Read by QxMD icon Read

fecal DNA extraction

Scott W Korte, Craig L Franklin, Rebecca A Dorfmeyer, Aaron C Ericsson
To protect the biosecurity of research rodent colonies, research institutions frequently require a quarantine period for live animals transferred into their facilities. Quarantine practices often include antibiotic and antiparasitic treatment with drugs such as fenbendazole and macrolide lactones. The influence of these compounds on the resident gut microbiota of mice is unknown, and any effects might subsequently affect model reproducibility. To test the influence of standard quarantine procedures on the composition of the microbiota, C57BL/6 mice, purchased from 2 different commercial suppliers, were randomly assigned to treatment groups (n = 12) by vendor and treated with fenbendazole-supplemented feed, topical moxidectin, both treatments, or no treatment (control), according to our institution's standard treatment regimen and duration...
May 1, 2018: Journal of the American Association for Laboratory Animal Science: JAALAS
Letizia Mazzini, Luca Mogna, Fabiola De Marchi, Angela Amoruso, Marco Pane, Irene Aloisio, Nicole Bozzi Cionci, Francesca Gaggìa, Ausiliatrice Lucenti, Enrica Bersano, Roberto Cantello, Diana Di Gioia, Giovanni Mogna
BACKGROUND: Recent preclinical studies suggest that dysfunction of gastrointestinal tract may play a role in amyotrophic lateral sclerosis (ALS) pathogenesis through a modification of the gut microbiota brain axis. Our study is the first focused on microbiota analysis in ALS patients. AIM: Our aim was to study the main human gut microbial groups and the overall microbial diversity in ALS and healthy subjects. Moreover we have examined the influence of a treatment with a specific bacteriotherapy composed of Lactobacillus strains (Lactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus salivarius) acting on the gastrointestinal barrier...
May 18, 2018: Journal of Clinical Gastroenterology
Margaret H Ainslie-Garcia, Abdolvahab Farzan, Mohsen Jafarikia, Brandon N Lillie
Foodborne human salmonellosis is an important food safety concern worldwide. Food-producing animals are one of the major sources of human salmonellosis, and thus control of Salmonella at the farm level could reduce Salmonella spread in the food supply system. Genetic selection of pigs with resistance to Salmonella infection may be one way to control Salmonella on swine farms. The objective of this study was to investigate the association between genetic variants in the porcine innate immune system with on-farm Salmonella shedding and Salmonella colonization tested at slaughter...
June 2018: Veterinary Microbiology
Nitsan Maharshak, Yehuda Ringel, David Katibian, Ashley Lundqvist, R Balfour Sartor, Ian M Carroll, Tamar Ringel-Kulka
BACKGROUND: Irritable bowel syndrome (IBS) has been associated with changes in the intestinal microbiota. Only a few studies have explored differences in the mucosa-associated microbiota between IBS patients and healthy controls (HC). AIMS: To characterize and compare the microbiota in mucosal and fecal samples from carefully selected patients with IBS-D and HC. METHODS: The cohort was composed of 23 diarrhea-predominant IBS (IBS-D) patients and 24 HC...
May 17, 2018: Digestive Diseases and Sciences
Sun-Young Kook, Yunjeong Kim, Ben Kang, Yon Ho Choe, Young-Ho Kim, Seokjin Kim
Background/Aims: Tens of trillions of microorganisms constitute the gut microbiota of the human body. The microbiota plays a critical role in maintaining host immunity and metabolism. Analyses of the gut microbial composition in Korea are limited to a few studies consisting of small sample sizes. To investigate the gut microbial community in a large sample of healthy Koreans, we analyzed the 16S ribosomal RNA of 4 representative bacterial genera Lactobacillus , Bifidobacterium , Bacteroides , and Clostridium ...
April 2018: Intestinal Research
Nidia Maradiaga, Brian Aldridge, Mohamed Zeineldin, James Lowe
Cross fostering is employed to equalize the number of piglet between litters ensuring colostrum intake for their survival and growth. However, little is known about the impact of cross fostering on the intestinal microbiota and mucosal immune gene expression of the neonatal pig. The objective of this study was to determine the influence of maternal microbial communities on the gastrointestinal (GI) microbiota and mucosal immune gene expression in young pigs reared in a cross-fostering model. Piglets were given high quality colostrum from birth dam or foster dam upon birth...
