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Microbial diversity

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https://www.readbyqxmd.com/read/27933544/dissection-of-host-susceptibility-to-bacterial-infections-and-its-toxins
#1
Aysar Nashef, Mahmoud Agbaria, Ariel Shusterman, Nicola Ivan Lorè, Alessandra Bragonzi, Ervin Wiess, Yael Houri-Haddad, Fuad A Iraqi
Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933101/study-of-holtermanniella-wattica-leucosporidium-creatinivorum-naganishia-adeliensis-solicoccozyma-aeria-and-solicoccozyma-terricola-for-their-lipogenic-aptitude-from-different-carbon-sources
#2
Sara Filippucci, Giorgia Tasselli, Alessandro Scardua, Simone Di Mauro, Maria Rita Cramarossa, Davide Perini, Benedetta Turchetti, Andrea Onofri, Luca Forti, Pietro Buzzini
BACKGROUND: The ability of some microorganisms to accumulate lipids is well known; however, only recently the number of studies on microbial lipid biosynthesis for obtaining oleochemical products, namely biofuels and some building blocks for chemistry, is rapidly and spectacularly increased. Since 1990s, some oleaginous yeasts were studied for their ability to accumulate lipids up to 60-70% of their dry weight. Due to the vast array of engineering techniques currently available, the recombinant DNA technology was the main approach followed so far for obtaining lipid-overproducing yeasts, mainly belonging to the Yarrowia lipolytica...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27933047/diazotroph-diversity-in-the-sea-ice-melt-ponds-and-surface-waters-of-the-eurasian-basin-of-the-central-arctic-ocean
#3
Mar Fernández-Méndez, Kendra A Turk-Kubo, Pier L Buttigieg, Josephine Z Rapp, Thomas Krumpen, Jonathan P Zehr, Antje Boetius
The Eurasian basin of the Central Arctic Ocean is nitrogen limited, but little is known about the presence and role of nitrogen-fixing bacteria. Recent studies have indicated the occurrence of diazotrophs in Arctic coastal waters potentially of riverine origin. Here, we investigated the presence of diazotrophs in ice and surface waters of the Central Arctic Ocean in the summer of 2012. We identified diverse communities of putative diazotrophs through targeted analysis of the nifH gene, which encodes the iron protein of the nitrogenase enzyme...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27932907/optimized-r-functions-for-analysis-of-ecological-community-data-using-the-r-virtual-laboratory-rvlab
#4
Constantinos Varsos, Theodore Patkos, Anastasis Oulas, Christina Pavloudi, Alexandros Gougousis, Umer Zeeshan Ijaz, Irene Filiopoulou, Nikolaos Pattakos, Edward Vanden Berghe, Antonio Fernández-Guerra, Sarah Faulwetter, Eva Chatzinikolaou, Evangelos Pafilis, Chryssoula Bekiari, Martin Doerr, Christos Arvanitidis
BACKGROUND: Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27931360/molecular-biological-methods-in-environmental-engineering
#5
Guocai Zhang, Li Wei, Chein-Chi Chang, Yuhua Zhang, Dong Wei
Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification...
October 2016: Water Environment Research: a Research Publication of the Water Environment Federation
https://www.readbyqxmd.com/read/27930854/the-water-kefir-grain-inoculum-determines-the-characteristics-of-the-resulting-water-kefir-fermentation-process
#6
David Laureys, Luc De Vuyst
AIMS: To investigate the influence of the water kefir grain inoculum on the characteristics of the water kefir fermentation process. METHODS AND RESULTS: Three water kefir fermentation processes were started with different water kefir grain inocula and followed as a function of time regarding microbial species diversity, community dynamics, substrate consumption profile, and metabolite production course. The inoculum determined the water kefir grain growth, the viable counts on the grains, the time until total carbohydrate exhaustion, the final metabolite concentrations, and the microbial species diversity...
