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Dna extraction microbes

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https://www.readbyqxmd.com/read/29433218/application-of-high-throughput-pyrosequencing-in-the-analysis-of-microbiota-of-food-commodities-procured-from-small-and-large-retail-outlets-in-a-u-s-metropolitan-area-a-pilot-study
#1
Daleniece Higgins, Chandan Pal, Irshad M Sulaiman, Chunrong Jia, Tyler Zerwekh, Scot E Dowd, Pratik Banerjee
With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA...
March 2018: Food Research International
https://www.readbyqxmd.com/read/29361962/evaluation-of-biological-potential-of-selected-species-of-family-poaceae-from-bahawalpur-pakistan
#2
Iram Fatima, Sobia Kanwal, Tariq Mahmood
BACKGROUND: Oxidative stress as well as bacterial and fungal infections are common source of diseases while plants are source of medication for curative or protective purposes. Hence, aim of study was to compare the pharmacological potential of seven grass species in two different solvents i.e. ethanol and acetone. METHODS: Preliminary phytochemical tests were done and antioxidant activities were evaluated using ELISA and their IC50 values and AAI (%) were recorded...
January 24, 2018: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/29322917/identification-of-natural-antimicrobial-peptides-from-bacteria-through-metagenomic-and-metatranscriptomic-analysis-of-high-throughput-transcriptome-data-of-taiwanese-oolong-teas
#3
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29310749/culture-independent-approaches-to-chlamydial-genomics
#4
Alyce Taylor-Brown, Danielle Madden, Adam Polkinghorne
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement...
January 3, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29305057/comparison-of-dna-extraction-methods-for-human-gut-microbial-community-profiling
#5
Mi Young Lim, Eun-Ji Song, Sang Ho Kim, Jangwon Lee, Young-Do Nam
The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29295716/first-detection-and-genetic-characterisation-of-enterocytozoon-bieneusi-in-wild-deer-in-melbourne-s-water-catchments-in-australia
#6
Yan Zhang, Anson V Koehler, Tao Wang, Shane R Haydon, Robin B Gasser
BACKGROUND: Enterocytozoon bieneusi is reported to be a common microsporidian of humans and animals in various countries. However, E. bieneusi has yet to be recorded in animals in Australia. Here, we undertook the first molecular epidemiological investigation of E. bieneusi in three species of deer (Cervus elaphus, Dama dama and Rusa unicolor) that live in the catchment areas that supply the city of Melbourne with drinking water. METHODS: Genomic DNA was extracted from a total of 610 individual faecal samples from wild deer, including sambar deer (Rusa unicolor) (n = 516), red deer (Cervus elaphus) (n = 77) and fallow deer (Dama dama) (n = 17) from nine catchment areas, and then tested using a nested PCR-based sequencing approach employing internal transcribed spacer (ITS) of nuclear ribosomal DNA as the genetic marker...
January 3, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29274973/short-communication-signs-of-host-genetic-regulation-in-the-microbiome-composition-in-2-dairy-breeds-holstein-and-brown-swiss
#7
O Gonzalez-Recio, I Zubiria, A García-Rodríguez, A Hurtado, R Atxaerandio
This study aimed to evaluate whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Microbial DNA was extracted from 18 samples of ruminal content from 2 breeds (Holstein and Brown Swiss). Reads were processed using mothur (https://www.mothur.org/) in 16S and 18S rRNA gene-based analyses. Then, reads were classified at the genus clade, resulting in 3,579 operational taxonomic units (OTU) aligned against the 16S database and 184 OTU aligned against the 18S database...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29224074/sampling-extraction-and-high-throughput-sequencing-methods-for-environmental-microbial-and-viral-communities
#8
Pedro J Torres, Scott T Kelley
The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29207565/delivery-mode-and-the-transition-of-pioneering-gut-microbiota-structure-composition-and-predicted-metabolic-function
#9
Noel T Mueller, Hakdong Shin, Aline Pizoni, Isabel C Werlang, Ursula Matte, Marcelo Z Goldani, Helena A S Goldani, Maria G Dominguez-Bello
Cesarean (C-section) delivery, recently shown to cause excess weight gain in mice, perturbs human neonatal gut microbiota development due to the lack of natural mother-to-newborn transfer of microbes. Neonates excrete first the in-utero intestinal content (referred to as meconium) hours after birth, followed by intestinal contents reflective of extra-uterine exposure (referred to as transition stool) 2 to 3 days after birth. It is not clear when the effect of C-section on the neonatal gut microbiota emerges...