May 6, 2018: Microbial Pathogenesis
Yun Huang, Si-Cheng Li, Ji Hu, Hai-Bin Ruan, He-Ming Guo, Hong-Hong Zhang, Xin Wang, Yu-Fang Pei, Yang Pan, Chen Fang
AIMS: To investigate whether microbial dysbiosis is associated with T1D in Chinese population and to explore relationships between the composition of gut microbiome and clinical data. METHODS: In this study, we recruited 10 healthy and 12 T1D Han Chinese subjects between the ages of 12 to 33. Fecal samples were collected for DNA extraction and 16S rRNA sequencing, followed by analyses of the gut microbiota composition. RESULTS: Bacterial communities differed between healthy and T1D subjects...
May 4, 2018: Diabetes Research and Clinical Practice
Yiping Cao, Meredith R Raith, John F Griffith
qPCR has become increasingly popular for microbial water quality testing because it is faster, more specific, and more flexible than culture-based methods. However, qPCR method limitations such as quantification bias introduced by reliance on standards and susceptibility to PCR inhibitors are major obstacles for implementation in water testing. This is because water testing requires accurate quantification of rare targets and because environmental waters often contain PCR inhibitors. Digital PCR offers the opportunity to maintain qPCR's advantages over culture-based methods while ameliorating two of qPCR's major limitations: the necessity to run standard curves and high susceptibility to inhibition...
2018: Methods in Molecular Biology
Hongxing Qiao, Liheng Zhang, Hongtao Shi, Yuzhen Song, Chuanzhou Bian
The gut microbiota play important roles in the degradation of chemical compounds of herbal medicines (HMs). However, little information regarding the interplay between HMs and the gut microbiota is available. Thus, the aim of this study was to investigate the composition of the fecal microbiota of young (age, 11 weeks) hens fed a conventional diet containing a crude Astragalus (0.5%) additive for 21 days (group A) vs. controls (group B) that were fed only conventional feed. The fecal contents of 14-week-old hens were collected for DNA extraction, and then the V3 and V4 hyper-variable regions of the 16S rRNA gene were amplified and analyzed using high-throughput sequencing technology...
April 30, 2018: AMB Express
Blair Lawley, Manuela Centanni, Jun Watanabe, Ian Sims, Susan Carnachan, Roland Broadbent, Pheng Soon Lee, Khai Hong Wong, Gerald W Tannock
Members of the bacterial genus Bifidobacterium generally dominate the faecal microbiota of infants. The species B. longum is prevalent, but the subspecies longum and infantis that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacity to metabolize Human Milk Oligosaccharides (HMO) and may have differing ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms...
April 27, 2018: Applied and Environmental Microbiology
Jyoti K Lama, Dave S Bachoon
Feral pigs (Sus scrofa) are an environmentally destructive invasive species that act as a reservoir for zoonotic pathogens. The aim of this study was to determine the presence of Brucella suis, Campylobacter jejuni, and of Escherichia coli in feces of feral pigs from Georgia. Fecal samples were collected from 87 feral pigs from forested and agricultural regions of Georgia. DNA was extracted from the fecal samples and quantitative PCR (qPCR) was used to screen for each of the four pathogens. The qPCR assays indicated that B...
April 26, 2018: Vector Borne and Zoonotic Diseases
D I Ayala, J Chen, M Bugarel, G H Loneragan, H C den Bakker, K R Kottapalli, M M Brashears, K K Nightingale
Lactobacillus animalis NP51 is a direct-fed microbial strain (DFM) extensively used as a pre-harvest food safety mitigation in feedlot cattle due to its antagonistic effects against human foodborne pathogens such as Salmonella and Escherichia coli O157:H7. NP51 not only promotes overall gut health but interferes with the ability of these pathogens to colonize the gastrointestinal tract of cattle. As a result, NP51 reduces fecal shedding of Salmonella and E. coli O157:H7 in cattle presented for harvest and the load of these pathogens that enter the human food chain...
April 16, 2018: Journal of Microbiological Methods
Mamta Rani, Deepti Narang, Dinesh Kumar, Mudit Chandra, Sikh Tejinder Singh, G Filia
Background and Aim: Johne's disease is chronic granulomatous enteritis which affects ruminants. There are many diagnostic approaches for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) of which molecular detection methods using various elements are less time consuming and more accurate. The present study was conducted using ISMap 02 element for nested polymerase chain reaction (nPCR) based detection of MAP in fecal samples. The aim was to test the sensitivity and specificity of the ISMap 02 element and also to use this element for the detection of MAP in fecal samples of cattle and buffaloes...
