keyword
MENU ▼
Read by QxMD icon Read
search

fecal DNA extraction

keyword
https://www.readbyqxmd.com/read/28544222/usefulness-of-detection-of-clarithromycin-resistant-helicobacter-pylori-from-fecal-specimens-for-young-adults-treated-with-eradication-therapy
#1
Takako Osaki, Katsuhiro Mabe, Cynthia Zaman, Hideo Yonezawa, Masumi Okuda, Kenji Amagai, Shinji Fujieda, Mitsuhide Goto, Wataru Shibata, Mototsugu Kato, Shigeru Kamiya
BACKGROUND: To prevent Helicobacter pylori infection in the younger generation, it is necessary to investigate the prevalence of antibiotic-resistant H. pylori. OBJECTIVE: The aim of this study was to evaluate the method of PCR-based sequencing to detect clarithromycin (CAM) resistance-associated mutations using fecal samples as a noninvasive method. METHODS: DNA extracted from fecal specimens and isolates from gastric biopsy specimens were collected from patients with H...
May 22, 2017: Helicobacter
https://www.readbyqxmd.com/read/28541661/a-complementary-isothermal-amplification-method-to-the-us-epa-qpcr-approach-for-the-detection-of-enterococci-in-environmental-waters
#2
Claudia Kolm, Roland Martzy, Kurt Brunner, Robert L Mach, Rudolf Krska, Georg Heinze, Regina Sommer, Georg H Reischer, Andreas H Farnleitner
We report a novel molecular assay, based on helicase-dependent amplification (HDA), for the detection of enterococci as markers for fecal pollution in water. This isothermal assay targets the same Enterococcus 23S rRNA gene region as the existing quantitative polymerase chain reaction (qPCR) assays of the US Environmental Protection Agency Methods 1611 and 1609 but can be entirely performed on a simple heating block. The developed Enterococcus HDA assay successfully discriminated 15 enterococcal from 15 non-enterococcal reference strains and reliably detected 48 environmental isolates of enterococci...
May 25, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28533898/reconstructing-a-herbivore-s-diet-using-a-novel-rbcl-dna-mini-barcode-for-plants
#3
David L Erickson, Elizabeth Reed, Padmini Ramachandran, Norman A Bourg, William J McShea, Andrea Ottesen
Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer (Odocoileus virginianus) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce...
May 2017: AoB Plants
https://www.readbyqxmd.com/read/28484128/characterizing-the-temporal-patterns-of-avian-influenza-virus-introduction-into-japan-by-migratory-birds
#4
Manabu Onuma, Masayoshi Kakogawa, Masae Yanagisawa, Atsushi Haga, Tomomi Okano, Yasuko Neagari, Tsukasa Okano, Koichi Goka, Mitsuhiko Asakawa
The objectives of the present study were to observe the temporal pattern of avian influenza virus (AIV) introduction into Japan and to determine which migratory birds play an important role in introducing AIV. In total, 19,407 fecal samples from migratory birds were collected at 52 sites between October 2008 and May 2015. Total nucleic acids extracted from the fecal samples were subjected to reverse transcription loop-mediated isothermal amplification to detect viral RNA. Species identification of host migratory birds was conducted by DNA barcoding for positive fecal samples...
May 7, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28475713/tcdd-influences-reservoir-of-antibiotic-resistance-genes-in-murine-gut-microbiome
#5
Robert D Stedtfeld, Tiffany M Stedtfeld, Kelly A Fader, Maggie R Williams, Prianca Bhaduri, John Quensen, Timothy R Zacharewski, James M Tiedje, Syed A Hashsham
Dysbiosis of the gut microbiome via antibiotics, changes in diet, and infection can select for bacterial groups that more frequently harbor antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, the impact of environmental toxicants on the reservoir of ARGs in the gut microbiome has received less attention. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist with multiple toxic health effects including immune dysfunction. The selective pressure of TCDD on the abundance of ARG and MGE harboring gut populations was examined using C57BL/6 mice exposed to 0-30 μg/kg TCDD for 28 and 92 days with the latter having a 30-day recovery period...
