flow cytometric data acquisition of microbial aggregates

Analyse quantitative de l’auto-agrégation microbienne à l’aide de la cytométrie en flux d’imagerie

Bacterial autoaggregation is considered a primary step in biofilm formation. In this process (sometimes also called autoagglutination or flocculation), bacteria of the same type form multicellular clumps that eventually settle at the bottom of culture tubes or attach to their target tissue or surface1.
Autoaggregation is a widely observed phenomenon and has been shown so far in Gram-negative pathogens such as the opportunistic pathogen Acinetobacter baumannii2, the dental pathogen Aggregobacter actinomycetemcomitans3, and the emerging pathogen Burkholderia pseudomallei4. Autoaggregation has also been described in several probiotic Gram-positive strains5,6,7,8. In Lactobacillus (L.) acidophilus, autoaggregation was partially mediated by S-layer proteins and correlated with an adhesion to xylan7. Similarly, we found a correlation between glucose-dependent autoaggregation and induction of the adhesive properties (as judged by adhesion to mucin) of the probiotic species Lacticaseibacillus rhamnosus GG, Lacticaseibacillus casei, L. acidophilus, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum5. The increased autoaggregation most likely reflected changes in the expression of cellular adhesins in response to glucose and its catabolites9. While the molecular mechanisms of autoaggregation remain to be determined, it has been shown that this process alters the phenotype of the aggregated bacteria and grants them enhanced tolerance to environmental stressors1, as well as increased sensitivity to quorum sensing molecules10.
Several approaches have been used to measure autoaggregation; one experimental approach is to let cultures stand statically in narrow culture tubes for a given time. Control cultures remain turbid, whereas autoaggregation cultures will settle at the bottom of the tube. A more quantitative approach measures autoaggregation by sedimentation or settling assay11.
Flow cytometry has also been increasingly employed in recent years to investigate bacterial autoaggregation. This method is appropriate for analyzing particles between approximately 0.5 and 1000 &#181;m in size. The single bacterium or formed aggregates are suspended in fluid, fed into a stream, and can be detected one by one11. Recording forward scattered light allows measuring the relative size of the cell or aggregate. It is relatively fast and straightforward but cannot detect several parameters, such as aggregate size or the average number of cells in aggregates. Therefore, this approach can be complemented microscopically, allowing more parameters to be checked12. However, traditional microscopy is time-consuming and thereby limits the number of tested samples and the statistical power of the analysis. In general, imaging flow cytometry provides several features compared to traditional flow cytometry, such as simultaneous analysis of cell morphology and phenotype, conducting image-based analysis, detecting rare events, and validating flow cytometry data13. These advantages enhance the capabilities of flow cytometry and facilitate a more detailed examination of cell populations.
This study provides a valuable protocol for imaging flow cytometry to monitor autoaggregation in lactic acid bacteria (LAB). These Gram-positive rods are facultative anaerobes and belong to the LAB group. These efficient glucose fermenters generate lactic acid as their main end-product of carbohydrate metabolism14. These bacteria are beneficial core members of the microbiome and are naturally found in the gastrointestinal tract (GIT) of humans and animals, as well as in the urogenital tract of females15. Therefore, the exact characterization of their autoaggregation properties is of high biotechnological and clinical interest.
Our previous findings indicated that the basal level of autoaggregation differs between different probiotic strains. This heterogeneity is affected by the different carbohydrates used as a carbon source5. To overcome this fundamental property of probiotic bacteria, the effects of carbohydrates from the diet were monitored on autoaggregation on the single-cell level using IFC. This IFC-based approach combines the power and speed of traditional flow cytometers with the microscope&#39;s resolution. Therefore, it allows high-rate complex morphometric measurements in a phenotypically defined way16,17. This approach can be extended to other probiotic and pathogenic bacteria, combined with fluorescent reporters to monitor gene expression, and fluorescently labeled strains to monitor the presence and abundance of specific bacterial species in heterogeneous aggregates.

Pleins feux sur l’auteur : Faire progresser la recherche sur l’auto-agrégation microbienne à l’aide de la cytométrie en flux d’imagerie

Cytométrie en flux d’imagerie pour étudier l’auto-agrégation microbienne

This study utilized Lactobacillus species as a model to demonstrate the effectiveness of imaging flow cytometry analysis in studying microbial autoaggregation. The focus is on analyzing the response of autoaggregation of Lactobacillus species to simple carbohydrates from the diet. The most used methods for measuring autoaggregation are spectral photometry, which measures microbial suspensions, turbidity, or optical density, and traditional microscopy techniques, such as bright field, phase contrast, and fluorescent microscopy.When talking about hight-throughput imaging, one major experimental challenge is single event segmentation. In this protocol, it is a single aggregate. Imaging flow cytometry addresses this challenge elegantly and give researchers a powerful tool for studying autoaggregation.

