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

Objective Clinical diagnostics often requires the detection of multiple bacterial species in limited clinical samples with a single DNA extraction method. This study aimed to compare the bacterial DNA extraction efficiency of two lysis methods automated with the MagNA-Pure LC instrument. The samples included five oral bacterial species (three Gram-positive and two Gram-negative) with or without human saliva background. Methods Genomic DNA (gDNA) was extracted from bacterial cultures by bead-beating lysis (BMP) or chemical lysis (MP), followed by automated purification and measurement by quantitative PCR. Results For pure bacterial cultures, the MP method yielded higher quantities of extracted DNA and a lower detection limit than the BMP method, except where the samples contained high numbers of Gram-positive bacteria. For bacterial cultures with a saliva background, no difference in gDNA extraction efficacy was observed between the two methods. Conclusions The efficiency of a bacterial DNA extraction method is not only affected by the bacterial cell wall structure but also by the sample milieu. The MP method provided superior gDNA extraction efficiency when the samples contained a single bacterial species, whereas either of the BMP and MP methods could be applied with similar efficiencies to samples containing multiple species of bacteria.

Download Full-text

A comparison of different DNA extraction methods and molecular techniques for the detection and identification of foodborne pathogens

AIMS Microbiology ◽

10.3934/microbiol.2021019 ◽

2021 ◽

Vol 7 (3) ◽

pp. 304-319

Author(s):

Spyridon Andreas Papatheodorou ◽

◽

Panagiotis Halvatsiotis ◽

Dimitra Houhoula ◽

Keyword(s):

Dna Extraction ◽

Foodborne Pathogens ◽

Extraction Method ◽

Pathogenic Bacteria ◽

Low Cost ◽

Isoamyl Alcohol ◽

Extraction Methods ◽

Molecular Techniques ◽

Bacterial Dna ◽

Dna Extraction Method

<abstract> <p>Foodborne infections continue to plague Europe. Food safety monitoring is in crisis as the existing techniques for detecting pathogens do not keep up with the global rising of food production and consumption. Thus, the development of innovative techniques for detecting and identifying pathogenic bacteria has become critical. The aim of the present study was firstly to develop an innovative simple and low cost method of extracting bacterial DNA from contaminated food and water samples with <italic>Salmonella enteric</italic> subsp. <italic>enteric</italic> serovar Typhimurium and <italic>Listeria monocytogenes</italic> and its comparison with two commercial DNA extraction kits (Qiagen, Macherey-Nagel). Finally, pathogens' detection using two molecular techniques (PCR-electrophoresis, LAMP), in order to evaluate the best combination of DNA extraction and identification based on their sensitivity, cost, rapidity and simplicity. Considering the above criteria, among them, best was proved an in-house bacterial DNA extraction method, based on the chloroform-isoamyl alcohol protocol, with certain modifications. This technique showed statistically similar results in terms of sensitivity, compared to the commercial kits, while at the same time maintained high rapidity and much lower cost. Lastly, between the molecular techniques, LAMP was found more promising considering its simplicity, high rapidity and sensitivity. Conclusively, the in-house DNA extraction method along with the LAMP technique, was proven to be the best among the presented combinations.</p> </abstract>

Download Full-text

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis

MicrobiologyOpen ◽

10.1002/mbo3.453 ◽

2017 ◽

Vol 6 (4) ◽

pp. e00453 ◽

Cited By ~ 19

Author(s):

Sylwia Zielińska ◽

Piotr Radkowski ◽

Aleksandra Blendowska ◽

Agnieszka Ludwig-Gałęzowska ◽

Joanna M. Łoś ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Dna Extraction ◽

Structure Analysis ◽

Microbial Community Structure ◽

Soil Microbial Community ◽

Extraction Method ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Dna Extraction Method

Download Full-text

BACTERIAL DNA EXTRACTION METHOD FOR THE DETECTION OF HELICOBACTER PYLORI FROM HUMAN FECAL SAMPLES

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2020.v13i6.37344 ◽

2020 ◽

pp. 38-40

Author(s):

JHOAN GUAMÁN ◽

FAVIAN BAYAS-MOREJÓN ◽

ELENA BRITO ◽

NORMA PAREDES

Keyword(s):

Helicobacter Pylori ◽

Dna Extraction ◽

Conventional Polymerase Chain Reaction ◽

Chain Reaction ◽

Bacterial Dna ◽

Dna Extraction Method ◽

Stool Samples ◽

Chelex Resin ◽

Polymerase Chain ◽

Bacterial Dna Extraction

Objective: The work proposed the implementation of a method of DNA extraction for the detection of the pathogen from 50 stool samples. Methods: A method of DNA extraction with Chelex resin was applied and then detected by conventional polymerase chain reaction (PCR). Results: By PCR, 11 samples were positive for Helicobacter pylori. Conclusions: The Chelex extraction methodology allows obtaining DNA with quality necessary to be detected by PCR, making it a fast methodology for its diagnostic application.

Download Full-text

Sensitivity detection of Abacavir in human through SNP detection of HLA-B*5701 allele

International Journal of Bioassays ◽

10.21746/ijbio.2016.08.006 ◽

2016 ◽

Vol 5 (08) ◽

pp. 4754

Author(s):

Tanushree Mitra* ◽

Shivshankar Kumdale ◽

Sameer Chowdhary ◽

Amol D. Raut

Keyword(s):

Blood Sample ◽

Dna Extraction ◽

Genomic Dna ◽

Extraction Method ◽

Snp Detection ◽

Dna Extraction Method ◽

Sensitivity Detection

The main objective of this study was to make sure whether randomly taken 12 samples were sensitive to abacavir. The genomic DNA from 12 blood sample were extracted by phenol chloroform DNA extraction method, extracted genomic DNA were amplified and sequenced, thereafter SNPs were detected. Every sample had shown the presence of normal base at SNP position. This study indicated, those randomly taken 12 patients were sensitive to abacavir, so they can consume abacavir if they get infected with HIV.

Download Full-text