keyword
MENU ▼
Read by QxMD icon Read
search

fecal DNA extraction

keyword
https://www.readbyqxmd.com/read/29138113/prevalence-of-extended-spectrum-beta-lactamase-and-carbapenemase-encoding-genes-in-poultry-feces-from-algeria-and-marseille-france
#1
Chabou Selma, Leulmi Hamza, Davoust Bernard, Aouadi Atef, Jean-Marc Rolain
OBJECTIVE: The aim of this study was to evaluate the prevalence of extended-spectrum beta lactamase (ESBLs) and carbapenemase-encoding genes in poultry from Algeria and Marseille, France. MATERIALS AND METHODS: The samples consisted of feces from broilers from France and Algeria between 2014 and 2015. DNA extraction and quantitative PCR were performed on 833 fecal samples to screen for the presence of ESBLs (TEM, SHV, CTX-M) and carbapenemase-encoding genes (NDM, OXA48, OXA58)...
November 11, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29126996/blastocystis-genetic-diversity-among-children-of-low-income-daycare-center-in-southeastern-brazil
#2
Ana Paula Oliveira-Arbex, Érica Boarato David, Semíramis Guimarães
Blastocystis, an unicellular anaerobic eukaryote, is known to be a very common intestinal parasite found in humans and animals fecal samples worldwide. Currently, there is an increasing interest to yield insights into its prevalence and diversity in human populations living in poor and deprived areas. In this study, we describe the prevalence and genetic variability of Blastocystis isolates obtained from daycare center attendees aged 0 to 6years and staff, as well as some children family members and their dogs in a low-income community in São Paulo State, Brazil...
November 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29120399/a-microbiomic-analysis-in-african-americans-with-colonic-lesions-reveals-streptococcus-sp-vt162-as-a-marker-of-neoplastic-transformation
#3
Hassan Brim, Shibu Yooseph, Edward Lee, Zaki Sherif, Muneer Abbas, Adeyinka O Laiyemo, Sudhir Varma, Manolito Torralba, Scot E Dowd, Karen E Nelson, Wimal Pathmasiri, Susan Sumner, Willem de Vos, Qiaoyi Liang, Jun Yu, Erwin Zoetendal, Hassan Ashktorab
Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC). To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to determine the microbiota composition (using 16S rDNA) and genomic content (metagenomics). Metagenomic functions with discriminative power between healthy and neoplastic specimens were established...
November 9, 2017: Genes
https://www.readbyqxmd.com/read/29079861/impact-of-dna-extraction-sample-dilution-and-reagent-contamination-on-16s-rrna-gene-sequencing-of-human-feces
#4
Eliana P Velásquez-Mejía, Jacobo de la Cuesta-Zuluaga, Juan S Escobar
Culture-independent methods have granted the possibility to study microbial diversity in great detail, but technical issues pose a threat to the accuracy of new findings. Biases introduced during DNA extraction can result in erroneous representations of the microbial community, particularly in samples with low microbial biomass. We evaluated the DNA extraction method, initial sample biomass, and reagent contamination on the assessment of the human gut microbiota. Fecal samples of 200 mg were subjected to 1:10 serial dilutions; total DNA was obtained using two commercial kits and the microbiota assessed by 16S ribosomal RNA (rRNA) gene sequencing...
