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fecal DNA extraction

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https://www.readbyqxmd.com/read/28737135/a-flotation-sieving-method-to-detect-echinococcus-multilocularis-and-toxocara-spp-eggs-in-soil-by-real-time-pcr
#1
Gérald Umhang, Matthieu Bastien, Camille Renault, Marine Faisse, Christophe Caillot, Jean-Marc Boucher, Vanessa Hormaz, Marie-Lazarine Poulle, Franck Boué
Soil can be a source of human infection by many zoonotic helminth species including Echinococcus multilocularis and Toxocara spp. The prevention of alveolar echinococcosis could be greatly improved through the identification of at-risk areas. Yet very few data are available about the detection of E. multilocularis in soil, while more studies have been reported for Toxocara spp. Identification of soil contamination by E. multilocularis eggs requires the use of specific methods. This study describes the development of a method for the detection of E...
2017: Parasite: Journal de la Société Française de Parasitologie
https://www.readbyqxmd.com/read/28713847/next-generation-sequencing-of-the-dna-virome-from-fecal-samples
#2
Cynthia L Monaco, Douglas S Kwon
Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand displacement amplified (MDA) and fragmented; and 4) libraries are constructed and sequenced using Illumina Miseq. Subsequent sequence analysis for viral sequence identification should be sensitive but stringent...
March 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28683838/a-novel-ultra-high-throughput-16s-rrna-gene-amplicon-sequencing-library-preparation-method-for-the-illumina-hiseq-platform
#3
Eric J de Muinck, Pål Trosvik, Gregor D Gilfillan, Johannes R Hov, Arvind Y M Sundaram
BACKGROUND: Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. METHODS: We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods...
July 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28668239/association-of-altered-gut-microbiota-composition-with-chronic-urticaria
#4
Edris Nabizadeh, Nima Hosseini Jazani, Morteza Bagheri, Shahram Shahabi
BACKGROUND: An altered gut microbiota composition has recently been linked to some types of allergies. OBJECTIVE: To compare the relative amounts of Akkermansia muciniphila, Clostridium leptum, Faecalibacterium prausnitzii, and Enterobacteriaceae as members of gut microbiota among patients with chronic urticaria (CU) and healthy controls. METHODS: A total of 20 patients with CU and 20 healthy individuals matched by age and sex participated in the study...
July 2017: Annals of Allergy, Asthma & Immunology
https://www.readbyqxmd.com/read/28659635/method-for-preparing-dna-from-feces-in-guanidine-thiocyanate-solution-affects-16s-rrna-based-profiling-of-human-microbiota-diversity
#5
Koji Hosomi, Harumi Ohno, Haruka Murakami, Yayoi Natsume-Kitatani, Kumpei Tanisawa, Soichiro Hirata, Hidehiko Suzuki, Takahiro Nagatake, Tomomi Nishino, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa
Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compared with a frozen method to transport and stock fecal samples at room temperature for DNA analysis; however, optimal methods to measure fecal bacterial composition in GuSCN solution remain to be investigated. Here, we examined the influence of various factors such as pretreatment (e...
June 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28624295/molecular-characterization-of-sarcocystis-spp-in-intestine-mucosal-scrapings-and-fecal-samples-of-pampas-fox-lycalopex-gymnocercus
#6
Nathalia Paula Scioscia, María Laura Gos, Guillermo María Denegri, Gastón Moré
Sarcocystis spp. are obligatory intracellular protozoan parasites which can infect humans and animals. Most of Sarcocystis species were identified based on the detection of muscle cysts in different intermediate hosts (IH). Regarding to natural infection in definitive host, there are few reports which have reached to determining species of Sarcocystis. The present work was aimed to studying the occurrence of Sarcocystis spp. (oocysts and sporocysts) in mucosal scrapings of small intestine and fecal samples of one the most abundant wild canids from South America, Lycalopex gymnocercus (Pampas fox), and to identify the Sarcocystis spp...
