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fecal DNA extraction

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https://www.readbyqxmd.com/read/29346412/a-comparative-analysis-of-preservation-techniques-for-the-optimal-molecular-detection-of-hookworm-dna-in-a-human-fecal-specimen
#1
Marina Papaiakovou, Nils Pilotte, Ben Baumer, Jessica Grant, Kristjana Asbjornsdottir, Fabian Schaer, Yan Hu, Raffi Aroian, Judd Walson, Steven A Williams
BACKGROUND: Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29342372/enrichment-of-antibiotic-resistance-genes-in-soil-receiving-composts-derived-from-swine-manure-yard-wastes-or-food-wastes-and-evidence-for-multi-year-persistence-of-swine-i-i-clostridium-i-i-spp
#2
Andrew Scott, Yuan-Ching Tien, Craig F Drury, W Daniel Reynolds, Edward Topp
The impact of amendment with swine manure composts (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared to untreated control soil, all three amendment types increased the abundance of gene targets for up to four years post-application...
January 17, 2018: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/29317877/phylogenetic-analysis-of-giardia-lamblia-human-genotypes-in-fars-province-southern-iran
#3
Mohammad Rayani, Gholamreza Hatam, Ngah Zasmy Unyah, Abdolmajid Ashrafmansori, Wan Omar Abdullah, Rukman Awang Hamat
Background: This study is the first phylogenetic genotype analysis of Giardia lamblia in Iran. The main objective was to determine genotyping and identify the sub-assemblages of Giardia lamblia isolates involved in the transmission of giardiasis in Fars Province, south of Iran, in 2012. Methods: Forty G. lamblia isolates were collected from the patient's fecal samples with gastrointestinal discomfort referred to the health centers and hospitals in Shiraz, Fars Province, south of Iran...
October 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/29305057/comparison-of-dna-extraction-methods-for-human-gut-microbial-community-profiling
#4
Mi Young Lim, Eun-Ji Song, Sang Ho Kim, Jangwon Lee, Young-Do Nam
The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29300934/effects-of-sample-preservation-and-dna-extraction-on-enumeration-of-antibiotic-resistance-genes-in-wastewater
#5
An-Dong Li, Jacob W Metch, Yulin Wang, Emily Garner, An Ni Zhang, Maria V Riquelme, Peter J Vikesland, Amy Pruden, Tong Zhang
With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move towards standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit, and ZR Fecal DNA MiniPrep™), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA...
December 27, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29300319/surveillance-of-foodborne-pathogens-towards-diagnostic-metagenomics-of-fecal-samples
#6
REVIEW
Sandra Christine Andersen, Jeffrey Hoorfar
Diagnostic metagenomics is a rapidly evolving laboratory tool for culture-independent tracing of foodborne pathogens. The method has the potential to become a generic platform for detection of most pathogens and many sample types. Today, however, it is still at an early and experimental stage. Studies show that metagenomic methods, from sample storage and DNA extraction to library preparation and shotgun sequencing, have a great influence on data output. To construct protocols that extract the complete metagenome but with minimal bias is an ongoing challenge...
January 4, 2018: Genes
https://www.readbyqxmd.com/read/29290650/structural-shift-of-gut-microbiota-during-chemo-preventive-effects-of-epigallocatechin-gallate-on-colorectal-carcinogenesis-in-mice
#7
Xin Wang, Tao Ye, Wen-Jie Chen, You Lv, Zong Hao, Jun Chen, Jia-Ying Zhao, Hui-Peng Wang, Yuan-Kun Cai
AIM: To investigate the effect of epigallocatechin gallate (EGCG) on structural changes of gut microbiota in colorectal carcinogenesis. METHODS: An azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colitis mouse model was established. Forty-two female FVB/N mice were randomly divided into the following three groups: group 1 (10 mice, negative control) was treated with vehicle, group 2 (16 mice, positive control) was treated with AOM plus vehicle, and group 3 (16 mice, EG) was treated with AOM plus EGCG...
December 14, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29281808/evaluation-of-the-novel-crassphage-marker-for-sewage-pollution-tracking-in-storm-drain-outfalls-in-tampa-florida
#8
Warish Ahmed, Aldo Lobos, Jacob Senkbeil, Jayme Peraud, Javier Gallard, Valerie J Harwood
CrAssphage are recently-discovered DNA bacteriophages that are prevalent and abundant in human feces and sewage. We assessed the performance characteristics of a crAssphage quantitative PCR (qPCR) assay for quantifying sewage impacts in stormwater and surface water in subtropical Tampa, Florida. The mean concentrations of crAssphage in untreated sewage ranged from 9.08 to 9.98 log10 gene copies/L. Specificity was 0.927 against 83 non-human fecal reference samples and the sensitivity was 1.0. Cross-reactivity was observed in DNA extracted from soiled poultry litter but the concentrations were substantially lower than untreated sewage...
