Microbe Profile: Escherichia coli O157 : H7 - notorious relative of the microbiologist's workhorse

Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples

As the amount of metagenomic sequencing continues to increase, there is a growing need for tools that help biologists make sense of the data. Specifically, researchers are often interested in the potential of a microbial community to carry out a metabolic reaction, but this analysis requires knitting together multiple software tools into a complex pipeline. Thanos offers a user-friendly R package designed for the pathway-centric analysis and visualization of the functions encoded within metagenomic samples. It allows researchers to go beyond taxonomic profiles and find out, quantitatively, which pathways are prevalent in an environment, as well as comparing different environments in terms of their functional potential. The analysis is based on the sequencing depth of the genes of interest, either in the metagenome-assembled genomes (MAGs) or in the assembled reads (contigs), using a normalization strategy that enables comparison across samples. The package can import the data from multiple formats and offers functions for the visualization of the results as bar plots of the functional profile, box plots of compare functions across samples, and annotated pathway graphs. By streamlining the analysis of the functional potential encoded in microbial communities, Thanos can enable impactful discoveries in all the fields touched by metagenomics, from human health to the environmental sciences.

Rapid and sensitive detection of E. coli O157:H7 by lateral flow immunoassay and silver enhancement

The aim of this study was to develop a sensitive lateral flow immunoassay (LFIA) for the rapid detection of Escherichia coli (E. coli) O157:H7, a pathogen contributor to diseases and fatalities worldwide. Au nanoparticles with high stability, uniform size, and shape were synthesized and coated with heterobifunctional PEG polymer with carboxyl groups, and they were bioconjugated to be used as label in sandwich-LFIA. Then, a silver enhancement strategy was developed as an accessible, rapid, and cost-effective approach for signal amplification to reduce the limit of detection (LOD). The optimal results were achieved when a solution of silver nitrate and hydroquinone/citrate buffer was added to the strips for 4 min. This led to a decrease in the visual LOD from 2 × 10⁶ (CFU mL^-1) to 2 × 10³ (CFU mL^-1), resulting in a threefold improvement in sensitivity compared to the conventional LFIA system. The specificity of the system was evaluated by using non-target bacteria (E. coli BL21 and E. coli T515) and its reliability was determined by testing commercial food samples (milk, tap water, and orange juice), demonstrating its effectiveness for quickly detecting pathogenic bacteria in food products.

Influence of pressurization rate and mode on cell damage of Escherichia coli and Staphyloccocus aureus by high hydrostatic pressure

As a non-thermal technology, high hydrostatic pressure (HHP) has been widely investigated for inactivating microorganisms in food. Few studies have been presented on the pressurization/depressurization rate and mode of microbial inactivation. In this study, effect of pressurization rate and mode on Escherichia coli and Staphylococcus aureus cell damage during HHP treatment was investigated. The results showed that fast pressurization + linear mode (FL) treatment has the best bactericidal effect on E. coli and S. aureus, followed by fast pressurization + stepwise mode (FS) and slow pressurization + stepwise mode (SS) treatments. FL treatment caused more morphological damage to the cell wall, cell membrane, and cytoplasmic components compared with FS and SS treatment detected by SEM and TEM. Additionally, the damage to membrane permeability of them was also enhanced after FL treatment. Therefore, our results indicated that FL treatment could be applied to enhance the bactericidal effect of HHP on bacteria by increasing the damage to cell morphological structure and membrane integrity.

The Patrol Yeast: A new biosensor armed with antibody-receptor chimera detecting a range of toxic substances associated with food poisoning

Baker's yeast is an attractive host with established safety and stability characteristics. Many yeast-based biosensors have been developed, but transmembrane signal transduction has not been used to detect membrane-impermeable substances using antigen-antibody interactions. Therefore, we created Patrol Yeast, a novel yeast-based immunosensor of various targets, particularly toxic substances in food. A membrane-based yeast two-hybrid system using split-ubiquitin was successfully used to detect practically important concentration ranges of caffeine and aflatoxins using separated variable regions of an antibody. Moreover, enterohemorrhagic Escherichia coli O157 was detected using a specific single-chain antibody, in which Zymolyase was added to partially destroy the cell wall. The incorporation of secreted Cypridina luciferase reporter further simplified the signal detection procedures without cell lysis. The methodology is more cost-effective and faster than using mammalian cells. The ability to detect various targets renders Patrol Yeast a valuable tool for ensuring food and beverage safety and addressing other environmental and technological issues.

Interdigitated Electrode Biosensor Based on Plasma-Deposited TiO2 Nanoparticles for Detecting DNA

Bioelectrodes mediated by metal oxide nanoparticles have facilitated the development of new sensors in medical diagnosis. High-purity TiO₂ nanoparticles (NPs) were synthesized through thermal plasma and deposited directly on an interdigitated electrode. The surface of the TiO₂-deposited electrode was activated with (3-aminopropyl) triethoxysilane (APTES) followed by fixing the single-stranded probe deoxyribonucleic acid (DNA) to fabricate the DNA biosensor. The structural properties of the deposited TiO₂ nanoparticles were analyzed using a transmission electron microscope (TEM), X-ray diffraction (XRD), and a dynamic light scattering (DLS) system. The chemical composition and structural properties of the TiO₂ nanoparticle layer and the fixed layer were analyzed by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). E. coli O157:H7, a well-known pernicious pathogenic bacterial species, was detected as a target DNA of the prepared DNA biosensor, and the characteristics of DNA detection were determined by the current change using a picoammeter. The degree of binding between the probe DNA and the target DNA was converted into an electrical signal using the picoammeter method to quantitatively analyze the concentration of the target DNA. With the specificity experiment, it was confirmed that the biosensor was able to discriminate between nucleotides with mismatched, non-complementary, or complementary sequences.

A critical review: Recent advances in "digital" biomolecule detection with single copy sensitivity

Detection of a single biomolecule, ranging from nucleic acids, proteins, viruses to bacteria, is of paramount importance in various fields including biology, environment, food and agriculture industry, public health, and medicine. With the understanding of the biological functions of these biomolecules (or bioparticles) and their impacts on public health, environmental pollution, and food safety, advanced detection techniques are unprecedentedly demanded for their early and/or sensitive detection. In this critical review, a series of elegant research about digital detection of biomolecules with potential single copy sensitivity is reviewed and summarized with the focus on the design principle and the innovation of how to accomplish the “digital” detection concept. Starting with a brief introduction on the importance of digital detection, recent advances in “digital” biomolecule detection with single copy sensitivity are grouped and discussed based on the difference of signal reporting systems, including surrogate signal development for “digital” detection, direct visualization for “digital” detection, and nucleic acid amplification enabled “digital” detection. Interdisciplinary combination and integration of different cutting-edge techniques are also discussed with details. The review is closed with the conclusion and future trends.