PVP-I was also highly effective at eradicating bacterial biofilms, which is a vitally important consideration for wound care and infection control. Despite a long history of extensive use, no resistance or cross-resistance to PVP-I has been recorded, which is in contrast with other antiseptics. Despite previous misconceptions, it has been shown that PVP-I has low allergenic properties, low cytotoxicity and can promote wound healing through increased expression of transforming growth factor beta. CONCLUSION With increased understanding of the importance of tackling antimicrobial resistance and bacterial biofilms in acute and chronic wound care, alongside improved understanding of the challenges of antiseptic use, PVP-I remains a promising agent for the management of antisepsis.
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Successive use of microorganisms to remove chromium from wastewater.
Elahi, A, Arooj, I, Bukhari, DA, Rehman, A
Applied microbiology and biotechnology. 2020;(9):3729-3743
Abstract
Heavy metal pollution is a direct consequence of the extensive utilization of heavy metals in various industrial processes. The persistence and nondegradability of heavy metals cause them to bioaccumulate in nature, and when they come in direct contact with the pristine environment, they not only contaminate it severely but also pose dire consequences to the health of all living forms on earth, including humans. Chromium (Cr) is one of the heavy metals which has been extensively used in various industrial processes such as mining, alloy manufacturing, tanning of hides and skins, pigment production, etc. However, it is regarded as a priority pollutant due to its highly toxic, teratogenic, mutagenic, and carcinogenic nature, and the U.S. Environmental Protection Agency (EPA) also categorized it into group "A" human carcinogen. In contrast to water-soluble hexavalent chromium (Cr6+), its reduced form, trivalent chromium (Cr3+), is relatively benign and readily precipitated at environmental pH. Thus, bioremediation of Cr6+ through microorganisms including bacteria, yeast, and algae provides a promising approach to decontaminate a metal-polluted environment. This review describes an overview of the microbial reduction of Cr6+, resistance mechanism, and the antioxidant profiling exhibited by these microorganisms when exposed to Cr6+. It also describes the pilot-scale study of the successive use of bacterial, fungal, and algal strains and the subsequent use of microbially purified water for the cultivation of plant growth. Multiple metal-resistant microorganisms are a good bioresource for green chemistry to eradicate environmental Cr6+. KEY POINTS • Hexavalent chromium (Cr6+) is highly toxic for living organisms including humans. • Microbial Cr resistance is mediated at the genetic, proteomic, and molecular levels. • Successive use of microorganisms is the best strategy to exterminate Cr6+from the environment.