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Dna extraction microbes

Katherine R Amato
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health...
October 20, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
Elisabeth Schrumpf, Martin Kummen, Laura Valestrand, Thomas U Greiner, Kristian Holm, Velmurugesan Arulampalam, Henrik M Reims, John Baines, Fredrik Bäckhed, Tom H Karlsen, Richard S Blumberg, Johannes R Hov, Espen Melum
BACKGROUND & AIMS: A strong association between human inflammatory biliary diseases and gut inflammation has led to the hypothesis that gut microbes and lymphocytes activated in the intestine play a role in biliary inflammation. The NOD.c3c4 mouse model develops spontaneous biliary inflammation in extra- and intra-hepatic bile ducts. We aimed to clarify the role of the gut microbiota in the biliary disease of NOD.c3c4 mice. METHODS: We sampled cecal content and mucosa from conventionally raised (CONV-R) NOD...
October 5, 2016: Journal of Hepatology
Shariq Qayyum, Asad Ullah Khan
Silver nanoparticles (AgNPs) were biosynthesized via a green route using ten different plants extracts (GNP1- Caryota urens, GNP2-Pongamia glabra, GNP3- Hamelia patens, GNP4-Thevetia peruviana, GNP5-Calendula officinalis, GNP6-Tectona grandis, GNP7-Ficus petiolaris, GNP8- Ficus busking, GNP9- Juniper communis, GNP10-Bauhinia purpurea). AgNPs were tested against drug resistant microbes and their biofilms. These nanoparticles (NPs) were characterised using UV-vis spectroscopy, transmission electron microscope, Fourier transform infrared spectroscopy, X-ray diffraction and Image J software...
October 2016: IET Nanobiotechnology
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
Ericka L Anderson, Weizhong Li, Niels Klitgord, Sarah K Highlander, Mark Dayrit, Victor Seguritan, Shibu Yooseph, William Biggs, J Craig Venter, Karen E Nelson, Marcus B Jones
As reports on possible associations between microbes and the host increase in number, more meaningful interpretations of this information require an ability to compare data sets across studies. This is dependent upon standardization of workflows to ensure comparability both within and between studies. Here we propose the standard use of an alternate collection and stabilization method that would facilitate such comparisons. The DNA Genotek OMNIgene∙Gut Stool Microbiome Kit was compared to the currently accepted community standard of freezing to store human stool samples prior to whole genome sequencing (WGS) for microbiome studies...
2016: Scientific Reports
Jacobo de la Cuesta-Zuluaga, Juan S Escobar
Next-generation sequencing technologies have found a widespread use in the study of host-microbe interactions due to the increase in their throughput and their ever-decreasing costs. The analysis of human-associated microbial communities using a marker gene, particularly the 16S rRNA, has been greatly benefited from these technologies - the human gut microbiome research being a remarkable example of such analysis that has greatly expanded our understanding of microbe-mediated human health and disease, metabolism, and food absorption...
2016: Frontiers in Nutrition
Mercedes E Gonzalez, Julie V Schaffer, Seth J Orlow, Zhan Gao, Huilin Li, Alexander V Alekseyenko, Martin J Blaser
BACKGROUND: Patients with atopic dermatitis (AD) are prone to skin infections, with microbes such as Staphylococcus aureus suspected of contributing to pathogenesis. Bleach baths might improve AD by reducing skin microbial burden. OBJECTIVE: We sought to characterize the microbiota of lesional and nonlesional skin in young children with AD and control subjects and compare changes after treatment with a topical corticosteroid (TCS) alone or TCS + dilute bleach bath...
September 2016: Journal of the American Academy of Dermatology
Kate M O'Brien, Michael S Chimenti, Morgan Farnell, Tom Tabler, Thomas Bair, Joey L Bray, Matthew W Nonnenmann
Chronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes. However, the microbial composition and abundance has not been fully elucidated. Genomic DNA was extracted from settled dust and personal inhalable dust collected while performing litter sampling or mortality collection tasks. DNA libraries were sequenced using a paired-end sequencing-by-synthesis approach on an Illumina HiSeq 2500...
July 28, 2016: Microbial Biotechnology
Varsik Martirosyan, Adrian Unc, Gad Miller, Tirza Doniger, Chaim Wachtel, Yosef Steinberger
Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1)...
October 2016: Microbial Ecology
Shintaro Hara, Masanori Saito
Phytate (inositol hexaphosphate; IHP)-degrading microbes have been suggested to contribute to arbuscular mycorrhizal fungi (AMF)-mediated P transfer from IHP to plants; however, no IHP degrader involved in AMF-mediated P transfer has been isolated to date. We herein report the isolation of IHP-degrading bacteria using a modified baiting method. We applied alginate beads as carriers of IHP powder, and used them as recoverable IHP in the AM fungal compartment of plant cultivation experiments. P transfer from IHP in alginate beads via AMF was confirmed, and extracted DNA from alginate beads was analyzed by denaturing gradient gel electrophoresis targeting the 16S rRNA gene and a clone library method for the beta-propeller phytase (BPP) gene...
