keyword
MENU ▼
Read by QxMD icon Read
search

fecal DNA extraction

keyword
https://www.readbyqxmd.com/read/28886400/breastfeeding-increases-microbial-community-resilience
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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)...
July 4, 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
#7
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
https://www.readbyqxmd.com/read/28761476/prevalence-clinical-manifestations-and-genotyping-of-cryptosporidium-spp-in-patients-with-gastrointestinal-illnesses-in-western-iran
#8
Hamed Kiani, Ali Haghighi, Seyyed Javad Seyyedtabaei, Eznollah Azargashsb, Nozhat Zebardast, Niloofar Taghipour, Ali Rostami, Lihua Xiao
BACKGROUND: Cryptosporidium species are recognized as important gastrointestinal pathogens. This study was conducted to identify the prevalence, clinical manifestations and genotyping of Cryptosporidium spp. in patients with gastrointestinal illnesses (GIs) in western Iran. METHODS: Overall, 1301 fecal samples were collected from patients with GIs referred to the 12 clinical laboratories in Nahavand County, west of Iran. Modified Ziehl-Neelsen staining method was used to identify the oocysts...
April 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28740461/down-for-the-count-cryptosporidium-infection-depletes-the-gut-microbiome-in-coquerel-s-sifakas
#9
Erin A McKenney, Lydia K Greene, Christine M Drea, Anne D Yoder
Background: The gut microbiome (GMB) is the first line of defense against enteric pathogens, which are a leading cause of disease and mortality worldwide. One such pathogen, the protozoan Cryptosporidium, causes a variety of digestive disorders that can be devastating and even lethal. The Coquerel's sifaka (Propithecus coquereli) - an endangered, folivorous primate endemic to Madagascar - is precariously susceptible to cryptosporidiosis under captive conditions. If left untreated, infection can rapidly advance to morbidity and death...
2017: Microbial Ecology in Health and Disease
https://www.readbyqxmd.com/read/28740351/partners-of-patients-with-ulcerative-colitis-exhibit-a-biologically-relevant-dysbiosis-in-fecal-microbial-metacommunities
#10
Guang-Lan Chen, Ye Zhang, Wang-Yue Wang, Xue-Liang Ji, Fei Meng, Pei-Song Xu, Ning-Min Yang, Fu-Qiang Ye, Xiao-Chen Bo
AIM: To investigate alterations in the fecal microbiome using 16S rRNA amplicon sequencing in couples in the same cohabitation environment. METHODS: Fecal samples were collected from eight ulcerative colitis (UC) patients and their healthy partners at Lishui People's Hospital, Zhejiang Province, China. DNA was extracted and the variable regions V3 and V4 of the 16S rRNA genes were PCR amplified using a two-step protocol. Clear reads were clustered into operational taxonomic units (OTUs) at the 97% sequence similarity level using UCLUST v1...
July 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28737135/a-flotation-sieving-method-to-detect-echinococcus-multilocularis-and-toxocara-spp-eggs-in-soil-by-real-time-pcr
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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"