Background Continuous transformation and development of new detection tools for bacteria has converted the laborious scientific work into smart apparatus in recent years. The journey had begun with the culture-based plate enumeration, and now it has evolved into several culture-independent techniques. Polymerase chain reaction (PCR) is on the top of the list that is now a routinely used biological approach to detect bacterial cells. Instrumental techniques are also helpful in this regard, as they are more sensitive for detection of various microbes. Scope and approach In this review, we described new trends and their practical application in the fields of detection microbiology and food technology. This study provides a brief overview of conventional and modern detection techniques which includes nucleic-acid sequence based techniques to non-destructive imaging techniques. Key findings and conclusions Besides the availability of antibiotics and clinical treatments, bacterial infections significantly increase the mortality rate. It is necessary to detect apparent infectious agents beforehand. Therefore, the detection methods for microorganisms should be more rapid, smart and reliable in response to the need. Conventional detection techniques are slow and time-consuming but more accurate and reliable than the modern detection techniques. By combing the mentioned techniques, scientists can achieve better results.

Conventional and emerging detection techniques for pathogenic bacteria in food science: A review

Contribution of non-Saccharomyces yeasts to wine volatile and sensory diversity: A study on Lachancea thermotolerans, Metschnikowia spp. and Starmerella bacillaris strains isolated in Italy.

Food safety is a major concern in the context of rising population and decreasing earth resources. Food is often contaminated by bacteria, viruses, fungi and parasites, which induce disease such as hemolytic uremic, irritable bowel and Guillain–Barre syndromes. Detection of pathogenic microbes is therefore essential for food safety. Detection methods include biological methods, biosensors and methods based on spectroscopy, immunology and nucleic acids. Here, we review advanced detection techniques used to analyze toxic substances in food.

Methods of detection of food-borne pathogens: a review

Bacterial viability currently refers to ability of a cell to grow and reproduce itself under a set of defined environmental conditions (Kennedy, Cronin, & Wilkinson, 2011). The characteristics of viable cells include the presence and functioning of a range of structural, metabolic, physiological and genetic properties. However, this traditional definition requires that a single “viable” cell must grow and subsequently generate a colony of cells which can be measured optically either in liquid or solid media, thus forming the basis of Koch's principles (Muller & Nebe-von-Caron, 2010). Hence, viability is generally equated with the ability to reproduce and subsequently by cultivability. However, it is clear that not all bacterial cells obey this relationship and indeed, while they may lack the ability to reproduce and grow under certain conditions, they may possess many of the properties of fully functioning viable cells. Hence, we arrive at another classification based on the term “vitality” or the degree to which a cell can perform various aspects of metabolic, physiological and genetic functionality and the extent of structural and morphological integrity (Kramer & Thielman, 2016). In this case, cell vitality is not exclusively related to reproducibility or cultivability and in certain aspects the cell can be described as being in a viable-but-non-culturable state (VBNC) as reviewed by Zhao, Zhong, Wei, Lin, and Ding (2017). A truly “dead” cell may therefore lack the minimal structural integrity and ability to carry out basic cell functionality such as control and activity of physiology, metabolism and genetic material and possess neither vitality or viability characteristics (Davis, 2014). Based on these various states, enumeration of bacterial cells has evolved into two general methodologies; (1) culture dependent and (2) culture independent (Davis, 2014). In the former technique, a liquid sample is plated onto solid media, incubated under defined conditions of time and temperature with data expressed as numbers of colony forming units per gram of original material (cfu/g) (Davey, 2011). This traditional methodology is still the “gold standard” and is backed by legal status for use in routine enumeration and identification of live/ viable microorganisms in food samples (FAO/WHO (2002); ISO (2002); Ministero della Salute (2013); Hill et al., 2014; Sanders et al. (2016)). This methodology is a classic example of where viability depends exclusively on the ability of the cell to reproduce with visual inspection of the colony formed from the original single cell. Culture-independent methodologies for bacterial enumeration involve DNA based technologies such as polymerase chain reaction (PCR) or quantitative PCR (qPCR) whereby a specific gene fragment within a DNA sample is amplified and the fluorescent signal directly related to the number of cells in the original sample. This technology is highly useful but may not always distinguish DNA originating from viable or non-viable cells. However, reagents such as ethidium monoazide (EMA) or propidium monoazide (PMA) can be included in the assay to prevent amplification of DNA from dead cells (Martinon, Cronin, Quealy, Stapleton, & Wilkinson, 2012). Another emerging rapid culture-independent technique for bacterial enumeration is flow cytometry, which utilises a combination of light scattering and emitted fluorescence to detect cells having various structural, physiological and genetic states (Cronin & Wilkinson, 2010).

