keyword
MENU ▼
Read by QxMD icon Read
search

Dna extraction microbes

keyword
https://www.readbyqxmd.com/read/28177784/effects-of-several-in-feed-antibiotic-combinations-on-the-abundance-and-diversity-of-fecal-microbes-in-weaned-pigs
#1
Huizhi Li, Tingting Liang, Qingpo Chu, Feilong Xu, Yuan Li, Lingling Fu, Bo Zhou
To characterize the effects of several subtherapeutic antibiotic combinations on the abundance and diversity of fecal microbes, 400 weaned pigs were selected and randomly assigned to 8 groups, where they were continuously fed different antibiotic combinations for 28 days. Then, a total of 48 pigs were randomly selected to individually collect the feces for DNA extraction and 16S rRNA high-throughput sequencing. Compared with the pigs without antibiotic administration, the diversities of fecal microbes were decreased in the pigs fed chlortetracycline (CTC), olaquindox (OLA) and enramycin (ER)/ virginiamycin (VIR), where the relative abundance of the phymum Bacteroidetes and the genus Prevotella were increased...
January 24, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28174737/metagenomic-characterization-of-microbial-communities-in-situ-within-the-deeper-layers-of-the-ileum-in-crohn-s-disease
#2
Chandra Sekhar Pedamallu, Ami S Bhatt, Susan Bullman, Sharyle Fowler, Samuel S Freeman, Jacqueline Durand, Joonil Jung, Fujiko Duke, Veronica Manzo, Diana Cai, Ashwin Ananthakrishnan, Akinyemi I Ojesina, Aruna Ramachandran, Dirk Gevers, Ramnik J Xavier, Atul K Bhan, Matthew Meyerson, Vijay Yajnik
BACKGROUND & AIMS: Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28161601/messages-from-the-first-international-conference-on-clinical-metagenomics-iccmg
#3
Etienne Ruppé, Gilbert Greub, Jacques Schrenzel
Metagenomics is recently entering in the clinical microbiology and an increasing number of diagnostic laboratories are now proposing the sequencing & annotation of bacterial genomes and/or the analysis of clinical samples by direct or PCR-based metagenomics with short time to results. In this context, the first International Conference on Clinical Metagenomics (ICCMg) was held in Geneva in October 2016 and several key aspects have been discussed including: i) the need for improved resolution, ii) the importance of interpretation given the common occurrence of sequence contaminants, iii) the need for improved bioinformatic pipelines, iv) the bottleneck of DNA extraction, v) the importance of gold standards, vi) the need to further reduce time to results, vii) how to improve data sharing, viii) the applications of bacterial genomics and clinical metagenomics in better adapting therapeutics and ix) the impact of metagenomics and new sequencing technologies in discovering new microbes...
February 1, 2017: Microbes and Infection
https://www.readbyqxmd.com/read/28125031/phylogenetic-heatmaps-highlight-composition-biases-in-sequenced-reads
#4
Sulbha Choudhari, Andrey Grigoriev
Due to advancements in sequencing technology, sequence data production is no longer a constraint in the field of microbiology and has made it possible to study uncultured microbes or whole environments using metagenomics. However, these new technologies introduce different biases in metagenomic sequencing, affecting the nucleotide distribution of resulting sequence reads. Here, we illustrate such biases using two methods. One is based on phylogenetic heatmaps (PGHMs), a novel approach for compact visualization of sequence composition differences between two groups of sequences containing the same phylogenetic groups...
January 24, 2017: Microorganisms
https://www.readbyqxmd.com/read/28070089/development-of-a-one-run-real-time-pcr-detection-system-for-pathogens-associated-with-bovine-respiratory-disease-complex
#5
Mai Kishimoto, Shinobu Tsuchiaka, Sayed Samim Rahpaya, Ayako Hasebe, Keiko Otsu, Satoshi Sugimura, Suguru Kobayashi, Natsumi Komatsu, Makoto Nagai, Tsutomu Omatsu, Yuki Naoi, Kaori Sano, Sachiko Okazaki-Terashima, Mami Oba, Yukie Katayama, Reiichiro Sato, Tetsuo Asai, Tetsuya Mizutani
Bovine respiratory disease complex (BRDC) is frequently found in cattle worldwide. The etiology of BRDC is complicated by infections with multiple pathogens, making identification of the causal pathogen difficult. Here, we developed a detection system by applying TaqMan real-time PCR (Dembo respiratory-PCR) to screen a broad range of microbes associated with BRDC in a single run. We selected 16 bovine respiratory pathogens (bovine viral diarrhea virus, bovine coronavirus, bovine parainfluenza virus 3, bovine respiratory syncytial virus, influenza D virus, bovine rhinitis A virus, bovine rhinitis B virus, bovine herpesvirus 1, bovine adenovirus 3, bovine adenovirus 7, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, Trueperella pyogenes, Mycoplasma bovis and Ureaplasma diversum) as detection targets and designed novel specific primer-probe sets for nine of them...
