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https://www.readbyqxmd.com/read/28742161/abundance-and-co-occurrence-of-extracellular-capsules-increases-environmental-breadth-implications-for-the-emergence-of-pathogens
#1
Olaya Rendueles, Marc Garcia-Garcerà, Bertrand Néron, Marie Touchon, Eduardo P C Rocha
Extracellular capsules constitute the outermost layer of many bacteria, are major virulence factors, and affect antimicrobial therapies. They have been used as epidemiological markers and recently became vaccination targets. Despite the efforts to biochemically serotype capsules in a few model pathogens, little is known of their taxonomic and environmental distribution. We developed, validated, and made available a computational tool, CapsuleFinder, to identify capsules in genomes. The analysis of over 2500 prokaryotic genomes, accessible in a database, revealed that ca...
July 24, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28738824/visibiome-an-efficient-microbiome-search-engine-based-on-a-scalable-distributed-architecture
#2
Syafiq Kamarul Azman, Muhammad Zohaib Anwar, Andreas Henschel
BACKGROUND: Given the current influx of 16S rRNA profiles of microbiota samples, it is conceivable that large amounts of them eventually are available for search, comparison and contextualization with respect to novel samples. This process facilitates the identification of similar compositional features in microbiota elsewhere and therefore can help to understand driving factors for microbial community assembly. RESULTS: We present Visibiome, a microbiome search engine that can perform exhaustive, phylogeny based similarity search and contextualization of user-provided samples against a comprehensive dataset of 16S rRNA profiles environments, while tackling several computational challenges...
July 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#3
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/28714894/carbonic-anhydrase-from-porphyromonas-gingivalis-as-a-drug-target
#4
REVIEW
Claudiu T Supuran, Clemente Capasso
Periodontitis originates from a microbial synergy causing the development of a mouth microbial imbalance (dysbiosis), consisting of a microbial community composed of anaerobic bacteria. Most studies concerning the treatment of periodontitis have primarily take into account the Gram-negative bacterium Porphyromonas gingivalis, because it is a prominent component of the oral microbiome and a successful colonizer of the oral epithelium. Here, we focus our attention on the study of the carbonic anhydrases (CAs, EC 4...
July 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28710141/perspective-improving-nutritional-guidelines-for-sustainable-health-policies-current-status-and-perspectives
#5
Paolo Magni, Dennis M Bier, Sergio Pecorelli, Carlo Agostoni, Arne Astrup, Furio Brighenti, Robert Cook, Emanuela Folco, Luigi Fontana, Robert A Gibson, Ranieri Guerra, Gordon H Guyatt, John Pa Ioannidis, Ann S Jackson, David M Klurfeld, Maria Makrides, Basil Mathioudakis, Alessandro Monaco, Chirag J Patel, Giorgio Racagni, Holger J Schünemann, Raanan Shamir, Niv Zmora, Andrea Peracino
A large body of evidence supports the notion that incorrect or insufficient nutrition contributes to disease development. A pivotal goal is thus to understand what exactly is appropriate and what is inappropriate in food ingestion and the consequent nutritional status and health. The effective application of these concepts requires the translation of scientific information into practical approaches that have a tangible and measurable impact at both individual and population levels. The agenda for the future is expected to support available methodology in nutrition research to personalize guideline recommendations, properly grading the quality of the available evidence, promoting adherence to the well-established evidence hierarchy in nutrition, and enhancing strategies for appropriate vetting and transparent reporting that will solidify the recommendations for health promotion...
July 2017: Advances in Nutrition
https://www.readbyqxmd.com/read/28698533/prevention-and-management-of-cow-s-milk-allergy-in-non-exclusively-breastfed-infants
#6
REVIEW
Yvan Vandenplas
Introduction: The prevention and management of cow milk allergy (CMA) is still debated. Since CMA is much less frequent in breastfed infants, breastfeeding should be stimulated. Method: Literature was searched using databases to find original papers and reviews on this topic. Results: Hydrolysates with a clinical proof of efficacy are recommended in the prevention and treatment of CMA. However, not all meta-analyses conclude that hydrolysates do prevent CMA or other atopic manifestations such as atopic dermatitis...
