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https://www.readbyqxmd.com/read/27933456/penicillin-v-acylases-from-gram-negative-bacteria-degrade-n-acylhomoserine-lactones-and-attenuate-virulence-in-pseudomonas-aeruginosa
#1
Avinash Vellore Sunder, Putri Dwi Utari, Sureshkumar Ramasamy, Ronald van Merkerk, Wim Quax, Archana Pundle
Virulence pathways in gram-negative pathogenic bacteria are regulated by quorum sensing mechanisms, through the production and sensing of N-acylhomoserine lactone (AHL) signal molecules. Enzymatic degradation of AHLs leading to attenuation of virulence (quorum quenching) could pave the way for the development of new antibacterials. Penicillin V acylases (PVAs) belong to the Ntn hydrolase superfamily, together with AHL acylases. PVAs are exploited widely in the pharmaceutical industry, but their role in the natural physiology of their native microbes is not clearly understood...
December 8, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27933039/the-contribution-of-mathematical-modeling-to-understanding-dynamic-aspects-of-rumen-metabolism
#2
André Bannink, Henk J van Lingen, Jennifer L Ellis, James France, Jan Dijkstra
All mechanistic rumen models cover the main drivers of variation in rumen function, which are feed intake, the differences between feedstuffs and feeds in their intrinsic rumen degradation characteristics, and fractional outflow rate of fluid and particulate matter. Dynamic modeling approaches are best suited to the prediction of more nuanced responses in rumen metabolism, and represent the dynamics of the interactions between substrates and micro-organisms and inter-microbial interactions. The concepts of dynamics are discussed for the case of rumen starch digestion as influenced by starch intake rate and frequency of feed intake, and for the case of fermentation of fiber in the large intestine...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27932684/standardizing-the-microbiota-of-fish-used-in-research
#3
REVIEW
I N Vatsos
Little attention has been paid to the effects of fish microbiotas on the reproducibility and comparability of fish studies so far. Extrinsic and intrinsic factors, such as water quality, environmental microbial populations, diet, host genetic profile, gender, age and stress status, affect fish microbiotas and create significant inter- and intra-species variations. Fish microbiotas play critical roles in many key aspects of host physiology, such as protection against pathogens, digestion and development of the digestive tract and the local immune system...
December 8, 2016: Laboratory Animals
https://www.readbyqxmd.com/read/27929086/the-e3-ubiquitin-ligase-trim31-attenuates-nlrp3-inflammasome-activation-by-promoting-proteasomal-degradation-of-nlrp3
#4
Hui Song, Bingyu Liu, Wanwan Huai, Zhongxia Yu, Wenwen Wang, Jing Zhao, Lihui Han, Guosheng Jiang, Lining Zhang, Chengjiang Gao, Wei Zhao
The NLRP3 inflammasome has a fundamental role in host defence against microbial pathogens and its deregulation may cause diverse inflammatory diseases. NLRP3 protein expression is a rate-limiting step for inflammasome activation, thus its expression must be tightly controlled to maintain immune homeostasis and avoid detrimental effects. However, how NLRP3 expression is regulated remains largely unknown. In this study, we identify E3 ubiquitin ligase TRIM31 as a feedback suppressor of NLRP3 inflammasome. TRIM31 directly binds to NLRP3, promotes K48-linked polyubiquitination and proteasomal degradation of NLRP3...
December 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27918230/mechanisms-of-cross-talk-between-the-diet-the-intestinal-microbiome-and-the-undernourished-host
#5
Helene Velly, Robert A Britton, Geoffrey A Preidis
Undernutrition remains one of the most pressing global health challenges today, contributing to nearly half of all deaths in children under five years of age. Although insufficient dietary intake and environmental enteric dysfunction are often inciting factors, evidence now suggests that unhealthy gut microbial populations perpetuate the vicious cycle of pathophysiology that results in persistent growth impairment in children. The metagenomics era has facilitated new research identifying an altered microbiome in undernourished hosts and has provided insight into a number of mechanisms by which these alterations may affect growth...