October 27, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29075474/pellets-of-proof-first-glimpse-of-the-dietary-composition-of-adult-odonates-as-revealed-by-metabarcoding-of-feces
#5
Kari M Kaunisto, Tomas Roslin, Ilari E Sääksjärvi, Eero J Vesterinen
Recent advances in molecular techniques allow us to resolve the diet of unstudied taxa. Odonates are potentially important top-down regulators of many insects. Yet, to date, our knowledge of odonate prey use is based mainly on limited observations of odonates catching or eating their prey. In this study, we examine the potential use of metabarcoding in establishing the diet of three adult odonate species (Lestes sponsa, Enallagma cyathigerum, and Sympetrum danae) at a site in southwestern Finland. To this purpose, we compared three different methods for extracting DNA from fecal samples: the Macherey-Nagel Nucleospin XS kit, a traditional salt extraction, and the Zymo Research Fecal Microprep kit...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29058768/the-impact-of-endogenous-content-replicates-and-pooling-on-genome-capture-from-fecal-samples
#6
J Hernandez-Rodriguez, M Arandjelovic, J Lester, C de Filippo, A Weihmann, M Meyer, S Angedakin, F Casals, A Navarro, L Vigilant, H S Kühl, K Langergraber, C Boesch, D Hughes, T Marques-Bonet
Target capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of non-invasive samples such as feces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution, and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries...
October 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29051757/role-of-gut-microbiota-on-cardio-metabolic-parameters-and-immunity-in-coronary-artery-disease-patients-with-and-without-type-2-diabetes-mellitus
#7
Lidia Sanchez-Alcoholado, Daniel Castellano-Castillo, Laura Jordán-Martínez, Isabel Moreno-Indias, Pilar Cardila-Cruz, Daniel Elena, Antonio J Muñoz-Garcia, Maria I Queipo-Ortuño, Manuel Jimenez-Navarro
Gut microbiota composition has been reported as a factor linking host metabolism with the development of cardiovascular diseases (CVD) and intestinal immunity. Such gut microbiota has been shown to aggravate CVD by contributing to the production of trimethylamine N-oxide (TMAO), which is a pro-atherogenic compound. Treg cells expressing the transcription factor Forkhead box protein P3 (FoxP3) play an essential role in the regulation of immune responses to commensal microbiota and have an atheroprotective role...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29035858/detection-of-small-number-of-giardia-in-biological-materials-prepared-from-stray-dogs
#8
Leila Esmailikia, Elahe Ebrahimzade, Parviz Shayan, Narges Amininia
Giardia lamblia is an intestinal protozoa with intermittent and low shedding especially in dogs, and the detection of Giardia is accompanied with problems such as sampling and diagnostic method. The objective of this study was to detection of Giardia in biological materials with low number of parasite using parasitological and molecular methods, and also to determine whether the examined stray dogs harbor known zoonotic genotype of Giardia. For this aim 85 fecal and duodenal samples were studied from which 1 was positive by Trichrome staining of stool, 4 were positive by staining of duodenal samples...
December 20, 2017: Acta Parasitologica
https://www.readbyqxmd.com/read/29030042/genetic-variability-and-transcontinental-sharing-of-giardia-duodenalis-infrapopulations-determined-by-glutamate-dehydrogenase-gene
#9
Adel Spotin, Majid Karamat, Mahmoud Mahami-Oskouei, Abbas Shahbazi, Ehsan Ahmadpour, Tahereh Mikaeili Galeh, Shirzad Fallahi
Microevolutionary data of Giardia duodenalis sub-assemblages is a prerequisite for determining the invasion zoonotic patterns of the parasite. To infer transmission patterns that could not be differentiated by the phenotypic features, a population genetic investigation is crucial for the elucidation of the genetic structure of G. duodenalis among the continents. Forty G. duodenalis positive fecal samples were collected from different foci of Northwest Iran. The specimens were subjected to Trichrome staining and sucrose gradient flotation...
