scholarly journals Comparison of Two Methods of Bacterial DNA Extraction from Human Fecal Samples Contaminated with Clostridium perfringens, Staphylococcus aureus, Salmonella Typhimurium, and Campylobacter jejuni

2014 ◽  
Vol 67 (6) ◽  
pp. 441-446 ◽  
Author(s):  
Jun Kawase ◽  
Morito Kurosaki ◽  
Yuta Kawakami ◽  
Takashi Kashimoto ◽  
Yoshie Tsunomori ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Salmonella Typhimurium ◽  
Dna Extraction ◽  
Campylobacter Jejuni ◽  
Clostridium Perfringens ◽  
Bacterial Dna ◽  
Fecal Samples ◽  
Bacterial Dna Extraction

scholarly journals Impact of sequence variant detection and bacterial DNA extraction methods on the measurement of microbial community composition in human stool

2017 ◽  
Author(s):  
Riley Hughes ◽  
Zeynep Alkan ◽  
Nancy L. Keim ◽  
Mary E. Kable
Keyword(s):  
Microbial Community ◽  
Dna Extraction ◽  
Community Composition ◽  
Sequence Variant ◽  
Mock Community ◽  
Bacterial Dna ◽  
Fecal Samples ◽  
Yield Quality ◽  
Bacterial Dna Extraction ◽  
Dna Stabilization

ABSTRACTBackgroundThe human gut microbiome has been widely studied in the context of human health and metabolism, however the question of how to analyze this community remains contentious. This study compares new and previously well established methods aimed at reducing bias in bioinformatics analysis (QIIME 1 and DADA2) and bacterial DNA extraction of human fecal samples in 16S rRNA marker gene surveys.ResultsAnalysis of a mock DNA community using DADA2 identified more chimeras (QIIME 1: 0.70% of total reads vs DADA2: 1.96%), fewer sequence variants, (QIIME 1: 1297.4 + 98.88 vs. DADA2: 136.27 + 11.35, mean + SD) and correct taxa at a higher resolution of classification (i.e. genus-level) than open reference OTU picking in QIIME 1. Additionally, the extraction of whole cell mock community bacterial DNA using four commercially available kits resulted in varying DNA yield, quality and bacterial community composition. Of the four kits compared, ZymoBIOMICS DNA Miniprep Kit provided the greatest yield, with a slight enrichment of Enterococcus. However, QIAamp Fast DNA Stool Mini Kit resulted in the highest DNA quality. Mo Bio PowerFecal DNA Kit had the most dramatic effect on the mock community composition, resulting in an increased proportion of members of the family Enterobacteriaceae and genus Eshcerichia as well as members of genera Lactobacillus and Pseudomonas. The presence of a sterile fecal matrix had a slight, but inconsistent effect on the yield, quality and taxa identified after extraction with all four DNA extraction kits. Extraction of bacterial DNA from native stool samples revealed a distinct effect of the DNA stabilization reagent DNA/RNA Shield on community composition, causing an increase in the detected abundance of members of orders Bifidobacteriales, Bacteroidales, Turicibacterales, Clostridiales and Enterobacteriales.ConclusionThese results confirm that the DADA2 algorithm is superior to sequence clustering by similarity to determine microbial community structure. Additionally, commercially available kits used for bacterial DNA extraction from fecal samples have some effect on the proportion of high abundance members detected in a microbial community, but it is less significant than the effect of using DNA stabilization reagent, DNA/RNA Shield.

Fate of Selected Pathogens Inoculated into Foods Prepared in Slow Cookers1,2

1979 ◽  
Vol 42 (11) ◽  
pp. 872-876 ◽  
Author(s):  
J. RITTER ◽  
J. O'LEARY ◽  
B. E. LANGLOIS
Keyword(s):  
Staphylococcus Aureus ◽  
Low Temperature ◽  
Salmonella Typhimurium ◽  
Clostridium Perfringens ◽  
Health Hazard ◽  
Green Bean ◽  
Vegetative Cells ◽  
Salmonella Choleraesuis ◽  
Navy Beans ◽  
The Mean

Staphylococcus aureus, Clostridium perfringens. Salmonella choleraesuis, and Salmonella typhimurium were inoculated (108 cells or spores) into two slow cookers containing green bean casserole, baked navy beans, chicken cacciatore, barbecued ribs or pork pot roast, and their fate determined after cooking. Heating patterns also were determined at three positions inside the two cookers. None of the foods cooked in either of the slow cookers contained detectable levels of S. aureus or salmonellae. The similarity between C. perfringens vegetative and spore counts indicate that only spores were present in the cooked foods. Except for the green bean casserole cooked using a low temperature setting, cooking resulted in a 0.44–1.67 and 0.36–1.54 log count reduction, respectively, of vegetative cells and spores of C. perfringens. Counts of vegetative cells and spores after cooking the green bean casserole were approximately .18 and .30 log counts higher than the uncooked counts. The mean times for the coldest areas in Cooker A to reach 50 C were 2.57 and 0.97 h, respectively, for the low (80 watts) and high (160 watts) temperature settings. The mean times for the coldest areas in Cooker B (removable liner) to reach 50 C were 2.35 and 0.52 h for the low (130 watts) and high (260 watts) temperature settings, respectively. Results suggest that when the recommended quantities of ingredients are used and the proper cooking procedure followed, foods prepared in the slow cookers studied do not present a health hazard.