Flow cytometry as a potential method of measuring bacterial viability in probiotic products: A review

Aroma profile is one of the main features for the acceptance of wine. Yeasts and bacteria are the responsible organisms to carry out both, alcoholic and malolactic fermentation. Alcoholic fermentation is in turn, responsible for transforming grape juice into wine and providing secondary aromas. Secondary aroma can be influenced by different factors; however, the influence of the microorganisms is one of the main agents affecting final wine aroma profile. Saccharomyces cerevisiae has historically been the most used yeast for winemaking process for its specific characteristics: high fermentative metabolism and kinetics, low acetic acid production, resistance to high levels of sugar, ethanol, sulfur dioxide and also, the production of pleasant aromatic compounds. Nevertheless, in the last years, the use of non-saccharomyces yeasts has been progressively growing according to their capacity to enhance aroma complexity and interact with S. cerevisiae, especially in mixed cultures. Hence, this review article is aimed at associating the main secondary aroma compounds present in wine with the microorganisms involved in the spontaneous and guided fermentations, as well as an approach to the strain variability of species, the genetic modifications that can occur and their relevance to wine aroma construction.

https://www.mdpi.com/2304-8158/10/1/51/pdf

Secondary Aroma: Influence of Wine Microorganisms in Their Aroma Profile.

Influence of cell-cell contact between L. thermotolerans and S. cerevisiae on yeast interactions and the exo-metabolome.

Flow cytometry (FCM) is a powerful technique allowing detection and enumeration of microbial populations in food and during food process. Thanks to the fluorescent dyes used and specific probes, FCM provides information about cell physiological state and allows enumeration of a microorganism in a mixed culture. Thus, this technique is increasingly used to quantify pathogen, spoilage microorganisms and microorganisms of interest. Since one decade, FCM applications to the wine field increase greatly to determine population and physiological state of microorganisms performing alcoholic and malolactic fermentations. We will describe FCM principles and the available techniques allowing quantification of wine microorganisms by FCM using fluorescent dyes. Different examples of FCM analysis regarding monitoring of alcoholic fermentation, malolactic fermentation (total population, viable population, physiological state), specific detection and quantification of spoilage microorganisms like Brettanomyces will be presented.

/pdf/la-cytometrie-appliquee-aux-mircoorganismes-du-vin-3f75ldlv75.pdf

La cytométrie appliquée aux mircoorganismes du vin

The cell surface is the primary recognition site between the bacterium and the host. An operon of three genes, LSEI_0219 (cwaR), LSEI_0220 (cwaS), and LSEI_0221 (ldcA), has been previously identified as required for the establishment of Lactobacillus paracasei in the gut. The genes cwaR and cwaS encode a predicted two-component system (TCS) and ldcA a predicted D-alanyl-D-alanine carboxypeptidase which is a peptidoglycan (PG) biosynthesis enzyme. We explored the functionality and the physiological role of these three genes, particularly their impact on the bacterial cell wall architecture and on the bacterial adaptation to environmental perturbations in the gut. The functionality of CwaS/R proteins as a TCS has been demonstrated by biochemical analysis. It is involved in the transcriptional regulation of several genes of the PG biosynthesis. Analysis of the muropeptides of PG in mutants allowed us to re-annotate LSEI_0221 as a putative L,D-carboxypeptidase (LdcA). The absence of this protein coincided with a decrease of two surface antigens: LSEI_0020, corresponding to p40 or msp2 whose implication in the host epithelial homeostasis has been recently studied, and LSEI_2029 which has never been functionally characterized. The inactivation of each of these three genes induces susceptibility to antimicrobial peptides (hBD1, hBD2, and CCL20), which could be the main cause of the gut establishment deficiency. Thus, this operon is necessary for the presence of two surface antigens and for a suitable cell wall architecture.

/pdf/study-of-the-cwars-ldca-operon-coding-a-two-component-system-53jttk1c4n.pdf

Study of the cwaRS-ldcA Operon Coding a Two-Component System and a Putative L,D-Carboxypeptidase in Lactobacillus paracasei.

Application of flow cytometry to wine microorganisms

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Influence of cell-cell contact between L. thermotolerans and S. cerevisiae on yeast interactions and the exo-metabolome.

La cytométrie appliquée aux mircoorganismes du vin

Study of the cwaRS-ldcA Operon Coding a Two-Component System and a Putative L,D-Carboxypeptidase in Lactobacillus paracasei.

Application of flow cytometry to wine microorganisms