Acquisition de données de cytométrie en flux d’agrégats microbiens

Pour commencer l’analyse cytométrique en flux, réglez d’abord le laser de 785 nanomètres sur une puissance de cinq milliwatts pour les mesures en fond noir. Utilisez un objectif 60X avec une ouverture numérique de 0,9. Sélectionnez ensuite le réglage haute sensibilité et réglez la vitesse sur faible.Pour assurer la stabilité du cordon d’étalonnage, appuyez sur le bouton Lecture dans la boîte fluidique et examinez les images du talon, qui doivent apparaître nettes et claires. Générez un nouveau nuage de points dans la zone de l’espace de travail en sélectionnant Nouveau nuage de points. Sélectionnez ensuite la zone du canal Brightfield qui correspond à l’intensité du canal SSC et excluez les billes d’étalonnage qui s’exécutent simultanément dans l’échantillon.Ensuite, appuyez sur le bouton Load et positionnez un tube contenant l’échantillon de lactobacilles dans le support. Dans la zone Paramètres d’acquisition, entrez le nom de l’échantillon et spécifiez l’emplacement de stockage des données. Définissez le nombre d’événements à collecter, généralement compris entre 10 000 et 20 000 événements.Maintenant, commencez le processus d’acquisition en cliquant sur le bouton Enregistrer situé dans la boîte Acquisition. Le processus s’arrêtera une fois le volume d’événements spécifié atteint. Appuyez sur le bouton Retour pour décharger le tube et le retirer du support comme indiqué dans la fenêtre contextuelle.Après avoir répété le processus pour tous les échantillons, enregistrez le modèle pour maintenir l’uniformité de l’acquisition des données. Pour l’analyse des données, pour charger le fichier brut dans le logiciel d’analyse, cliquez sur Fichier et ouvrez le fichier rif. Dans la fenêtre qui s’ouvre, sélectionnez Utiliser l’analyse d’acquisition, puis cliquez sur OK. Ensuite, pour créer un histogramme du carré moyen de la racine du gradient, cliquez sur le bouton Nouvel histogramme et choisissez la population de l’acquisition à analyser.Sous la fonction Axe X, sélectionnez Dégradé RMS du canal Fond clair. Ensuite, placez une porte pour exclure les événements non ciblés en cliquant sur le bouton Créer une région de ligne dans la zone d’analyse. Créez un nuage de points de la zone en fonction des proportions en cliquant sur le bouton Nouveau nuage de points dans la zone d’analyse.Sélectionnez la population ciblée dans la fenêtre Nouveau nuage de points. Sélectionnez ensuite la zone du canal Fond clair pour la fonction Axe X. Choisissez le rapport hauteur/largeur de la fonction Axe Y.Dessinez une porte sur le nuage de points à l’aide du bouton Créer un rectangle en fonction de la valeur de surface de la population d’événements agrégés. De même, dessinez une autre porte pour la population des célibataires et des petits agrégats. Enregistrez votre analyse de données en tant que modèle en cliquant sur l’onglet Fichier, en choisissant Enregistrer en tant que modèle ast, puis ouvrez l’exemple de fichier suivant sous le même modèle pour créer le fichier d’analyse de données.Pour mesurer la distribution de la taille agrégée, commencez par tracer un histogramme de la zone de la population des événements d’agrégation. Enregistrez l’analyse des données en cliquant sur le fichier et en sélectionnant l’option Enregistrer en tant que modèle. Après l’enregistrement, ouvrez le fichier d’exemple suivant sous le même modèle que celui du fichier d’analyse de données.Des cellules uniques, de petits agrégats, de grands agrégats et des chaînes ont été observés chez LGG et L. paracasei, mais il n’a pas été possible de distinguer les chaînes des agrégats plus grands. Des variations significatives dans les caractéristiques d’agrégation des différentes souches de LAB ont été observées en réponse aux sucres fermentescibles ou non fermentescibles.

