Electron microscope imaging was conducted at the Electron Microscopy Unit of the Weizmann Institute of Science, supported in part by the Irving and Cherna Moskowitz Center for Nano and Bio-Nano Imaging. This research was also supported by the ISF I-CORE grant 152/1, Mr. and Mrs. Dan Kane, Ms. Lois Rosen, by a Yeda-Sela research grant, by the Larson Charitable Foundation, by Ruth and Herman Albert Scholars Program for New Scientists, by the Ilse Katz Institute for Materials Sciences and Magnetic Resonance Research grant, by the Ministry of Health grant for alternative research methods, and by the France-Israel Cooperation - Maimonide-Israel Research Program. IKG is a recipient of the Rowland and Sylvia Career Development Chair.

1. Assessing the Effect of Small Molecule Inhibitors on Pellicle and Biofilm Colony Formation
<ol>
	<li>Prepare a 2x solution of defined biofilm-inducing MSgg medium25 without the calcium chloride and iron(III) chloride hexahydrate. After filter sterilization, add the calcium chloride. The medium is ready to use directly or it can be stored at 4 &#176;C in the dark.</li>
	<li>Prepare the 1x MSgg dilution on the day of the experiment.
	<ol>
		<li>Dilute the 2x MSgg medium to 1x with sterile distilled water (pellicles) or sterile 3% hot (80 &#176;C) agar (biofilms) and add iron(III) chloride hexahydrate to a final concentration of 50 &#956;M (pellicles) or 250 &#181;M (biofilms). Add antibiotics or small molecule inhibitors to the desired concentration and mix well. For example, to obtain a final concentration of 0.5 mM D-leucine in 30 ml to establish pellicles or biofilms, add 196.6 &#181;l of a 76.3 mM (10 mg/ml) D-leucine stock solution. 
		NOTE: The final 1x MSgg composition is described in Table 1. Compared to the original recipe25, the medium contained 50 &#181;g/ml threonine and the iron concentration to grow biofilm colonies on solid MSgg medium was increased 2.5x to optimize the wrinkled colony morphology.</li>
	</ol>
	</li>
	<li>After solidification of the agar, dry the solid MSgg plates in a biological hood for 30-45 min prior to the inoculation.</li>
	<li>To select specific inhibitors that interfere with the mechanisms of pellicle formation (Figure 1), rule out that the concentrations used affect planktonic and static growth.
	<ol>
		<li>Determine planktonic growth (increase in optical density over time in liquid culture) in a simple growth curve by measuring the optical density at 600 nm every hour until the stationary growth phase.</li>
		<li>To confirm that the measured culture turbidity represents live cell counts, determine the numbers of colony forming units (CFU) of cells in the planktonic growth phase from a shaking culture after several time points.</li>
		<li>To assess the effect of small molecule inhibitors on static pellicle growth, harvest cells at the end of a 3-day incubation at 23 &#176;C from a 24-well cell-culture well, inoculated under the same conditions as described in sections 1.7-1.9 and determine the CFU. For this control, use a pellicle-deficient strain that lacks the operons encoding for the extracellular matrix components (i.e., B. subtilis &#916;epsH, &#916;tasA). 
		NOTE: This strain is capable of growing under static conditions, but in contrast to a pellicle-forming wild type, it is deficient in the ability to float to the liquid-air interface, where growth is favored due to increased oxygen levels26. Thus, this extracellular matrix- and pellicle-deficient strain is a recommended reference strain to assess growth under static conditions. 
		NOTE: For the specific example of the non-canonical D-amino acid D-leucine described below, an effect on planktonic and static growth at concentrations that interfered with pellicle formation was ruled out12,17. The methods to determine planktonic and static growth are described in detail17.</li>
	</ol>
	</li>
</ol>
<img alt="Figure 1" src="/files/ftp_upload/54612/54612fig1.jpg" /> 
Figure 1. Conceptual overview for the identification of a robust experimental setup to assess the specific inhibition of biofilm formation. Selection criteria for small molecule inhibitors that indicate specific interference with biofilm formation without pronounced effect on planktonic growth. <a href="https://www.jove.com/files/ftp_upload/54612/54612fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol start="5">
	<li>Streak out B. subtilis from a -80 &#176;C stock (LB culture of 109 cells/ml frozen in 20% glycerol) to isolate single colonies on a LB-1.5% agar plate with a sterile tip or applicator stick.</li>
	<li>Grow overnight at 30 &#176;C.</li>
	<li>CRITICAL STEP: For a robust pellicle inhibition by the non-canonical D-amino acids such as D-leucine, grow a single colony picked from the LB-1.5% agar plate in 3 ml LB broth at 37 &#176;C for 4 hr in a shaking incubator (shaking speed 200 rpm). Replace the LB broth with biofilm-inducing MSgg medium prior to inoculation by centrifuging 1.5 ml starter culture for 4 min at 6,000 x g, carefully removing the supernatant and re-suspending the pellet in 1.5 ml MSgg medium. The rest of the culture can be discarded. 