December 24, 2017: Water Research
https://www.readbyqxmd.com/read/29275129/dysbiosis-of-the-fecal-microbiota-in-feedlot-cattle-with-hemorrhagic-diarrhea
#9
Mohamed Zeineldin, Brian Aldridge, James Lowe
The bovine gastrointestinal microbiota is a complex polymicrobial ecosystem that plays an important role in maintaining mucosal health. The role of mucosal microbial populations in the pathogenesis of gastrointestinal diseases has been well established in other species. However, limited information is available about changes in the fecal microbiota that occur under disease conditions, such as hemorrhagic diarrhea in feedlot cattle. The objectives of this study were to characterize the differences in fecal microbiota composition, diversity and functional gene profile between feedlot calves with, and without, hemorrhagic diarrhea...
December 21, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29250161/detection-of-k-ras-gene-mutations-in-feces-by-magnetic-nanoprobe-in-patients-with-pancreatic-cancer-a-preliminary-study
#10
Xiaoguang Wang, Jingshuai Wang, Fei Chen, Zhengxiang Zhong, Lifeng Qi
The present study aimed to investigate the feasibility and effectiveness of detecting K-ras mutation by using magnetic nanoparticles in fecal samples of patients with pancreatic cancer at different stages. The novel methodology of K-ras mutation detection was compared to the existing methodology of cancer antigen (CA)19-9 examination. Patients with pancreatic cancer (n=88), pancreatic benign diseases who displayed chronic pancreatitis (n=35), pancreatic mucinous cyst neoplasms (n=10) and pancreatic serous cyst (n=9) admitted to the Department of Surgery, Jiaxing Second Hospital were enrolled in the present study...
January 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29228270/influenza-a-virus-subtype-h9n2-infection-disrupts-the-composition-of-intestinal-microbiota-of-chickens
#11
Alexander Yitbarek, J Scott Weese, Tamiru Negash Alkie, John Parkinson, Shayan Sharif
The impact of low pathogenic influenza viruses such as subtype H9N2, which infect the respiratory and the gastrointestinal tracts of chickens, on microbial composition are not known. Twenty day-old specific pathogen free chickens were assigned to two treatment groups, control (Uninfected) and H9N2-infected (challenged via the oral-nasal route). Fecal genomic DNA was extracted, and the V3-V4 regions of the 16S rRNA gene was sequenced using the Illumina Miseq® platform. Sequences were curated using Mothur as described in the MiSeq SOP...
December 6, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29224863/quantifying-fecal-shedding-of-mycobacterium-avium-ssp-paratuberculosis-from-calves-after-experimental-infection-and-exposure
#12
Caroline S Corbett, Herman W Barkema, Jeroen De Buck
Johne's disease, a chronic enteritis caused by Mycobacterium avium ssp. paratuberculosis (MAP), causes large economic losses to the dairy industry worldwide. Fecal shedding of MAP contaminates the environment, feed, and water and contributes to new infections on farm, yet there is limited knowledge regarding mechanisms of shedding, extent of intermittent shedding, and numbers of MAP bacteria shed. The objectives were to (1) compare (in an experimental setting) the frequency at which intermittent shedding occurred and the quantity of MAP shed among pen mates that were inoculated or contact-exposed (CE); and (2) determine whether an association existed between inoculation dose and quantity of MAP shed...
December 7, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29221852/captive-bred-neotropical-birds-diagnosed-with-cryptosporidium-avian-genotype-iii
#13
Ricardo Silva Novaes, Marcus Sandes Pires, Adriana Pittella Sudré, Teresa Cristina Bergamo do Bomfim
Currently, there are only three valid species of Cryptosporidium infecting avian hosts, namely, Cryptosporidium meleagridis, Cryptosporidium baileyi, and Cryptosporidium galli, in addition to 13 genotypes of unknown species status, such as Avian genotypes I-VI, the black duck genotype, the Eurasian woodcock genotype, and goose genotypes I-V. The objectives of this study were to microscopically diagnose the presence of Cryptosporidium in birds from a commercial aviary located in Rio de Janeiro, Brazil; genotypically characterize species and/or genotypes of genus Cryptosporidum; and conduct sequencing and phylogenetic analyses to compare the obtained DNA sequences with those deposited in GenBank...
