Method for absolute quantification of microbial communities by using both microarrays and competitive PCR.

08:00 EDT 9th September 2019 | BioPortfolio

Summary of "Method for absolute quantification of microbial communities by using both microarrays and competitive PCR."

Methods for the robust quantification of bacterial communities are still under development. In this context, the present study aimed to evaluate a method combining competitive PCR (cPCR) and microarray assays for the determination of absolute content of total bacteria and individual bacterial species in samples. For this, a competitor DNA for cPCR and microarrays containing three types of DNA probes was prepared. A calibration curve was generated with genomic DNA samples as standards, which was then utilized for cPCR-based determination of the total number (in moles) of 16S rRNA genes in other bacterial samples. Moreover, scatter plots of species-specific probes versus total bacteria probe for each genomic DNA of known concentration was fit to the regression model, and the obtained slope value was defined as the hybridization affinity ratio. The cPCR assay was performed for both a commercially available mixed genomic DNA sample and human oral bacterial DNA samples, and the total number of moles of 16S rRNA genes was determined. These values were distributed among each species on the basis of the signal intensities of species-specific probes and the hybridization affinity ratio. The total number of bacterial genomes and those of individual species were determined by dividing the copy number of 16S rRNA genes per genome. The obtained results were confirmed by quantitative real-time PCR (qPCR). For values of >1 × 10 copies determined by qPCR, the ratio of the values measured by DNA chips to by qPCR was 1.53-fold on average and <2.6-fold for all data. These results show that the combined method of cPCR and microarray is useful to quantify the absolute numbers of several types of bacteria in a sample at one time.


Journal Details

This article was published in the following journal.

Name: Journal of microbiological methods
ISSN: 1872-8359
Pages: 105718


DeepDyve research library

PubMed Articles [12449 Associated PubMed Articles listed on BioPortfolio]

Improved measurement of absolute mRNA quantity without reverse transcription.

Gene expression studies using microarrays have provided important insights into understanding the mechanisms of transcriptional regulation in a variety of biological and disease phenomena. In a previo...

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities.

Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level...

Microbial Interaction Network Inference in Microfluidic Droplets.

Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantifica...

Quantifying bacterial cell lysis using GFP based fluorimetric assay.

Quantitative measurement of cell lysis against a given microbial strain is essential to calculate the antimicrobial potency of protein/peptide/nanomaterial based formulations. Fluorescence spectroscop...

Feasibility of absolute quantification for P MRS at 7 T.

Phosphorus spectroscopy can differentiate among liver disease stages and types. To quantify absolute concentrations of phosphorus metabolites, sensitivity calibration and transmit field ( ) correctio...

Clinical Trials [3259 Associated Clinical Trials listed on BioPortfolio]

Single-scan Rest/Stress Imaging With Cadmium Zinc Telluride-based SPECT for Coronary Flow Quantification

The investigators aim to address this issue with novel image quantification methods using CZT-based SPECT, which is capable of dynamic data acquisition and therefore feasible for the quant...

Validation of a Diagnostic Method for Quantification of Sleep Bruxism

This study aims to validate a new diagnostic method for quantification and monitoring of sleep bruxism.

Host Response to Pessaries in Microbial Communities of the Postmenopausal Vagina

The ability to determine the postmenopausal vaginal environment and the impact of pessary use could help to maximize pessary therapy and non-surgical treatment for such a prevalent problem...

Micro-Technique Sampling

This is a single-center, exploratory comparative pilot study to identify the most appropriate method for microbial consortia sampling from the skin. Ten subjects are expected to complete ...

Absolute Quantification of Coronary Flow Reserve by Stress Perfusion MRI

Coronary artery disease (CAD, coronary heart disease) is the leading cause of death in the U.S., causing 1 in 5 deaths in 2005. The current method for diagnosing coronary artery disease th...

Medical and Biotech [MESH] Definitions

Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. Each colony (i.e., microbial colony-forming unit) represents the progeny of a single cell in the original inoculum. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.

An ethnic group with shared religious beliefs in PROTESTANISM. Originating in Switzerland in the late 1600s, and first migrating to the mid-Atlantic, they now live throughout Eastern and Mid-Western United States and elsewhere. Communities are usually close-knit and marriage is within the community.

A frequent complication of drug therapy for microbial infection. It may result from opportunistic colonization following immunosuppression by the primary pathogen and can be influenced by the time interval between infections, microbial physiology, or host resistance. Experimental challenge and in vitro models are sometimes used in virulence and infectivity studies.

Light absorbing proteins and protein prosthetic groups found in certain microorganisms. Some microbial photoreceptors initiate specific chemical reactions which signal a change in the environment, while others generate energy by pumping specific ions across a cellular membrane.

A material transfer technique used for assembling biological material or cells into a prescribed organization to create functional structures such as MICROCHIP ANALYTICAL DEVICES, cell microarrays, or three dimensional anatomical structures.

Quick Search

DeepDyve research library

Relevant Topics

Polymerase Chain Reaction (PCR)
PCR (Polymerase Chain Reaction) uses the ability of DNA polymerase (enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two ident...

DNA Microarray
A DNA microarray or biochip is a collection of microscopic DNA spots attached to a solid surface used to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome.

Immunoassay - ELISA
Immunoassays are quick and accurate tests to detect specific molecules. Immunoassays rely on an antibody to bind to the specific structure of a molecule. Antibodies are proteins generated by animals in response to the invasion of a foreign molecule (anti...

Searches Linking to this Article