June 15, 2017: Parasitology International
https://www.readbyqxmd.com/read/28616082/prevalence-of-pks-positive-escherichia-coli-in-japanese-patients-with-or-without-colorectal-cancer
#7
Takayuki Shimpoh, Yoshihiro Hirata, Sozaburo Ihara, Nobumi Suzuki, Hiroto Kinoshita, Yoku Hayakawa, Yumiko Ota, Akiko Narita, Shuntaro Yoshida, Atsuo Yamada, Kazuhiko Koike
BACKGROUND: Recent studies show that some Escherichia coli strains possessing a gene cluster named the pks island might have a causative role in the development of human colorectal cancer (CRC). In several reports from Europe, they are found more prevalently in colon tissue specimens derived from CRC patients compared to those from controls. In this study we sought to clarify the difference in pks prevalence between CRC patients and non-CRC controls in the Japanese population, by using non-invasive sample collection technique during colonoscopy...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28613041/genotyping-horse-epithelial-cells-from-fecal-matter-by-isolation-of-polymerase-chain-reaction-products
#8
Pero Dimsoski
AIM: To show that application of the polymerase chain reaction (PCR) method modified for amplification of a low-copy number DNA samples, ie, the isolation of PCR products (IPCRp), would represent improvement in obtaining genotypes from a fecal DNA compared with previously used genotyping methods. METHODS: The DNA from the horse fecal matter was extracted by modified Qiagen DNA Stool Mini Kit protocol. Following the extraction, the DNA genotypes from fecal samples were obtained by the most powerful PCR amplification method, the IPCRp...
June 14, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28595822/a-multiplex-restriction-enzyme-pcr-for-unequivocal-identification-and-differentiation-of-trichostrongylus-species-in-human-samples
#9
Azadeh Mizani, Pooria Gill, Ahmad Daryani, Shahabeddin Sarvi, Afsaneh Amouei, Ali Bakooie Katrimi, Eissa Soleymani, Siavash Mirshafiee, Sara Gholami, Seyed Abdollah Hosseini, Shirzad Gholami, Mohammad-Taghi Rahimi, Mohammad Bagher Hashemi-Soteh, Mehdi Sharif
Trichostrongylus species remain one of the major health challenges in the tropical and summer rainfall regions worldwide. Identification of strongylid species diagnostic methods is vital for obtaining a deep understanding of the epidemiology, population biology, anthelmintic treatment efficacy, and drug resistance in order to design effective parasite control strategies. We evaluated a multiplex RE-PCR for the diagnosis of key Trichostrongylus spp. Genomic DNA amplification of Trichostrongylus colubriformis, Trichostrongylus axei and Trichostrongylus vitrinus was achieved as standard sample using specific primers located in the second internal transcribed spacer (ITSII) of nuclear ribosomal DNA (rDNA)...
June 21, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28578061/effects-of-the-combination-of-%C3%AF-3-pufas-and-proanthocyanidins-on-the-gut-microbiota-of-healthy-rats
#10
Sara Ramos-Romero, Mercè Hereu, Eunice Molinar-Toribio, María Pilar Almajano, Lucía Méndez, Isabel Medina, Núria Taltavull, Marta Romeu, Maria Rosa Nogués, Josep Lluís Torres
ω-3 Polyunsaturated fatty acids (PUFAs) reduce risk factors for cardiovascular diseases (CVD) and other pathologies that involve low-grade inflammation. They have recently been shown to exert complementary functional effects with proanthocyanidins. As the reduction of health-promoting gut bacteria such as lactobacilli and bifidobacteria has been linked to a number of alterations in the host, the aim of this study was to determine whether PUFAs and proanthocyanidins also cooperate in maintaining well-balanced microbiota...
July 2017: Food Research International
https://www.readbyqxmd.com/read/28571671/the-microbiome-of-infants-recruited-to-a-randomised-placebo-controlled-probiotic-trial-pips-trial
#11
Michael Millar, Jo Seale, Melanie Greenland, Pollyanna Hardy, Edmund Juszczak, Mark Wilks, Nicola Panton, Kate Costeloe, William G Wade
The microbial dysbiosis associated with necrotizing enterocolitis (NEC) in preterm infants suggests that early exposure to probiotics may decrease and antibiotics may increase NEC risk. However, administration of Bifidobacterium breve strain BBG-001 to preterm infants did not affect NEC incidence in a multicenter randomised controlled phase 3 trial (PiPS trial). Using a subset of these subjects we compared the fecal microbiome of probiotic and placebo groups and assessed the impact of early antibiotic treatment...