flow-cytometric-data-acquisition-of-microbial-aggregates

Research

JoVE Journal

Biology

Flow Cytometric Data Acquisition of Microbial Aggregates

Imaging Flow Cytometry to Study Microbial Autoaggregation

Beneficial and probiotic bacteria play essential roles in their hosts, providing various health benefits, including immunity to infectious diseases. The Lactobacillaceae family consists of Gram-positive bacteria with confirmed probiotic properties. This study utilizes Lactobacillaceae species as a model to demonstrate the effectiveness of single-cell high throughput analysis in studying cellular aggregation. The focus is on analyzing the response of these beneficial species to simple carbohydrates from the diet.
The study showcases how Imaging Flow Cytometry (IFC) can overcome the fundamental differences in the assembly of probiotic bacteria in the presence and absence of carbohydrates. IFC combines the power and speed of conventional flow cytometry with the spatial resolution of microscopy, enabling high-rate complex morphometric measurements in a phenotypically defined manner across a library of beneficial bacterial strains and conditions. This protocol provides insights into the autoaggregation of Lactobacillaceae species and sheds light on their response to dietary carbohydrates, contributing to understanding the mechanisms behind the beneficial effects of these probiotic bacteria.

This protocol describes a quantitative approach to measure microbial autoaggregation using imaging flow cytometry.

Beneficial and probiotic bacteria play essential roles in their hosts, providing various health benefits, including immunity to infectious diseases. The ...

Recherche

Biologie

Lactobacillaceae Sample Preparation for Flow Cytometric Analysis

Start by inoculating five milliliters of lactobacilli MRS broth with a single colony of the lactobacilli strain, incubated at 37 degrees Celsius under static conditions overnight. Dilute the cell culture in a one-to-100 ratio in three milliliters of 50%supplemented tryptic soy broth, vortex the culture, and incubate it. Then invert the tube to mix the cells in the medium before transferring 200 to 300 microliters of the sample into a 1.5 milliliter micro centrifuge tube.

Lactobacillacées Préparation de l’échantillon pour l’analyse par cytométrie en flux

To begin the flow cytometric analysis, first set the 785-nanometer laser to a power of five milliwatts for dark field measurements. Use a 60X lens with a numerical aperture of 0.9. Then select the high-sensitivity setting and set the speed to low.To ensure calibration bead stability, press the Play button in the fluidics box and examine the bead images, which should appear sharp and clear. Generate a new scatterplot in the workspace box by selecting New Scatterplot. Then select the area in the Brightfield channel that corresponds to the SSC channel intensity and exclude the calibration beads that are running concurrently within the sample.Next, press the Load button and position a tube containing the Lactobacilli sample in the holder. In the Acquisition Settings box, enter the sample name and specify the location for data storage. Set the number of events to be collected, typically within the range of 10, 000 to 20, 000 events.Now, begin the acquisition process by clicking the Record button located in the Acquisition box. The process will halt after reaching the specified volume of events. Press the Return button to unload the tube and remove it from the holder as prompted in the popup window.After repeating the process for all samples, save the template to maintain data acquisition uniformity. For data analysis, to load the raw file into the analysis software, click on File and open the rif file. In the opened window, select Use Acquisition Analysis and then click OK.Next, to create a histogram of the gradient root mean square, click the New Histogram button and choose the population from the acquisition to analyze.Under the X Axis feature, select Gradient RMS of the Brightfield channel. Next, place a gate to exclude non-focused events by clicking the Create Line Region button in the analysis area. Create a scatterplot of the area versus the aspect ratio by clicking the New Scatterplot button in the analysis area.Select the focused population in the New Scatterplot window. Then select the area of the Brightfield channel for the X-Axis feature. Choose the aspect ratio for the Y-Axis feature.Draw a gate on the scatterplot using the Create Rectangle button based on the area value for the aggregate events population. Similarly, draw another gate for the singles and small aggregates population. Save your data analysis as a template by clicking the File tab, choosing Save As Template ast, and then open the next sample file under the same template to create the data analysis file.To measure the aggregate size distribution, start by plotting a histogram of the area of the aggregation events population. Save the data analysis by clicking on the file and selecting the Save As Template option. After saving, open the next sample file under the same template for the data analysis file.Single cells, small aggregates, large aggregates, and chains were observed in LGG and L.paracasei but it was not possible to distinguish between chains and larger aggregates. Significant variations in the aggregation characteristics of different LAB strains were observed in response to fermentable or non-fermentable sugars.