July 10, 2017: Nutrients
https://www.readbyqxmd.com/read/28696064/harnessing-microbiome-based-biotechnologies-for-sustainable-mitigation-of-nitrous-oxide-emissions
#7
Hang-Wei Hu, Ji-Zheng He, Brajesh K Singh
Achieving the Sustainable Development Goal of climate change mitigation within this century will require adoption of new innovative technologies to control emissions of nitrous oxide (N2 O), an important greenhouse gas leading to global warming. This is particularly important in the face of growing fertilizer consumption and continuous land degradation. Currently used tools to mitigate N2 O emissions are based on agrochemical inputs and agronomic practices. Emerging technologies include plant breeding approaches to manipulate microbiome activities in agro-ecosystems, and microbial biotechnology approaches for in situ microbiome manipulation and engineering via use of biochemical, cellular and genome-editing methods...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28690680/from-grass-to-gas-microbiome-dynamics-of-grass-biomass-acidification-under-mesophilic-and-thermophilic-temperatures
#8
Christian Abendroth, Claudia Simeonov, Juli Peretó, Oreto Antúnez, Raquel Gavidia, Olaf Luschnig, Manuel Porcar
BACKGROUND: Separating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28690156/the-microbiome-as-engineering-tool-manufacturing-and-trading-between-microorganisms
#9
REVIEW
Jo De Vrieze, Marlies E R Christiaens, Willy Verstraete
The integration of microbial technologies within the framework of the water-energy nexus has been taking place for over a century, but these mixed microbial communities are considered hard to deal with 'black boxes'. Process steering is mainly based on avoiding process failure by monitoring conventional parameters, e.g., pH and temperature, which often leads to operation far below the intrinsic potential. Mixed microbial communities do not reflect a randomised individual mix, but an interacting microbiological entity...
July 6, 2017: New Biotechnology
https://www.readbyqxmd.com/read/28686570/using-metagenomics-to-connect-microbial-community-biodiversity-and-functions
#10
Lucas William Mendes, Lucas Peres Palma Braga, Acacio Aparecido Navarrete, Dennis Goss de Souza, Genivaldo Gueiros Zacarias Silva, Siu Mui Tsai
Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28678528/21st-century-toolkit-for-optimizing-population-health-through-precision-nutrition
#11
Aifric O'Sullivan, Bethany Henrick, Bonnie Dixon, Daniela Barile, Angela Zivkovic, Jennifer Smilowitz, Danielle Lemay, William Martin, J Bruce German, Sara Elizabeth Schaefer
Scientific, technological, and economic progress over the last 100 years all but eradicated problems of widespread food shortage and nutrient deficiency in developed nations. But now society is faced with a new set of nutrition problems related to energy imbalance and metabolic disease, which require new kinds of solutions. Recent developments in the area of new analytical tools enable us to systematically study large quantities of detailed and multidimensional metabolic and health data, providing the opportunity to address current nutrition problems through an approach called Precision Nutrition...
July 5, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28674641/quantifying-the-human-vaginal-community-state-types-csts-with-the-species-specificity-index
#12
Zhanshan Sam Ma, Lianwei Li
The five community state types (CSTs) first identified by Ravel et al. (2011) offered a powerful scheme to classify the states of human vaginal microbial communities (HVMC). The classification is a significant advance because it devised an effective handle to deal with the enormous inter-subject heterogeneity and/or intra-subject temporal variability, the quantification of which is extremely difficult but of critical importance such as the understanding of BV (bacterial vaginosis) etiology. Indeed, arguably the most plausible ecological hypothesis for interpreting the BV etiology heavily depends on the CST classification (Gajer et al...