October 13, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28971851/time-of-day-and-eating-behaviors-are-associated-with-the-composition-and-function-of-the-human-gastrointestinal-microbiota
#10
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/28967887/towards-standards-for-human-fecal-sample-processing-in-metagenomic-studies
#11
Paul I Costea, Georg Zeller, Shinichi Sunagawa, Eric Pelletier, Adriana Alberti, Florence Levenez, Melanie Tramontano, Marja Driessen, Rajna Hercog, Ferris-Elias Jung, Jens Roat Kultima, Matthew R Hayward, Luis Pedro Coelho, Emma Allen-Vercoe, Laurie Bertrand, Michael Blaut, Jillian R M Brown, Thomas Carton, Stéphanie Cools-Portier, Michelle Daigneault, Muriel Derrien, Anne Druesne, Willem M de Vos, B Brett Finlay, Harry J Flint, Francisco Guarner, Masahira Hattori, Hans Heilig, Ruth Ann Luna, Johan van Hylckama Vlieg, Jana Junick, Ingeborg Klymiuk, Philippe Langella, Emmanuelle Le Chatelier, Volker Mai, Chaysavanh Manichanh, Jennifer C Martin, Clémentine Mery, Hidetoshi Morita, Paul W O'Toole, Céline Orvain, Kiran Raosaheb Patil, John Penders, Søren Persson, Nicolas Pons, Milena Popova, Anne Salonen, Delphine Saulnier, Karen P Scott, Bhagirath Singh, Kathleen Slezak, Patrick Veiga, James Versalovic, Liping Zhao, Erwin G Zoetendal, S Dusko Ehrlich, Joel Dore, Peer Bork
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis...
November 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28967572/validation-and-application-of-quantitative-pcr-assays-using-host-specific-bacteroidales-genetic-markers-for-swine-fecal-pollution-tracking
#12
Lihua Fan, Jiangbing Shuai, Ruoxue Zeng, Hongfei Mo, Suhua Wang, Xiaofeng Zhang, Yongqiang He
Genome fragment enrichment (GFE) method was applied to identify host-specific bacterial genetic markers that differ among different fecal metagenomes. To enrich for swine-specific DNA fragments, swine fecal DNA composite (n = 34) was challenged against a DNA composite consisting of cow, human, goat, sheep, chicken, duck and goose fecal DNA extracts (n = 83). Bioinformatic analyses of 384 non-redundant swine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode metabolism-associated, cellular processes and information storage and processing...
December 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28951300/effect-of-sea-buckthorn-protein-on-the-intestinal-microbial-community-in-streptozotocin-induced-diabetic-mice
#13
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/28886400/breastfeeding-increases-microbial-community-resilience
#14
Isabel I Carvalho-Ramos, Rubens T D Duarte, Katia Brandt, Marina B Martinez, Carla R Taddei
OBJECTIVE: Since the present group had already described the composition of the intestinal microbiota of Brazilian infants under low social economic level, the aim of the present study was to analyze the microbial community structure changes in this group of infants during their early life due to external factors. METHODS: Fecal samples were collected from 11 infants monthly during the first year of life. The infants were followed regarding clinical and diet information and characterized according to breastfeeding practices...
September 5, 2017: Jornal de Pediatria
https://www.readbyqxmd.com/read/28864945/fecal-microbiota-of-lambs-fed-purple-prairie-clover-dalea-purpurea-vent-and-alfalfa-medicago-sativa
#15
Qianqian Huang, Devin B Holman, Trevor Alexander, Tianming Hu, Long Jin, Zhongjun Xu, Tim A McAllister, Surya Acharya, Guoqi Zhao, Yuxi Wang
The present study assessed the effect of purple prairie clover (PPC) and PPC condensed tannins (CT) on the fecal microbiota of lambs using high-throughput 16S rRNA gene pyrosequencing. A total of 18 individual lambs were randomly divided into three groups and fed either green chop alfalfa (Alf), a 40:60 (DM basis; Mix) mixture of Alf and PPC, or Mix supplemented with polyethylene glycol (Mix-P) for 18 days. Fecal samples were collected on days 13 through 18 using digital rectal retrieval. The DNA of fecal samples was extracted and the microbial 16S rRNA gene amplicons were sequenced using 454 pyrosequencing...
September 1, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28821259/the-effect-of-storage-at-ambient-temperature-on-the-feline-fecal-microbiota
#16
Moran Tal, Adronie Verbrugghe, Diego E Gomez, Charlotte Chau, J Scott Weese
BACKGROUND: Feline fecal microbiota analyses can potentially be impacted by a variety of factors such as sample preparation, sequencing method and bioinformatics analyses. Another potential influence is changes in the microbiota from storage of samples prior to processing. This study examined the effect of ambient temperature exposure on the feline fecal microbiota composition. Fecal samples were collected from 12 healthy cats, within 15 min after defecation. Samples were aliquoted and the first aliquot was frozen at -80 °C within 1 hour of defecation...