December 5, 2017: Acta Tropica
https://www.readbyqxmd.com/read/29218079/vegf-c-mediated-enhancement-of-lymphatic-drainage-reduces-intestinal-inflammation-by-regulating-il-9-il-17-balance-and-improving-gut-microbiota-in-experimental-chronic-colitis
#14
Xiaolei Wang, Jin Zhao, Li Qin
BACKGROUND: Inflammation-associated lymphangiogenesis (IAL) induced by vascular endothelial growth factor (VEGF)-C/VEGF receptor-3 (VEGFR-3) pathway plays a crucial role in chronic intestinal inflammation. This study aimed to investigate the effects of VEGF-C mediated enhancement of lymphatic drainage on the intestinal inflammation in experimental chronic colitis (CC) and the potential mechanism was explored. METHODS: Mouse CC model was established by three cycles of 2% DSS administration for 5 days following water administration for 5 days...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/29198923/enteromorpha-and-polysaccharides-from-enteromorpha-ameliorate-loperamide-induced-constipation-in-mice
#15
Xinxiu Ren, Lei Liu, Yaser Gamallat, Bingqiang Zhang, Yi Xin
Slow-transit constipation(STC)is a disease characterized by functional gastrointestinal disorder. Common laxatives used in clinical practice against constipation such as Senna have side effects. Enteromorpha(EP)is a common marine alga, and the polysaccharide extracted from EP has been reported possessing anti-cancer and anti-inflammation effects. The aim of this study is to investigate the effects of EP and Polysaccharides from Enteromorpha (PEP) on loperamide induced constipated mice model and illustrating mechanism of action...
December 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29185906/molecular-identification-of-cryptosporidium-spp-in-iranian-dogs-using-seminested-pcr-a-first-report
#16
Reza Ranjbar, Hossein Mirhendi, Morteza Izadi, Bahador Behrouz, Reza Mohammadi Manesh
Cryptosporidium is a parasitic protozoon with a wide range of vertebrate hosts. Cryptosporidiosis has been reported from numerous countries, including Iran. Molecular identification can be applied to characterize Cryptosporidium, of which there are over 30 species and 50 genotypes. Herein, we report the genetic diversity of Cryptosporidium spp. in Iranian dogs for the first time based on 18S ribosomal RNA gene sequencing. One hundred forty fecal samples of herd dogs were collected from Isfahan, central Iran...
November 29, 2017: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/29181860/detection-of-helicobacter-pylori-in-stool-samples-of-young-children-using-real-time-polymerase-chain-reaction
#17
Gany Beer-Davidson, Musa Hindiyeh, Khitam Muhsen
BACKGROUND: The aims of this study were to develop and validate a multiplex real-time polymerase chain reaction (q-PCR) assay of Helicobacter pylori in stool samples of healthy children. Additionally, we determined the prevalence of clarithromycin resistance and cagA gene in H. pylori-positive samples. MATERIALS AND METHODS: Archived stool samples from 188 children aged 6-9 years and 272 samples of 92 infants aged 2-18 months were tested for H. pylori antigens using enzyme immunoassay (EIA)...
November 27, 2017: Helicobacter
https://www.readbyqxmd.com/read/29181448/direct-pcr-offers-a-fast-and-reliable-alternative-to-conventional-dna-isolation-methods-for-gut-microbiomes
#18
Elin Videvall, Maria Strandh, Anel Engelbrecht, Schalk Cloete, Charlie K Cornwallis
The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing...
November 2017: MSystems
https://www.readbyqxmd.com/read/29156877/comparison-of-microscopy-elisa-and-real-time-pcr-for-detection-of-giardia-intestinalis-in-human-stool-specimens
#19
Yunus Emre Beyhan, Zeynep Taş Cengiz
Background/aim: This study included patients who had digestive system complaints between August 2015 and October 2015. The research was designed to compare conventional microscopy with an antigen detection ELISA kit and the TaqMan-based real-time PCR (RT-PCR) technique for detection of Giardia intestinalis in human stool specimens. Materials and methods: Samples were concentrated by formalin-ether sedimentation technique and microscopic examinations were carried out on wet mount slides. A commercially available ELISA kit (Giardia CELISA, Cellabs, Brookvale, Australia) was used for immunoassay...
August 23, 2017: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/29156625/gene-based-pathogen-detection-can-we-use-qpcr-to-predict-the-outcome-of-diagnostic-metagenomics
#20
Sandra Christine Andersen, Mette Sofie Rousing Fachmann, Kristoffer Kiil, Eva Møller Nielsen, Jeffrey Hoorfar
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through screening of methods, whether qPCR can be used as an indicator for the optimization of sample preparation for NGS-based shotgun metagenomics with a diagnostic focus...
November 20, 2017: Genes
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