June 2017: EBioMedicine
https://www.readbyqxmd.com/read/28567559/diagnosis-of-canine-echinococcus-multilocularis-infections-by-copro-dna-tests-comparison-of-dna-extraction-techniques-and-evaluation-of-diagnostic-deworming
#12
Takao Irie, Takuya Ito, Hirokazu Kouguchi, Kimiaki Yamano, Kohji Uraguchi, Kinpei Yagi, Nariaki Nonaka
The use of copro-DNA detection methods for the diagnosis of canine Echinococcus multilocularis infection was evaluated with a focus on DNA extraction techniques: two commercial kits and a modified alkaline-sodium dodecyl sulfate (SDS) technique. Dog feces (0.2 g) mixed with a protoscolex or with 1 or 10 eggs of E. multilocularis were subjected to DNA detection following extraction by these methods. DNA was extracted from all protoscolex samples by all methods, but success for samples with eggs depended on extraction technique with the modified technique showing success on all samples...
May 31, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28566084/-multicenter-investigation-of-bufavirus-in-the-etiology-of-viral-central-nervous-system-infections-of-adults-and-children
#13
Aylin Altay Koçak, Murat Öcal, Meltem Polat, Saliha Kanık Yüksek, Anıl Aktaş Tapısız, Hasan Tezer, Aykut Özkul, Koray Ergünay, Gülendam Bozdayı, Kamruddin Ahmed
Bufavirus (BuV) is a newly-identified parvovirus in the family of Parvoviridae. Metagenomic analysis of fecal samples from children in Burkina Faso with acute diarrhea showed a highly divergent parvovirus, which was named bufavirus (BuV). The global distribution, epidemiology and genetic characteristics of BuVs infections are obscure. It was first discovered as an agent causing gastroenteritis but the association of BuV infections with various clinical presentations mostly remain to be explored. The aims of this study were to investigate probable impact of BuV in central nervous system infections in a region where it was previously reported to cause human infections and to detect enteroviruses (EV) which are reported as a cause of central nervous system infections in our country...
April 2017: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/28560114/differentiation-of-bifidobacterium-longum-subspecies-longum-and-infantis-by-quantitative-pcr-using-functional-gene-targets
#14
Blair Lawley, Karen Munro, Alan Hughes, Alison J Hodgkinson, Colin G Prosser, Dianne Lowry, Shao J Zhou, Maria Makrides, Robert A Gibson, Christophe Lay, Charmaine Chew, Pheng Soon Lee, Khai Hong Wong, Gerald W Tannock
BACKGROUND: Members of the genus Bifidobacterium are abundant in the feces of babies during the exclusively-milk-diet period of life. Bifidobacterium longum is reported to be a common member of the infant fecal microbiota. However, B. longum is composed of three subspecies, two of which are represented in the bowel microbiota (B. longum subsp. longum; B. longum subsp. infantis). B. longum subspecies are not differentiated in many studies, so that their prevalence and relative abundances are not accurately known...
2017: PeerJ
https://www.readbyqxmd.com/read/28544222/usefulness-of-detection-of-clarithromycin-resistant-helicobacter-pylori-from-fecal-specimens-for-young-adults-treated-with-eradication-therapy
#15
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-u-s-epa-quantitative-polymerase-chain-reaction-approach-for-the-detection-of-enterococci-in-environmental-waters
#16
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 U.S. 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...
June 9, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28533898/reconstructing-a-herbivore-s-diet-using-a-novel-rbcl-dna-mini-barcode-for-plants
#17
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
#18
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 23, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28475713/tcdd-influences-reservoir-of-antibiotic-resistance-genes-in-murine-gut-microbiome
#19
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 1, 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
#20
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
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