August 18, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28807288/prevalence-of-tritrichomonas-foetus-in-tennessee-bulls
#17
Chika C Okafor, Lew G Strickland, Brittni M Jones, Stephen Kania, David E Anderson, Brian K Whitlock
The prevalence of bovine trichomonosis (BT) in TN bulls was estimated through both active screening of bulls and review of previous laboratory records. During the active bull screening, preputial smegma specimens were collected from 458 TN beef bulls at 2 cattle slaughterhouses and 2 stockyards, which serve most beef bulls in TN, between March 2014 and June 2015. Each specimen was cultured for Tritrichomonas foetus (T. foetus) as well as evaluated microscopically every other day for seven days for any protozoa resembling T...
August 30, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28801119/stability-and-efficacy-of-frozen-and-lyophilized-fecal-microbiota-transplant-fmt-product-in-a-mouse-model-of-clostridium-difficile-infection-cdi
#18
Zhi-Dong Jiang, Ashley Alexander, Shi Ke, Evangelia M Valilis, Shaofan Hu, Bingjie Li, Herbert L DuPont
Freezing donor fecal microbiota has simplified fecal microbiota transplantation (FMT) in the treatment of recurrent C. difficile infection (CDI). However, the optimal storage time for the frozen FMT products remains unknown. Using an established murine model of CDI, stability and efficacy of frozen and lyophilized FMT product was studied at time points from 2 months to 15 months. DNA was extracted from fecal samples from the mice with identification of specific bacterial species by real-time quantitative PCR (qPCR)...
August 9, 2017: Anaerobe
https://www.readbyqxmd.com/read/28780245/prevalence-and-virulence-gene-profiling-of-enteroaggregative-escherichia-coli-in-malnourished-and-nourished-brazilian-children
#19
Alexandre Havt, Ila Fn Lima, Pedro Hqs Medeiros, Marco Af Clementino, Ana Ks Santos, Marília Smg Amaral, Herlice N Veras, Mara Mg Prata, Noélia L Lima, Alessandra Di Moura, Álvaro M Leite, Alberto M Soares, José Q Filho, Eric R Houpt, James P Nataro, Richard L Guerrant, Aldo Am Lima
The impact of enteroaggregative E. coli (EAEC) infection on childhood malnutrition and inflammation has been suggested, regardless of diarrhea. We investigated whether EAEC and its virulence-related genes (VRGs) are associated with malnutrition in a case-control study. Children aged 6-24 months from Brazil were enrolled as malnourished if weight-for-age Z-score (WAZ) ≤ -2 and nourished if WAZ > -1. Stools were cultured and examined for E. coli. DNA was extracted from fecal isolates and tested for EAEC by polymerase chain reaction (PCR)...
October 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28763566/metabolites-and-microbial-composition-of-stool-of-women-with-fecal-incontinence-study-design-and-methods
#20
Lily A Arya, Holly E Richter, Eric Jelovsek, Marie Gantz, Sara Cichowski, Halina Zyczynski, Keisha Dyer, Nazema Siddiqui, Cassandra Carberry, Corey Broeckling, Casey Morrow, Purna Kashyap, Susie Meikle
AIMS: This paper aims to report the rationale, design, and the specific methodology of an ongoing nested observational study that will determine the association of the metabolite and microbial composition of stool with fecal incontinence (FI). METHODS: Eligible cases are participants with FI enrolled in the Controlling Anal Incontinence in women by Performing Anal Exercises with Biofeedback or Loperamide (CAPABLe) trial, a Pelvic Floor Disorders Network trial across eight clinical centers in the United States...
August 1, 2017: Neurourology and Urodynamics
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"