May 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28467925/gut-microbiome-based-metagenomic-signature-for-non-invasive-detection-of-advanced-fibrosis-in-human-nonalcoholic-fatty-liver-disease
#6
Rohit Loomba, Victor Seguritan, Weizhong Li, Tao Long, Niels Klitgord, Archana Bhatt, Parambir Singh Dulai, Cyrielle Caussy, Richele Bettencourt, Sarah K Highlander, Marcus B Jones, Claude B Sirlin, Bernd Schnabl, Lauren Brinkac, Nicholas Schork, Chi-Hua Chen, David A Brenner, William Biggs, Shibu Yooseph, J Craig Venter, Karen E Nelson
The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis)...
May 2, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28448583/characterization-of-the-fecal-microbiome-during-neonatal-and-early-pediatric-development-in-puppies
#7
Blake C Guard, Hanna Mila, Jörg M Steiner, Claire Mariani, Jan S Suchodolski, Sylvie Chastant-Maillard
Limited information is available describing the development of the neonatal fecal microbiome in dogs. Feces from puppies were collected at 2, 21, 42, and 56 days after birth. Feces were also collected from the puppies' mothers at a single time point within 24 hours after parturition. DNA was extracted from fecal samples and 454-pyrosequencing was used to profile 16S rRNA genes. Species richness continued to increase significantly from 2 days of age until 42 days of age in puppies. Furthermore, microbial communities clustered separately from each other at 2, 21, and 42 days of age...
2017: PloS One
https://www.readbyqxmd.com/read/28414467/variation-of-bacterial-communities-with-water-quality-in-an-urban-tropical-catchment
#8
Jean Pierre Nshimyimana, Adam Joshua Ehrich Freedman, Peter Shanahan, Lloyd C H Chua, Janelle R Thompson
A major challenge for assessment of water quality in tropical environments is the natural occurrence and potential growth of Fecal Indicator Bacteria (FIB). To gain a better understanding of the relationship between measured levels of FIB and the distribution of sewage-associated bacteria, including potential pathogens, in the tropics this study compared the abundance of FIB (Total coliforms and E. coli) and the Bacteroidales (HF183 marker) with bacterial community structure determined by next-generation amplicon sequencing...
April 28, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28373017/conditional-postnatal-deletion-of-the-neonatal-murine-hepatic-circadian-gene-npas2-alters-the-gut-microbiome-following-restricted-feeding
#9
Derek S O'Neil, Christopher J Stewart, Derrick M Chu, Danielle M Goodspeed, Pablo J Gonzalez-Rodriguez, Cynthia D Shope, Kjersti M Aagaard
BACKGROUND: We have recently shown in both non-human primates and in rodents that fetal and neonatal hepatic expression of the circadian transcription factor, Npas2, is modulated by a high fat maternal diet and plays a critical role in establishing life-long metabolic homeostasis. Similarly, we and others have also established the importance of the maternal and early postnatal diet on establishment of the early gut microbiome. OBJECTIVE: We hypothesized that altered circadian gene expression solely in the neonatal liver would result in gut microbiome dysbiosis, especially with diet-induced metabolic stress (ie, restricted feeding)...
March 31, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28346925/microbiota-and-necrotizing-enterocolitis
#10
Sanjay Patole
Necrotizing enterocolitis (NEC) is an acquired gastrointestinal inflammatory condition with significant mortality and morbidity in preterm very low birth weight infants. The interplay between toll-like receptors, bacterial endotoxins, developmentally regulated excessive proinflammatory responses of the immature innate immune system, hypoxia, ischemia, reperfusion, free radicals, and the presence of substrates and bacterial endotoxins is thought to play an important role in the pathogenesis of NEC. The association (cause?) of various microbes (bacteria, viruses, and fungi) with NEC has intrigued researchers for many years...