December 4, 2017: Genes
https://www.readbyqxmd.com/read/29161268/nucleic-acid-purification-from-plants-animals-and-microbes-in-under-30-seconds
#10
Yiping Zou, Michael Glenn Mason, Yuling Wang, Eugene Wee, Conny Turni, Patrick J Blackall, Matt Trau, Jose Ramon Botella
Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed...
November 2017: PLoS Biology
https://www.readbyqxmd.com/read/29078799/comparing-microbiotas-in-the-upper-aerodigestive-and-lower-respiratory-tracts-of-lambs
#11
Laura Glendinning, David Collie, Steven Wright, Kenny M D Rutherford, Gerry McLachlan
BACKGROUND: Recently, the importance of the lung microbiota during health and disease has been examined in humans and in small animal models. Whilst sheep have been proposed as an appropriate large animal model for studying the pathophysiology of a number of important human respiratory diseases, it is clearly important to continually define the limits of agreement between these systems as new concepts emerge. In humans, it has recently been established that the lung microbiota is seeded by microbes from the oral cavity...
October 27, 2017: Microbiome
https://www.readbyqxmd.com/read/29057500/the-impact-of-rumen-cannulation-on-the-microbial-community-of-goat-rumens-as-measured-using-16s-rrna-high-throughput-sequencing
#12
L Wang, D Wu, T Yan, L Wang
The main objective of this study was to determine the impact of rumen cannulation on the microbial community of goat rumens using 16S rRNA high-throughput sequencing. Twelve Boer crossbred goats were used in the experiment: six goats were surgically fitted with rumen cannula, and the other six were used as controls. All goats were fed the same diet for 20 days, after which their rumen digesta were sampled once per week for three consecutive weeks. Total microbial DNA was extracted from the collected rumen fluid and was used as a template to amplify the V4 hypervariable region of the 16S rRNA gene...
October 22, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28971851/time-of-day-and-eating-behaviors-are-associated-with-the-composition-and-function-of-the-human-gastrointestinal-microbiota
#13
Jennifer L Kaczmarek, Salma Ma Musaad, Hannah D Holscher
Background: Preclinical research has shown that the gastrointestinal microbiota exhibits circadian rhythms and that the timing of food consumption can affect the composition and function of gut microbes. However, there is a dearth of knowledge on these relations in humans.Objective: We aimed to determine whether human gastrointestinal microbes and bacterial metabolites were associated with time of day or behavioral factors, including eating frequency, percentage of energy consumed early in the day, and overnight-fast duration...
November 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28956398/-discovery-and-analysis-of-staphylococcus-aureus-biofilm-inhibitors-using-functional-metagenomics-approach
#14
Ying Zhu, Shumao Chai, Mingming Cao, Shaochen Wang, Zhiyang Feng
Although most microbes are not readily cultured in the lab, microbial DNA can be extracted directly from an environmental sample and be functionally expressed in a suitable host for natural products discovery, and this approach has been termed "metagenomics". An E'mei Mountain soil metagenomic library was constructed using an Escherichia coli-Streptomyces shuttle vector for functional based screening of anti-bacterial clones in Streptomyces albus host. Two active clones were obtained and their fermentation broths were studied for the inhibitory effect on Staphylococcus aureus biofilm...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28951300/effect-of-sea-buckthorn-protein-on-the-intestinal-microbial-community-in-streptozotocin-induced-diabetic-mice
#15
Huaibo Yuan, Fangfang Shi, Lina Meng, Wenjuan Wang
This study investigated the intestinal microbial community distribution of Type 2 diabetic mice and discussed the effects of the sea buckthorn protein on the regulation of gut microbes. Date was collected for 12 cases of normal mice (NC group), 12 cases of Type 2 diabetic mice (DC group), and 12 cases of highly concentrated sea buckthorn seed protein dosed mice (SSPH group). This study analysed fecal samples, measured faecal pH value, and cultivated and determined intestinal bacteria count. This investigation also included the extraction of faecal samples for genomic DNA, PCR amplification of bacterial V3 16S rDNA products by denaturing gradient gel electrophoresis, DGGE map analysis of intestinal flora, determination of intestinal bacteria richness, Shannon-Wiener index and evenness index, and image similarity cluster analysis with UPGMA clustering...