January 8, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28005056/new-crispr-cas-systems-from-uncultivated-microbes
#6
David Burstein, Lucas B Harrington, Steven C Strutt, Alexander J Probst, Karthik Anantharaman, Brian C Thomas, Jennifer A Doudna, Jillian F Banfield
CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped...
February 9, 2017: Nature
https://www.readbyqxmd.com/read/28004217/lactobacillus-kefiri-shows-inter-strain-variations-in-the-amino-acid-sequence-of-the-s-layer-proteins
#7
Mariano Malamud, Paula Carasi, Sílvia Bronsoms, Sebastián A Trejo, María de Los Angeles Serradell
The S-layer is a proteinaceous envelope constituted by subunits that self-assemble to form a two-dimensional lattice that covers the surface of different species of Bacteria and Archaea, and it could be involved in cell recognition of microbes among other several distinct functions. In this work, both proteomic and genomic approaches were used to gain knowledge about the sequences of the S-layer protein (SLPs) encoding genes expressed by six aggregative and sixteen non-aggregative strains of potentially probiotic Lactobacillus kefiri...
December 21, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27988129/source-of-supplemental-dietary-copper-zinc-and-manganese-affects-fecal-microbial-relative-abundance-in-lactating-dairy-cows
#8
M J Faulkner, B A Wenner, L M Solden, W P Weiss
Appropriate trace mineral supplementation can improve immune response and hoof health in cattle and at much higher rates of supplementation to swine and poultry can alter microbial colonization of the gut, resulting in improved gut health. Diet can influence fecal microbial excretion in cattle, and the fecal microbiome may serve as a means for assessing gastrointestinal microbial changes. We hypothesized that feeding diets that differed in source of supplemental Cu, Zn, or Mn would alter the relative abundance of fecal microbes in lactating dairy cattle and that organic Zn would have the greatest effect...
February 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/27888152/an-improved-methodology-to-overcome-key-issues-in-human-fecal-metagenomic-dna-extraction
#9
Jitendra Kumar, Manoj Kumar, Shashank Gupta, Vasim Ahmed, Manu Bhambi, Rajesh Pandey, Nar Singh Chauhan
Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23kb) metagenomic DNA (260/280 ratio >1...
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27829577/chronic-early-life-stress-in-rat-pups-alters-basal-corticosterone-intestinal-permeability-and-fecal-microbiota-at-weaning-influence-of-sex
#10
Nabila Moussaoui, Jonathan P Jacobs, Muriel Larauche, Mandy Biraud, Mulugeta Million, Emeran Mayer, Yvette Taché
Background/Aims: Wistar rat dams exposed to limited nesting stress (LNS) from post-natal days (PND) 2 to 10 display erratic maternal behavior, and their pups show delayed maturation of the hypothalamic-pituitary-adrenal axis and impaired epithelial barrier at PND10 and a visceral hypersensitivity at adulthood. Little is known about the impact of early life stress on the offspring before adulthood and the influence of sex. We investigated whether male and female rats previously exposed to LNS displays at weaning altered corticosterone, intestinal permeability, and microbiota...
January 30, 2017: Journal of Neurogastroenterology and Motility
https://www.readbyqxmd.com/read/27762069/an-introduction-to-microbiome-analysis-for-human-biology-applications
#11
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
https://www.readbyqxmd.com/read/27754286/br-07-1-development-of-the-cell-microarray-for-high-throughput-analysis-of-gut-microbiota
#12
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
https://www.readbyqxmd.com/read/27720803/the-gut-microbiota-contributes-to-a-mouse-model-of-spontaneous-bile-duct-inflammation
#13
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 intrahepatic 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...
February 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/27676385/biofabrication-of-broad-range-antibacterial-and-antibiofilm-silver-nanoparticles
#14
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
https://www.readbyqxmd.com/read/27643284/br-07-1-development-of-the-cell-microarray-for-high-throughput-analysis-of-gut-microbiota
#15
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
https://www.readbyqxmd.com/read/27558918/a-robust-ambient-temperature-collection-and-stabilization-strategy-enabling-worldwide-functional-studies-of-the-human-microbiome
#16
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
https://www.readbyqxmd.com/read/27551678/considerations-for-optimizing-microbiome-analysis-using-a-marker-gene
#17
REVIEW
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
https://www.readbyqxmd.com/read/27543211/cutaneous-microbiome-effects-of-fluticasone-propionate-cream-and-adjunctive-bleach-baths-in-childhood-atopic-dermatitis
#18
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
https://www.readbyqxmd.com/read/27470660/high-throughput-genomic-sequencing-of-bioaerosols-in-broiler-chicken-production-facilities
#19
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
https://www.readbyqxmd.com/read/27450478/desert-perennial-shrubs-shape-the-microbial-community-miscellany-in-laimosphere-and-phyllosphere-space
#20
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
keyword
keyword
56892
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"