2017: Nestlé Nutrition Institute Workshop Series
https://www.readbyqxmd.com/read/28346396/a-pcr-based-molecular-detection-of-strongyloides-stercoralisin-human-stool-samples-from-tabriz-city-iran
#11
Reza Ghasemikhah, Mohammad Amin Tabatabaiefar, Seyed Ali Shariatzadeh, Abbas Shahbazi, Teymour Hazratian
Strongyloides stercoralis is a nematode causing serious infections in immunocompromised patients. In chronically infected patients, the low parasitic content as well as the resemblance of the larvae to several other species make diagnosis basedonmorphology difficult. In the present study, a PCR-based method targeting the internal transcribed sequence 2 (ITS2) of the rDNA region was examined for the molecular detection of S. stercoralis infection from the stool samples. A total of 1800 patients were included...
March 27, 2017: Scientia Pharmaceutica
https://www.readbyqxmd.com/read/28278278/dynamic-changes-of-the-respiratory-microbiota-and-its-relationship-to-fecal-and-blood-microbiota-in-healthy-young-cats
#12
Aida I Vientós-Plotts, Aaron C Ericsson, Hansjorg Rindt, Megan E Grobman, Amber Graham, Kaitlin Bishop, Leah A Cohn, Carol R Reinero
Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs...
2017: PloS One
https://www.readbyqxmd.com/read/28260371/analysis-of-100-year-old-beer-originated-from-the-czech-republic
#13
Jana Olšovská, Dagmar Matoulková, Martin Dušek, Jürgen Felsberg, Markéta Jelínková, Pavel Čejka, Karel Štěrba
Three bottles of different beers were found in 2015 during a reconstruction of the brewery of the Raven Trading s.r.o. company in Záhlinice, Czech Republic. Thanks to good storage conditions, it was possible to analyze their original characteristics. All three bottles contained most probably lager type beer. One beer had sulfuric and fecal off-flavors; it was bright with the original extract of 10.3° Plato. The second beer, with an original extract of 7.6° Plato, was dark and very acidic, resembling Lambic...
April 12, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28242041/a-novel-snapback-primer-probe-assay-for-the-detection-and-discrimination-of-sympatric-haemonchus-species-using-dna-melting-analysis
#14
Rudolf Pichler, Katja Silbermayr, Kathiravan Periasamy
Different sympatric species of Haemonchus parasites infecting ruminants and camels can be distinguished morphologically, but involves tedious microscopic examinations, measurements and several other limitations. Information on internal transcribed spacer-2 (ITS-2) sequence provides confirmatory differentiation of sympatric Haemonchus species. The present study introduces a novel, snapback primer probe based, real time PCR assay for the differentiation of three sympatric Haemonchus species, H. contortus (Hco), H...
February 20, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28239315/single-fecal-microbiota-transplantation-failed-to-change-intestinal-microbiota-and-had-limited-effectiveness-against-ulcerative-colitis-in-japanese-patients
#15
Shinta Mizuno, Kosaku Nanki, Katsuyoshi Matsuoka, Keiichiro Saigusa, Keiko Ono, Mari Arai, Shinya Sugimoto, Hiroki Kiyohara, Moeko Nakashima, Kozue Takeshita, Makoto Naganuma, Wataru Suda, Masahira Hattori, Takanori Kanai
BACKGROUND/AIMS: Recent developments in analytical techniques including next-generation sequencing have clarified the correlation between intestinal microbiota and inflammatory bowel disease. Fecal microbiota transplantation (FMT) for patients with ulcerative colitis (UC) is proposed as a potential approach to resolving their dysbiosis; however, its safety and efficacy have not been confirmed. This single-arm, open-label, non-randomized study aimed to evaluate the safety and efficacy of FMT for Japanese patients with UC as the first registered clinical trial in Japan...