December 5, 2016: Gut Microbes
https://www.readbyqxmd.com/read/27917161/the-interaction-between-plants-and-bacteria-in-the-remediation-of-petroleum-hydrocarbons-an-environmental-perspective
#6
REVIEW
Panagiotis Gkorezis, Matteo Daghio, Andrea Franzetti, Jonathan D Van Hamme, Wouter Sillen, Jaco Vangronsveld
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27912059/microbiota-diurnal-rhythmicity-programs-host-transcriptome-oscillations
#7
Christoph A Thaiss, Maayan Levy, Tal Korem, Lenka Dohnalová, Hagit Shapiro, Diego A Jaitin, Eyal David, Deborah R Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav
The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographical localization and metabolome patterns that determine the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27912009/resource-stoichiometry-and-the-biogeochemical-consequences-of-nitrogen-deposition-in-a-mixed-deciduous-forest
#8
Meghan G Midgley, Richard P Phillips
Ecosystems often show differential sensitivity to chronic nitrogen (N) deposition; hence, a critical challenge is to improve our understanding of how and why site-specific factors mediate biogeochemical responses to N enrichment. We examined the extent to which N impacts on soil carbon (C) and N dynamics depend on microbial resource stoichiometry. We added N to forest plots dominated by ectomycorrhizal (ECM) trees, which have litter and soil pools rich in organic N and relatively wide C:N ratios, and adjacent forest plots dominated by arbuscular mycorrhizal (AM) trees, which have litter and soil pools rich in inorganic N and relatively narrow C:N ratios...
December 2016: Ecology
https://www.readbyqxmd.com/read/27905920/synergistic-effects-and-related-bioactive-mechanism-of-potentilla-fruticosa-l-leaves-combined-with-ginkgo-biloba-extracts-studied-with-microbial-test-system-mts
#9
Ze-Hua Liu, Dong-Mei Wang, Su-Fang Fan, Deng-Wu Li, Zi-Wen Luo
BACKGROUND: Potentilla fruticosa, also called "Jinlaomei" and "Gesanghua", is widely used as folk herbs in traditional Tibetan medicine in China to treat inflammations, wounds, certain forms of cancer, diarrhoea, diabetes and other ailments. Previous research found P. fruticosa leaf extract (C-3) combined with Ginkgo biloba extracts (EGb) showed obvious synergistic effects in a variety of oxidation systems. The aim of the present study was to further confirm the synergy of P. fruticosa combined with EGb viewed from physiological bioavailability and explore the related bioactive mechanism behind the synergism...
December 1, 2016: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/27900689/novel-tools-for-the-functional-expression-of-metagenomic-dna
#10
Nadine Katzke, Andreas Knapp, Anita Loeschcke, Thomas Drepper, Karl-Erich Jaeger
Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900682/construction-and-screening-of-marine-metagenomic-large-insert-libraries
#11
Nancy Weiland-Bräuer, Daniela Langfeldt, Ruth A Schmitz
The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896730/scaling-up-the-phylogenetic-detection-of-lateral-gene-transfer-events
#12
Cheong Xin Chan, Robert G Beiko, Mark A Ragan
Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896478/soil-microbial-communities-buffer-physiological-responses-to-drought-stress-in-three-hardwood-species
#13
Steven A Kannenberg, Richard P Phillips
Trees possess myriad adaptations for coping with drought stress, but the extent to which their drought responses are influenced by interactions with soil microbes is poorly understood. To explore the role of microbes in mediating tree responses to drought stress, we exposed saplings of three species (Acer saccharum, Liriodendron tulipifera, and Quercus alba) to a four week experimental drought in mesocosms. Half of the pots were inoculated with a live soil slurry (i.e., a microbial inoculum derived from soils beneath the canopies of mature A...
November 28, 2016: Oecologia
https://www.readbyqxmd.com/read/27894645/microbes-dress-for-success-tolerance-or-resistance
#14
Janelle S Ayres
The intestinal microbiota performs essential functions for host physiology, but the specific constituents and the microbial factors required to promote host health remain largely unknown. A study by Rangan et al. suggests that members of the microbiota can modify microbial associated molecular patterns to promote host defense against invading pathogens.
November 25, 2016: Trends in Microbiology
https://www.readbyqxmd.com/read/27892936/influence-of-early-life-exposure-host-genetics-and-diet-on-the-mouse-gut-microbiome-and-metabolome
#15
Antoine M Snijders, Sasha A Langley, Young-Mo Kim, Colin J Brislawn, Cecilia Noecker, Erika M Zink, Sarah J Fansler, Cameron P Casey, Darla R Miller, Yurong Huang, Gary H Karpen, Susan E Celniker, James B Brown, Elhanan Borenstein, Janet K Jansson, Thomas O Metz, Jian-Hua Mao
Although the gut microbiome plays important roles in host physiology, health and disease(1), we lack understanding of the complex interplay between host genetics and early life environment on the microbial and metabolic composition of the gut. We used the genetically diverse Collaborative Cross mouse system(2) to discover that early life history impacts the microbiome composition, whereas dietary changes have only a moderate effect. By contrast, the gut metabolome was shaped mostly by diet, with specific non-dietary metabolites explained by microbial metabolism...
