flow cytometric data acquisition of microbial aggregates

イメージングフローサイトメトリーを用いた微生物オートアグリゲーションの定量解析

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.

著者スポットライト:イメージングフローサイトメトリーを使用した微生物オートアグリゲーションの研究の進展

微生物の自己凝集を研究するためのイメージングフローサイトメトリー

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.

微生物凝集体のフローサイトメトリーデータ取得

フローサイトメトリー解析を開始するには、まず785ナノメートルレーザーを暗視野測定用に5ミリワットの出力に設定します。60倍レンズを使用し、開口数が0.9です。次に、高感度設定を選択し、速度を低速に設定します。キャリブレーションビーズの安定性を確保するには、流路系ボックスの再生ボタンを押して、ビーズの画像を調べると、シャープでクリアに見えるはずです。ワークスペース ボックスで新しい散布図を生成するには、[新しい散布図] を選択します。次に、SSCチャンネルの強度に対応する明視野チャンネルの領域を選択し、サンプル内で同時に実行されているキャリブレーションビーズを除外します。次に、ロードボタンを押して、乳酸桿菌サンプルの入ったチューブをホルダーにセットします。[Acquisition Settings] ボックスにサンプル名を入力し、データ ストレージの場所を指定します。収集するイベントの数を設定します。通常は 10, 000 から 20, 000 のイベントの範囲内です。次に、取得ボックスにある[記録]ボタンをクリックして、取得プロセスを開始します。プロセスは、指定されたイベント量に達すると停止します。リターンボタンを押してチューブをアンロードし、ポップアップウィンドウの指示に従ってホルダーから取り外します。すべてのサンプルに対してこのプロセスを繰り返した後、データ取得の均一性を維持するためにテンプレートを保存します。データ分析の場合、RAWファイルを分析ソフトウェアにロードするには、[ファイル]をクリックしてrifファイルを開きます。開いたウィンドウで、[Use Acquisition Analysis] を選択し、[OK] をクリックします。次に、勾配平均平方根のヒストグラムを作成するには、[新規ヒストグラム] ボタンをクリックし、分析する母集団を取り込みから選択します。[X 軸] 機能で、明視野チャネルの [グラデーション RMS] を選択します。次に、解析領域の [Create Line Region] ボタンをクリックして、フォーカスされていないイベントを除外するゲートを配置します。エリアとアスペクト比の散布図を作成するには、解析エリアの [New Scatterplot] ボタンをクリックします。[新しい散布図]ウィンドウでフォーカスされた母集団を選択します。次に、X軸フィーチャーの明視野チャネルの領域を選択します。Y 軸機能のアスペクト比を選択します。[Create Rectangle] ボタンを使用して、集計イベント母集団の面積値に基づいて散布図にゲートを描画します。同様に、singles と small aggregates の母集団に対して別のゲートを描画します。「ファイル」タブをクリックし、「テンプレートとして保存」を選択してデータ分析をテンプレートとして保存し、同じテンプレートの下の次のサンプル・ファイルを開いてデータ分析ファイルを作成します。集計サイズの分布を測定するには、まず、集計イベント母集団の面積のヒストグラムをプロットします。ファイルをクリックし、[テンプレートとして保存]オプションを選択して、データ分析を保存します。保存後、データ分析ファイルと同じテンプレートで次のサンプルファイルを開きます。LGGとL.paracaseiでは、単一細胞、小さな凝集体、大きな凝集体、および鎖が観察されましたが、鎖と大きな凝集体を区別することはできませんでした。異なるLAB株の凝集特性には、発酵性糖または非発酵性糖に応答して有意な変動が観察されました。

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 ...

生物学

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.

ラクトバチル科 フローサイトメトリー解析のためのサンプル調製

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.