2017: PeerJ
https://www.readbyqxmd.com/read/28670307/synthetic-microbial-ecology-engineering-habitats-for-modular-consortia
#13
Sami Ben Said, Dani Or
The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28669592/personalized-microbiome-dynamics-cytometric-fingerprints-for-routine-diagnostics
#14
REVIEW
Christin Koch, Susann Müller
Microbiomes convoy human life in countless ways. They are an essential part of the human body and interact with its host in countless ways. Currently, extensive microbiome analyses assessing the microbiomes' composition and functions based on sequencing information are still far away from being routine analyses due to the complexity of applied techniques and data analysis, their time demand as well as high costs. With the growing demand for on-time community assessment and monitoring of its dynamic behavior with high resolution, alternative high-throughput methods such as microbial community flow cytometry come into focus...
June 29, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28662139/bacterial-microbiome-in-the-nose-of-healthy-cats-and-in-cats-with-nasal-disease
#15
Elisabeth S Dorn, Barbara Tress, Jan S Suchodolski, Tariq Nisar, Prajesh Ravindran, Karin Weber, Katrin Hartmann, Bianka S Schulz
BACKGROUND: Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD). METHODOLOGY/PRINCIPAL FINDINGS: DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced...
2017: PloS One
https://www.readbyqxmd.com/read/28654195/dynamics-of-the-oral-microbiota-as-a-tool-to-estimate-time-since-death
#16
Joe Adserias Garriga, Narciso M Quijada, Marta Hernandez, David Rodríguez Lázaro, Dawnie Steadman, Jesús Garcia-Gil
Oral cavity harbors one of the most diverse microbiomes in the human body. It has been shown to be the second most complex in the body after the gastro- intestinal tract. Upon death, the indigenous microorganisms lead the decomposition of the carcass. Therefore, oral cavity and gastro-intestinal tract microbiomes, play a key role in human decomposition. The aim of the present study is to monitor the microbiome of decaying bodies on a daily basis and to identify signature bacterial taxa, that can improve postmortem interval estimation...
June 27, 2017: Molecular Oral Microbiology
https://www.readbyqxmd.com/read/28650266/disease-suppressive-soils-new-insights-from-the-soil-microbiome
#17
Daniel Schlatter, Linda L Kinkel, Linda S Thomashow, David M Weller, Timothy Carl Paulitz
Soils suppressive to soilborne pathogens have been identified world-wide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils...
June 26, 2017: Phytopathology
https://www.readbyqxmd.com/read/28640599/a-high-throughput-dna-sequencing-approach-for-determining-sources-of-fecal-bacteria-in-a-lake-superior-estuary
#18
Clairessa M Brown, Christopher Staley, Ping Wang, Brent Dalzell, Chan Lan Chun, Michael J Sadowsky
Current microbial source-tracking (MST) methods, employed to determine sources of fecal contamination in waterways, use molecular markers targeting host-associated bacteria in animal or human feces. However, there is a lack of knowledge about fecal microbiome composition in several animals and imperfect marker specificity and sensitivity. To overcome these issues, a community-based MST method has been developed. Here, we describe a study done in the Lake Superior-Saint Louis River estuary using SourceTracker, a program that calculates the source contribution to an environment...
July 10, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28630614/a-plant-based-diet-for-the-prevention-and-treatment-of-type-2-diabetes
#19
REVIEW
Michelle McMacken, Sapana Shah
The prevalence of type 2 diabetes is rising worldwide, especially in older adults. Diet and lifestyle, particularly plant-based diets, are effective tools for type 2 diabetes prevention and management. Plant-based diets are eating patterns that emphasize legumes, whole grains, vegetables, fruits, nuts, and seeds and discourage most or all animal products. Cohort studies strongly support the role of plant-based diets, and food and nutrient components of plant-based diets, in reducing the risk of type 2 diabetes...
May 2017: Journal of Geriatric Cardiology: JGC
https://www.readbyqxmd.com/read/28628333/coupling-targeted-and-untargeted-mass-spectrometry-for-metabolome-microbiome-wide-association-studies-of-human-fecal-samples
#20
Alexey V Melnik, Ricardo R da Silva, Embriette R Hyde, Alexander A Aksenov, Fernando Vargas, Amina Bouslimani, Ivan Protsyuk, Alan K Jarmusch, Anupriya Tripathi, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays, and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies...
July 6, 2017: Analytical Chemistry
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