September 29, 2016: Microbes and Environments
I A Guillen, H Camacho, A D Tuero, D Bacardí, D O Palenzuela, A Aguilera, J A Silva, R Estrada, O Gell, J Suárez, J Ancizar, E Brown, A B Colarte, J Castro, L I Novoa
The study of the composition of the intestinal flora is important to the health of the host, playing a key role in maintaining intestinal homeostasis and the evolution of the immune system. For these studies, various universal primers of the 16S rDNA gene are used in microbial taxonomy. Here, we report an evaluation of 5 universal primers to explore the presence of microbial DNA in colon biopsies preserved in RNAlater solution. The DNA extracted was used for the amplification of PCR products containing the variable (V) regions of the microbial 16S rDNA gene...
September 2016: Journal of Biomolecular Techniques: JBT
Mansak Tantikachornkiat, Stacey Sakakibara, Marissa Neuner, Daniel M Durall
Culture-independent methods of microbial identification have been developed, which allow for DNA extraction directly from environmental samples without subjecting microbes to growth on nutrient media. These methods often involve next generation DNA sequencing (NGS) for identifying microbes and qPCR for quantifying them. Despite the benefits of extracting all DNA from the sample, results may be compromised by amplifying DNA from dead cells. To address this short-coming, the use of propidium monoazide (PMA) has been used to deactivate DNA in non-viable cells...
October 3, 2016: International Journal of Food Microbiology
Aina E F Moen, Tone M Tannæs, Simen Vatn, Petr Ricanek, Morten Harald Vatn, Jørgen Jahnsen
BACKGROUND: Nucleic acid purification methods are of importance when performing microbiota studies and especially when analysing the intestinal microbiota as we here find a wide range of different microbes. Various considerations must be taken to lyse the microbial cell wall of each microbe. In the present article, we compare several tissue lysis steps and commercial purification kits, to achieve a joint RNA and DNA purification protocol for the purpose of investigating the microbiota and the microbiota-host interactions in a single colonic mucosal tissue sample...
2016: BMC Research Notes
Wenfeng Wang, Yanyan Zhai, Lixiang Cao, Hongming Tan, Renduo Zhang
The objective of this study was to elucidate the endophytic microbiota in rice sprouts, roots, and stems, and their transmission in the plant development. Prior to DNA extraction, roots and stems were treated with 36% formaldehyde and 0.1M NaOH solutions to remove epiphytic bacterial whole 16S rRNA genes. Bacterial and fungal taxa in the sprout, root, and stem samples were analyzed using Illumina-based sequencing of the V3-V4 hyper variable regions of bacterial 16S rRNA genes and the ITS2 regions of fungal rRNA genes, respectively...
July 2016: Microbiological Research
Mark S Butler, Mark At Blaskovich, Jeremy G Owen, Matthew A Cooper
The discovery of new antibiotics is crucial if we are to avoid a future in which simple infections once again lead to death. New antibiotics were traditionally discovered by analyzing extracts from cultured soil-derived microbes. However, in the last few years only a few new antibiotic classes have been identified using this method. Attempts to apply target-based screening approaches to antibiotic discovery have also proven to be unproductive. In this article, we describe how DNA sequencing and bioinformatic techniques are revolutionizing natural product discovery leading to new natural product antibiotics sourced from both cultivated and uncultivated microbes...
June 2, 2016: Current Opinion in Microbiology
Joyce M McBeth, David Emerson
Microbiologically influenced corrosion (MIC) is a complex biogeochemical process involving interactions between microbes, metals, minerals, and their environment. We hypothesized that sediment-derived iron-oxidizing bacteria (FeOB) would colonize and become numerically abundant on steel surfaces incubated in coastal marine environments. To test this, steel coupons were incubated on sediments over 40 days, and samples were taken at regular intervals to examine microbial community succession. The experiments were conducted at two locations: (1) a brackish salt marsh stream and (2) a coastal marine bay...
2016: Frontiers in Microbiology
Angela Glassing, Scot E Dowd, Susan Galandiuk, Brian Davis, Rodrick J Chiodini
BACKGROUND: The advent and use of highly sensitive molecular biology techniques to explore the microbiota and microbiome in environmental and tissue samples have detected the presence of contaminating microbial DNA within reagents. These microbial DNA contaminants may distort taxonomic distributions and relative frequencies in microbial datasets, as well as contribute to erroneous interpretations and identifications. RESULTS: We herein report on the occurrence of bacterial DNA contamination within commonly used DNA extraction kits and PCR reagents and the effect of these contaminates on data interpretation...
2016: Gut Pathogens
James M Bardes, Christopher Waters, Hamed Motlagh, Alison Wilson
The endotracheal tube (ETT) is recognized as an independent factor for infection in intubated patients. The presence of biofilm contributes to the development of pneumonia. Standard culturing techniques are inadequate to detect many of the bacteria present in a biofilm. Delineation of the microbiota in the ETT is needed to further understand infections in ventilated patients. A prospective, observational study was performed at a university, Level I trauma center. Twenty ETT were collected at extubation. Bioluminal accretions were removed and quantified...
May 2016: American Surgeon
Junya Yamagishi, Yukuto Sato, Natsuko Shinozaki, Bin Ye, Akito Tsuboi, Masao Nagasaki, Riu Yamashita
The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we analyzed human oral microbes to compare the performance of three DNA extraction methods: PowerSoil (a method widely used in this field), QIAsymphony (a robotics method), and a simple boiling method. Dental plaque was initially collected from three volunteers in the pilot study and then expanded to 12 volunteers in the follow-up study...
2016: PloS One
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