September 23, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28894126/microbes-in-infant-gut-development-placing-abundance-within-environmental-clinical-and-growth-parameters
#16
Tanja Obermajer, Iztok Grabnar, Evgen Benedik, Tina Tušar, Tatjana Robič Pikel, Nataša Fidler Mis, Bojana Bogovič Matijašić, Irena Rogelj
Sound and timely microbial gut colonization completes newborn's healthy metabolic programming and manifests in infant appropriate growth and weight development. Feces, collected at 3, 30, and 90 days after birth from 60 breastfed Slovenian newborns, was submitted to microbial DNA extraction and qPCR quantification of selected gut associated taxa. Multivariate regression analysis was applied to evaluate microbial dynamics with respect to infant demographic, environmental, clinical characteristics and first year growth data...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28866213/multifunctional-biosynthesized-silver-nanoparticles-exhibiting-excellent-antimicrobial-potential-against-multi-drug-resistant-microbes-along-with-remarkable-anticancerous-properties
#17
Diksha Jha, Prasanna Kumar Thiruveedula, Rajiv Pathak, Bipul Kumar, Hemant K Gautam, Shrish Agnihotri, Ashwani Kumar Sharma, Pradeep Kumar
This study demonstrates the therapeutic potential of silver nanoparticles (AgNPs), which were biosynthesized using the extracts of Citrus maxima plant. Characterization through UV-Vis spectrophotometry, Dynamic Light Scattering (DLS), Fourier Transform Infrared spectroscopy (FTIR), X-ray Diffraction (XRD) and Transmission Electron Microscopy (TEM) confirmed the formation of AgNps in nano-size range. These nanoparticles exhibited enhanced antioxidative activity and showed commendable antimicrobial activity against wide range of microbes including multi-drug resistant bacteria that were later confirmed by TEM...
November 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28609785/comprehensive-analysis-of-microorganisms-accompanying-human-archaeological-remains
#18
Anna Philips, Ireneusz Stolarek, Bogna Kuczkowska, Anna Juras, Luiza Handschuh, Janusz Piontek, Piotr Kozlowski, Marek Figlerowicz
Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains...
July 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28555427/optimization-of-high-yielding-protocol-for-dna-extraction-from-the-forest-rhizosphere-microbes
#19
Sadam D V Satyanarayana, M S R Krishna, Pindi Pavan Kumar
Soil is major reservoir for microbes and harbors a vast microbial diversity. Soil microbiota plays a pivotal role in biogeochemical cycles, bioremediation, and in health and disease states of humans, animals, and plants. It is imperative to understand the microbial signatures which are specific in such an ecosystem to unravel their potential role and impact on environment. During the recent years, exploration of soil microbial communities has been geared up with the advent of advanced sequencing technologies...
June 2017: 3 Biotech
https://www.readbyqxmd.com/read/28494549/-changes-in-the-composition-of-intestinal-microbiota-in-mice-with-acute-liver-failure-induced-by-d-galactosamine
#20
Y X Hu, L Yu, H J Liu, M L Cheng
Objective: To investigate the changes in the composition of intestinal microbiota in mice with acute liver failure and identify characteristic bacteria, and to provide a basis for the diagnosis and treatment of acute liver failure with intestinal microbiota disorders. Methods: A total of 30 specific pathogen-free male BALB/c mice were used in this study, including 25 mice in the model group and 5 mice in the control group. An acute liver failure model was induced by D-galactosamine. Microbial DNA was extracted from intestinal contents in different segments of the lower digestive tract (ileum and colon) and feces and then were amplified using PCR...
April 20, 2017: Zhonghua Gan Zang Bing za Zhi, Zhonghua Ganzangbing Zazhi, Chinese Journal of Hepatology
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