December 8, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27930842/hydrolysis-of-nitriles-by-soil-bacteria-variation-with-soil-origin
#7
O K L Rapheeha, M P Roux-van der Merwe, J Badenhorst, V Chhiba, M L Bode, K Mathiba, D Brady
AIMS: The aim of the current study was to explore the bacterial soil diversity for nitrile biocatalysts, in particular those for hydrolysis of β-substituted nitriles, to the corresponding carboxamides and acids that may be incorporated into peptidomimetics. To achieve this we needed to compare the efficiency of isolation methods and determine the influence of land use and geographical origin of the soil sample. METHODS AND RESULTS: Nitrile-utilizing bacteria were isolated from various soil environments across a thousand kilometre long transect of South Africa, including agricultural soil, a gold mine tailings dam, and uncultivated soil...
December 8, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27930727/airway-microbiota-in-bronchoalveolar-lavage-fluid-from-clinically-well-infants-with-cystic-fibrosis
#8
Theresa A Laguna, Brandie D Wagner, Cynthia B Williams, Mark J Stevens, Charles E Robertson, Cole W Welchlin, Catherine E Moen, Edith T Zemanick, Jonathan K Harris
BACKGROUND: Upper airway cultures guide the identification and treatment of lung pathogens in infants with cystic fibrosis (CF); however, this may not fully reflect the spectrum of bacteria present in the lower airway. Our objectives were to characterize the airway microbiota using bronchoalveolar lavage fluid (BALF) from asymptomatic CF infants during the first year of life and to investigate the relationship between BALF microbiota, standard culture and clinical characteristics. METHODS: BALF, nasopharyngeal (NP) culture and infant pulmonary function testing data were collected at 6 months and one year of age during periods of clinical stability from infants diagnosed with CF by newborn screening...
2016: PloS One
https://www.readbyqxmd.com/read/27929086/the-e3-ubiquitin-ligase-trim31-attenuates-nlrp3-inflammasome-activation-by-promoting-proteasomal-degradation-of-nlrp3
#9
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/27928044/microbes-in-the-anthropocene-spillover-of-agriculturally-selected-bacteria-and-their-impact-on-natural-ecosystems
#10
REVIEW
Thomas Bell, Jason M Tylianakis
Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes...
December 14, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27925857/analysis-of-the-intestinal-microbial-community-and-inferred-functional-capacities-during-the-host-response-to-pneumocystis-pneumonia
#11
Derrick R Samuelson, Tysheena P Charles, Nicholas M de la Rua, Christopher M Taylor, Eugene E Blanchard, Meng Luo, Judd E Shellito, David A Welsh
BACKGROUND: Pneumocystis pneumonia is a major cause of morbidity and mortality in patients infected with HIV/AIDS. In this study, we evaluated the intestinal microbial communities associated with the development of experimental Pneumocystis pneumonia, as there is growing evidence that the intestinal microbiota is critical for host defense against fungal pathogens. METHODS: C57BL/6 mice were infected with live Pneumocystis murina (P. murina) via intratracheal inoculation and sacrificed 7 and 14 days postinfection for microbiota analysis...
December 7, 2016: Experimental Lung Research
https://www.readbyqxmd.com/read/27925209/dynamics-of-microbial-community-during-the-extremely-long-term-fermentation-process-of-a-traditional-soy-sauce
#12
Yang Yang, Yue Deng, Yulan Jin, Yanxi Liu, Baixue Xia, Qun Sun
BACKGROUND: Soy sauce produced by long-term natural fermentation is a traditional specialty in Asia, with a reputation for superior quality and rich flavor. In this study, both culture-dependent and independent approaches were used to investigate the microbial diversity and community dynamics during an extremely long-term (up to four years) natural fermentation of Xianshi Soy Sauce, a national intangible cultural heritage. RESULTS: Genera of Bacillus, Aspergillus, and Cladosporium were detected by both methods above...