March 2018: Veterinary World
Amr M Abdou, Riham H Hedia, Shimaa T Omara, Mohamed Abd El-Fatah Mahmoud, Mai M Kandil, M A Bakry
Aim: The aim of the current study was to isolate and identify naturally occurring probiotic Lactobacillus species in different animals with the different environmental background including fish, and farm animals to investigate interspecies differences in probiotics on the species level. Materials and Methods: A total of 44 fecal and milk samples were collected under aseptic conditions from cattle, buffalo, camel, sheep, goats, and fish. The samples were cultured, and the isolated strains were confirmed biochemically and molecularly using 16S rRNA multiplex polymerase chain reaction (PCR) analysis following DNA extraction from the bacterial isolates...
February 2018: Veterinary World
Malla I Neuvonen, Katri Korpela, Kristiina Kyrklund, Risto J Rintala, Mikko P Pakarinen
OBJECTIVES: To characterize the microbiota profiles of patients with Hirschsprung's disease (HD), and to evaluate this in relation to postoperative bowel function and the incidence of Hirschsprung-associated enterocolitis (HAEC). METHODS: All patients operated on for HD at our center between 1987-2011 were invited to answer questionnaires on bowel function and to participate in a clinical follow-up for laboratory investigations, including fecal DNA extraction, fecal calprotectin (FC), and brush border lactase (LCT) genotyping...
April 12, 2018: Journal of Pediatric Gastroenterology and Nutrition
Alanna Dubrovsky, Christopher L Kitts
A 20-year-old female was diagnosed with ulcerative colitis (UC) at age 14 and primary sclerosing cholangitis (PSC) at age 16. The PSC was successfully treated with high doses of oral vancomycin; however, the UC was more difficult to manage. After many drug treatments failed to treat the UC, the patient began following the specific carbohydrate diet (SCD). This report documents fecal microbiome changes resulting from following the SCD for two weeks. The DNA extracted from fecal samples was subjected to 16S rRNA gene sequencing to quantify bacterial species abundance...
February 9, 2018: Curēus
Xinyue Huang, Zi Ye, Qingfeng Cao, Guannan Su, Qingfeng Wang, Jing Deng, Chunjiang Zhou, Aize Kijlstra, Peizeng Yang
Purpose: To investigate gut microbiota composition and fecal metabolic phenotype in patients with acute anterior uveitis. Methods: Fecal DNA was extracted from 78 fecal samples (38 acute anterior uveitis (AAU) patients and 40 family members of patients or sex- and age-matched healthy controls) and then sequenced by high-throughput 16S rDNA analysis. Gas chromatographic mass spectrometry (GC-MS) based metabolomics was performed on 60 fecal samples (30 AAU patients and 30 healthy controls)...
March 1, 2018: Investigative Ophthalmology & Visual Science
Manuel Ares-Arroyo, Cristina Bernabe-Balas, Alfonso Santos-Lopez, Maria R Baquero, Kashi N Prasad, Dolores Cid, Carmen Martin-Espada, Alvaro San Millan, Bruno Gonzalez-Zorn
ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic analysis of these ColE1 replicons revealed a mosaic genetic structure consisting of a host-adapted conserved region responsible for the housekeeping functions of the plasmid, and a variable region encoding a wide variety of genes, including multiple antibiotic resistance determinants...
2018: Frontiers in Microbiology
Ayelet Di Segni, Tzipi Braun, Marina BenShoshan, Sarit Farage Barhom, Efrat Glick Saar, Karen Cesarkas, James E Squires, Nathan Keller, Yael Haberman
The human intestinal microbiome plays a central role in protecting cells from injury, in processing energy and nutrients, and in promoting immunity. Deviations from what is considered a healthy microbiota composition (dysbiosis) may impair vital functions leading to pathologic conditions. Recent and ongoing research efforts have been directed toward the characterization of associations between microbial composition and human health and disease. Advances in high-throughput sequencing technologies enable characterization of the gut microbial composition...
March 19, 2018: Journal of Visualized Experiments: JoVE
Ana Ramón-Laca, Daniel J White, Jason T Weir, Hugh A Robertson
Although some taxa are increasing in number due to active management and predator control, the overall number of kiwi ( Apteryx spp.) is declining. Kiwi are cryptic and rare, meaning current monitoring tools, such as call counts, radio telemetry, and surveys using detection dogs are labor-intensive, yield small datasets, and require substantial resources or provide inaccurate estimates of population sizes. A noninvasive genetic approach could help the conservation effort. We optimized a panel of 23 genetic markers (22 autosomal microsatellite loci and an allosomal marker) to discriminate between all species of kiwi and major lineages within species, while simultaneously determining sex...
March 2018: Ecology and Evolution
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"