January 2017: Intestinal Research
https://www.readbyqxmd.com/read/28223257/the-fecal-microbiome-of-dogs-with-exocrine-pancreatic-insufficiency
#16
Anitha Isaiah, Joseph Cyrus Parambeth, Jörg M Steiner, Jonathan A Lidbury, Jan S Suchodolski
Exocrine pancreatic insufficiency (EPI) in dogs is a syndrome of inadequate synthesis and secretion of pancreatic enzymes. Small intestinal bacterial dysbiosis occurs in dogs with EPI, and is reversed with pancreatic enzyme therapy. However, there are no studies evaluating the fecal microbiome of dogs with EPI. The objective of this study was to evaluate the fecal microbiome of dogs with EPI. Three day pooled fecal samples were collected from healthy dogs (n = 18), untreated (n = 7) dogs with EPI, and dogs with EPI treated with enzyme replacement therapy (n = 19)...
February 18, 2017: Anaerobe
https://www.readbyqxmd.com/read/28222192/blastocystis-subtyping-and-its-association-with-intestinal-parasites-in-children-from-different-geographical-regions-of-colombia
#17
Juan David Ramírez, Carolina Flórez, Mario Olivera, María Consuelo Bernal, Julio Cesar Giraldo
Blastocystis is a common enteric protist colonizing probably more than 1 billion people with a large variety of non-human hosts. Remarkable genetic diversity has been observed, leading to the subdivision of the genus into multiple subtypes (ST), some of which are exclusively found in non-human hosts. The aim of this study was to determine the distribution of Blastocystis STs/18S alleles in symptomatic (abdominal pain, anal pruritus, diarrhea, headache, nauseas and/or vomit) and asymptomatic children from nine geographical regions of Colombia...
2017: PloS One
https://www.readbyqxmd.com/read/28210245/pcr-inhibition-of-a-quantitative-pcr-for-detection-of-mycobacterium-avium-subspecies-paratuberculosis-dna-in-feces-diagnostic-implications-and-potential-solutions
#18
Kamal R Acharya, Navneet K Dhand, Richard J Whittington, Karren M Plain
Molecular tests such as polymerase chain reaction (PCR) are increasingly being applied for the diagnosis of Johne's disease, a chronic intestinal infection of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Feces, as the primary test sample, presents challenges in terms of effective DNA isolation, with potential for PCR inhibition and ultimately for reduced analytical and diagnostic sensitivity. However, limited evidence is available regarding the magnitude and diagnostic implications of PCR inhibition for the detection of MAP in feces...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28178984/bacteriological-water-quality-in-school-s-drinking-fountains-and-detection-antibiotic-resistance-genes
#19
Denize Gomes Freitas, Rassan Dyego Romão Silva, Luis Artur Mendes Bataus, Mônica Santiago Barbosa, Carla Afonso da Silva Bitencourt Braga, Lilian Carla Carneiro
The fecal coliform can contaminate water of human consumption causing problems to public health. Many of these microorganisms may contain plasmid and transfer them to other bacteria. This genetic material may confer selective advantages, among them resistance to antibiotics. The objectives of this study were to analyze the presence of fecal coliforms in water and at drinker surface, to identify the existence of plasmid, conducting studies of resistance to antibiotics, plasmid stability and capacity of bacterial conjugation...
February 8, 2017: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/28178033/social-influences-on-prevotella-and-the-gut-microbiome-of-young-monkeys
#20
Wellington Z Amaral, Gabriele R Lubach, Alexandra Proctor, Mark Lyte, Gregory J Phillips, Christopher L Coe
OBJECTIVE: Our aim was to evaluate the bacterial profiles of young monkeys as they were weaned into peer groups with a particular focus on Prevotella, an important taxon in both human and nonhuman primates. The weaning of infants and increased social contact with peers is a developmental stage that is likely to affect the gut microbiome. METHODS: Gut bacteria were assessed in 63 rhesus monkeys living in social groups comprised of 4-7 individuals. Two groups were assessed prospectively on Day 1 and 2 weeks after rehousing away from the mother and group formation...
February 7, 2017: Psychosomatic Medicine
keyword
keyword
57425
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"