November 28, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27892466/direct-evidence-for-microbial-derived-soil-organic-matter-formation-and-its-ecophysiological-controls
#16
Cynthia M Kallenbach, Serita D Frey, A Stuart Grandy
Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear...
November 28, 2016: Nature Communications
https://www.readbyqxmd.com/read/27891619/the-role-of-nutrients-in-drought-induced-tree-mortality-and-recovery
#17
REVIEW
Arthur Gessler, Marcus Schaub, Nate G McDowell
I. II. III. References SUMMARY: Global forests are experiencing rising temperatures and more severe droughts, with consistently dire forecasts for negative future impacts. Current research on the physiological mechanisms underlying drought impacts is focused on the water- and carbon-associated mechanisms. The role of nutrients is notably missing from this research agenda. Here, we investigate what role, if any, forest nutrition plays for survival and recovery of forests during and after drought. High nutrient availability may play a detrimental role in drought survival due to preferential biomass allocation aboveground that (1) predispose plants to hydraulic constraints limiting photosynthesis and promoting hydraulic failure, (2) increases carbon costs during periods of carbon starvation, and (3) promote biotic attack due to low tissue carbon: nitrogen (C : N)...
November 28, 2016: New Phytologist
https://www.readbyqxmd.com/read/27889451/diet-microbiota-interactions-mediate-global-epigenetic-programming-in-multiple-host-tissues
#18
Kimberly A Krautkramer, Julia H Kreznar, Kymberleigh A Romano, Eugenio I Vivas, Gregory A Barrett-Wilt, Mary E Rabaglia, Mark P Keller, Alan D Attie, Federico E Rey, John M Denu
Histone-modifying enzymes regulate transcription and are sensitive to availability of endogenous small-molecule metabolites, allowing chromatin to respond to changes in environment. The gut microbiota produces a myriad of metabolites that affect host physiology and susceptibility to disease; however, the underlying molecular events remain largely unknown. Here we demonstrate that microbial colonization regulates global histone acetylation and methylation in multiple host tissues in a diet-dependent manner: consumption of a "Western-type" diet prevents many of the microbiota-dependent chromatin changes that occur in a polysaccharide-rich diet...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27889152/application-of-flow-cytometry-to-wine-microorganisms
#19
REVIEW
Cédric Longin, Clément Petitgonnet, Michèle Guilloux-Benatier, Sandrine Rousseaux, Hervé Alexandre
Flow cytometry (FCM) is a powerful technique allowing detection and enumeration of microbial populations in food and during food process. Thanks to the fluorescent dyes used and specific probes, FCM provides information about cell physiological state and allows enumeration of a microorganism in a mixed culture. Thus, this technique is increasingly used to quantify pathogen, spoilage microorganisms and microorganisms of interest. Since one decade, FCM applications to the wine field increase greatly to determine population and physiological state of microorganisms performing alcoholic and malolactic fermentations...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27886541/long-term-effects-of-nickel-oxide-nanoparticles-on-performance-microbial-enzymatic-activity-and-microbial-community-of-a-sequencing-batch-reactor
#20
Sen Wang, Zhiwei Li, Mengchun Gao, Zonglian She, Liang Guo, Dong Zheng, Yangguo Zhao, Bingrui Ma, Feng Gao, Xuejiao Wang
The nitrogen and phosphorus removal, microbial enzymatic activity, and microbial community of a sequencing batch reactor (SBR) were evaluated under long-term exposure to nickel oxide nanoparticles (NiO NPs). High NiO NP concentration (over 5 mg L(-1)) affected the removal of chemical oxygen demand, nitrogen, and phosphorus. The presence of NiO NP inhibited the microbial enzymatic activities and reduced the nitrogen and phosphorus removal rates of activated sludge. The microbial enzymatic activities of the activated sludge showed a similar variation trend to the nitrogen and phosphorus removal rates with the increase in NiO NP concentration from 0 to 60 mg L(-1)...
November 22, 2016: Chemosphere
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