scholarly journals Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

Microbiome ◽  
2014 ◽  
Vol 2 (1) ◽  
pp. 19 ◽  
Author(s):  
Agata Wesolowska-Andersen ◽  
Martin Bahl ◽  
Vera Carvalho ◽  
Karsten Kristiansen ◽  
Thomas Sicheritz-Pontén ◽  
...  
Keyword(s):  
Community Structure ◽  
Dna Extraction ◽  
Extraction Method ◽  
Metagenomic Analysis ◽  
Fecal Material ◽  
Bacterial Dna ◽  
Dna Extraction Method ◽  
Bacterial Dna Extraction

scholarly journals Necessity of purification during bacterial DNA extraction with environmental soils

2017 ◽  
Vol 32 ◽  
pp. e2017013 ◽  
Author(s):  
Hyun Jeong Lim ◽  
Jung-Hyun Choi ◽  
Ahjeong Son
Keyword(s):  
Dna Extraction ◽  
Bacterial Dna ◽  
Bacterial Dna Extraction

Fate of Pathogens Inoculated onto Vacuum-Packaged Sliced Hams to Simulate Contamination During Packaging1

1979 ◽  
Vol 42 (6) ◽  
pp. 464-469 ◽  
Author(s):  
M. E. STILES ◽  
L.-K. NG
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Salmonella Typhimurium ◽  
Bacillus Cereus ◽  
Clostridium Perfringens ◽  
Subsequent Treatment ◽  
Vacuum Packaging ◽  
E Coli ◽  
Survival And Growth ◽  
And Staphylococcus Aureus

Ham and chopped ham from two manufacturers were contaminated with five enteropathogens: Bacillus cereus, Clostridium perfringens, Escherichia coli, Salmonella typhimurium and Staphylococcus aureus, at time of slicing and vacuum-packaging, to simulate contamination by manufacturer. Subsequent treatment of the samples, representing sound and undesirable retail handling and consumer use conditions, indicated marked differences in the fate of the pathogens between these products and within product type between the two manufacturers. Greatest differences were observed between the chopped ham products. All pathogens, except C. perfringens, grew actively in fresh ham and chopped ham with abusive holding at 30 and 21 C. After storage at 4 or 10 C for 30 days, B. cereus and C. perfringens were no longer detected, even after subsequent holding at 30 or 21 C for 24 h. E. coli survival and growth was variable, S. typhimurium survived well and grew under some conditions and S. aureus was generally inhibited at high levels of competition.

scholarly journals A New, Rapid, Efficient and Non-Toxic Method for Bacterial DNA Extraction

2019 ◽  
Vol 116 (3) ◽  
pp. 360a
Author(s):  
Semire Uzun Gocmen ◽  
Ahmet Aslan ◽  
Muhyittin Temiz
Keyword(s):  
Dna Extraction ◽  
Bacterial Dna ◽  
Bacterial Dna Extraction

Bacterial Cell Characteristics and Conditions Influencing Their Adhesion to Poultry Skin

1985 ◽  
Vol 48 (9) ◽  
pp. 803-807 ◽  
Author(s):  
H. S. LILLARD
Keyword(s):  
Staphylococcus Aureus ◽  
Salmonella Typhimurium ◽  
Clostridium Perfringens ◽  
Constant Pressure ◽  
Linear Increase ◽  
Bacterial Attachment ◽  
Sample Type ◽  
Proteus Vulgaris ◽  
Gram Negative ◽  
Salmonella Gallinarum

Conflicting reports appear in the literature regarding attachment of flagellated and nonflagellated bacteria to poultry skin. The following parameters which may influence bacterial attachment were examined: (a) sample type and size; (b) skin from fully processed and scalded but uneviscerated broilers; (c) skin from hard- and soft-scalded broilers; and (d) potentially variable tap rinse and constant pressure spray wash (50 psi). Gram-positive and gram-negative, flagellated and nonflagellated bacteria were used in suspension fluids (Salmonella typhimurium, Salmonella gallinarum, Proteus vulgaris, Pseudomonas fluoresces, Clostridium perfringens, Staphylococcus aureus and a nonflagellated species of Micrococcus). Results showed that none of the variables tested affected the ability of bacteria to adhere to poultry skin in 0.25 min. All species tested adhered to skin, and there was a generally linear increase in rate of attachment with time (0.25 to 60 min) following exposure of poultry skin to suspending fluid. It was concluded that nonflagellated bacteria attach as readily as flagellated bacteria under the same controlled conditions.

Development of a bacterial DNA extraction modular chip using a magnetic particle and portable vibration motor

2020 ◽  
Vol 12 (9) ◽  
pp. 1197-1202
Author(s):  
Sun Young Lim ◽  
Tae Jae Lee ◽  
Seol Yi Shin ◽  
Nam Ho Bae ◽  
Seok Jae Lee ◽  
...  
Keyword(s):  
Power System ◽  
Electric Power ◽  
Dna Extraction ◽  
Magnetic Particles ◽  
Magnetic Particle ◽  
Electric Power System ◽  
Bacterial Dna ◽  
System P ◽  
3D Printed ◽  
Bacterial Dna Extraction

The bacterial DNA was simply purified by magnetic particles with a portable vibration motor. To effectively extract DNA in the field, the 3D-printed device was employed with low electric power system.

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