December 7, 2016: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/27924596/methods-to-study-antagonistic-activities-among-oral-bacteria
#13
Fengxia Qi, Jens Kreth
Most bacteria in nature exist in multispecies communities known as biofilms. In the natural habitat where resources (nutrient, space, etc.) are usually limited, individual species must compete or collaborate with other neighboring species in order to perpetuate in the multispecies community. The human oral cavity is colonized by >700 microbial species known as the indigenous microbiota. This indigenous flora normally maintains an ecological balance through antagonistic as well as mutualistic interspecies interactions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924593/analysis-of-16s-rrna-gene-amplicon-sequences-using-the-qiime-software-package
#14
Blair Lawley, Gerald W Tannock
The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924592/microbial-community-profiling-using-terminal-restriction-fragment-length-polymorphism-t-rflp-and-denaturing-gradient-gel-electrophoresis-dgge
#15
José F Siqueira, Mitsuo Sakamoto, Alexandre S Rosado
In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924591/the-oral-microbiota-in-health-and-disease-an-overview-of-molecular-findings
#16
José F Siqueira, Isabela N Rôças
Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924137/exercise-induced-stress-behavior-gut-microbiota-brain-axis-and-diet-a-systematic-review-for-athletes
#17
REVIEW
Allison Clark, Núria Mach
Fatigue, mood disturbances, under performance and gastrointestinal distress are common among athletes during training and competition. The psychosocial and physical demands during intense exercise can initiate a stress response activating the sympathetic-adrenomedullary and hypothalamus-pituitary-adrenal (HPA) axes, resulting in the release of stress and catabolic hormones, inflammatory cytokines and microbial molecules. The gut is home to trillions of microorganisms that have fundamental roles in many aspects of human biology, including metabolism, endocrine, neuronal and immune function...
2016: Journal of the International Society of Sports Nutrition
https://www.readbyqxmd.com/read/27923915/late-phase-synthesis-of-i%C3%AE%C2%BAb%C3%AE-insulates-the-tlr4-activated-canonical-nf-%C3%AE%C2%BAb-pathway-from-noncanonical-nf-%C3%AE%C2%BAb-signaling-in-macrophages
#18
Budhaditya Chatterjee, Balaji Banoth, Tapas Mukherjee, Nandaraj Taye, Bharath Vijayaragavan, Samit Chattopadhyay, James Gomes, Soumen Basak
The nuclear factor κB (NF-κB) transcription factors coordinate the inflammatory immune response during microbial infection. Pathogenic substances engage canonical NF-κB signaling through the heterodimer RelA:p50, which is subjected to rapid negative feedback by inhibitor of κBα (IκBα). The noncanonical NF-κB pathway is required for the differentiation of immune cells; however, cross-talk between both pathways can occur. Concomitantly activated noncanonical signaling generates p52 from the p100 precursor...
December 6, 2016: Science Signaling
https://www.readbyqxmd.com/read/27922852/hiv-associated-changes-in-the-enteric-microbial-community-potential-role-in-loss-of-homeostasis-and-development-of-systemic-inflammation
#19
David B Gootenberg, Jeffrey M Paer, Jesus-Mario Luevano, Douglas S Kwon
PURPOSE OF REVIEW: Despite HIV therapy advances, average life expectancy in HIV-infected individuals on effective treatment is significantly decreased relative to uninfected persons, largely because of increased incidence of inflammation-related diseases, such as cardiovascular disease and renal dysfunction. The enteric microbial community could potentially cause this inflammation, as HIV-driven destruction of gastrointestinal CD4 T cells may disturb the microbiota-mucosal immune system balance, disrupting the stable gut microbiome and leading to further deleterious host outcomes...
December 2, 2016: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/27921148/metabolites-deciphering-the-molecular-language-between-dcs-and-their-environment
#20
REVIEW
Lucía Minarrieta, Peyman Ghorbani, Tim Sparwasser, Luciana Berod
Dendritic cells (DCs) determine the outcome of the immune response based on signals they receive from the environment. Presentation of antigen under various contexts can lead to activation and differentiation of T cells for immunity or dampening of immune responses by establishing tolerance, primarily through the priming of regulatory T cells. Infections, inflammation and normal cellular interactions shape DC responses through direct contact or via cytokine signaling. Although it is widely accepted that DCs sense microbial components through pattern recognition receptors (PRRs), increasing evidence advocates for the existence of a set of signals that can profoundly shape DC function via PRR-independent pathways...
December 5, 2016: Seminars in Immunopathology
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