	Important: To ensure the robustness of the system, the optical density at 600 nm (OD600) of the washed starter culture should be between 0.6 and 1.</li>
	<li>During the growth of the starter culture, prepare a 12-well cell-culture multidish plate containing 3 ml of MSgg medium without or with a concentration range of the small molecule inhibitor (e.g., 0.3, 0.5, 1 mM D-leucine17). To rule out edge effects, distribute the location of the different concentrations across the multidish plate. Alternatively, use 24-well cell-culture multidish plates containing 1.5 ml of MSgg medium.</li>
	<li>Inoculate the wells of the 12-well cell-culture multidish plate with 3 &#181;l of the washed starter culture (1:1,000 dilution). 
	NOTE: A lower dilution ratio, i.e., 1:500 can be used. This decreases the development time of the pellicles.</li>
	<li>Grow the pellicles at 23 &#176;C under static conditions for three days. Do not move the pellicles during this time, as it can affect the final surface morphology of the pellicle.</li>
	<li>Acquire pictures with a binocular and homogenous exposure of lightning. Alternatively, take a picture of the pellicles with a high resolution camera. To avoid artefacts caused by inconsistent light angles and shadows, take top-down pictures with the camera fixed on a tripod and use a soft and large light source at 45&#176; from both sides. 
	NOTE: An alternative method to study B. subtilis multicellularity is the biofilm colony assay on solid, biofilm-inducing MSgg medium. Like pellicles, this assay allows the study of spatiotemporal processes. Once the active range of small molecule inhibitors is determined, their effect on biofilm colony formation can be studied.</li>
	<li>To grow biofilm colonies, symmetrically spot 1.5 &#181;l of the unwashed pre-culture (Step 1.7) on the dried MSgg 1.5% agar plate with the help of a template &#8212; 4 drops per Petri dish of 8.5 cm diameter. Let the drops adsorb to the plate before moving them. 
	NOTE: The template helps to get an equal distribution of the biofilm colonies within the area where the cells are grown. To prepare the template, draw the total area of growth at original scales, divide it to equal sectors and mark the center. For a round Petri dish of 8.5 cm diameter, this assigns 14 cm2 to one biofilm colony.</li>
	<li>Incubate the plates at 30 &#176;C for three days. During this time, biofilm colonies develop and form a three-dimensional, wrinkled structure.</li>
	<li>Take pictures as in step 1.11.</li>
</ol>
2. Ethanol Resistance Assay
<ol>
	<li>Grow biofilms as described in steps 1.1-1.7 and 1.12-1.14.</li>
	<li>After 68 hr of growth at 30 &#176;C, cut the biofilm colonies into two equal parts with the help of a razor blade and the template.</li>
</ol>
<img alt="Figure 2" src="/files/ftp_upload/54612/54612fig2.jpg" /> 
Figure 2. Example experimental design to assess the resistance of biofilm colony cells to sterilizing agents. (A) Template used for the equal distribution of biofilm colonies across a Petri dish and for cutting. (B) Top-down images of untreated wild-type biofilm grown for 68 hr on solid, defined biofilm-inducing MSgg medium at 30 &#176;C. The enlargement shows how a biofilm colony can be cut in two equal halves. (C) The two equal biofilm halves are treated equally (control, PBS) or with either PBS or sterilizing agent and processed as described. Scale bar: 1 cm. <a href="https://www.jove.com/files/ftp_upload/54612/54612fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol start="3">
	<li>Carefully lift each half of the biofilm colony from the agar plate with a small spatula and move it to a 1.5 ml microcentrifuge tube containing 500 &#181;l of phosphate-buffered saline (PBS). If necessary, scrape the remaining cells from the plate and transfer them to the microcentrifuge tube as well. 
	NOTE: The second half of the biofilm colony is treated differentially, depending on whether it is the control or to test the resistance to sterilizing agents.</li>
	<li>For the control, incubate the second half of the biofilm colony in 500 &#181;l PBS as in step 2.3. To assess resistance to sterilizing agents, transfer the second half of the biofilm colony to 500 &#181;l 50% (v/v) ethanol. 
	NOTE: Alternative sterilizing agents such as sodium hypochlorite can be used. For all sterilizing agents used, determine the active concentration and incubation time in a preliminary experiment.</li>
	<li>Incubate the biofilm colonies for 10 min on the bench-top at room temperature.</li>
	<li>Centrifuge the biofilm colonies for 5 min at 18,000 x g and carefully remove the supernatant with a pipette. Add 300 &#181;l of PBS.</li>
	<li>Sonicate the cells mildly (amplitude 10%, pulse 5 sec) with the microtip of a sonicator. 
	NOTE: The sonication energy must be sufficient to separate biofilm aggregates. However, too harsh sonication may lyse the cells. Confirm in advance by light microscopy that the sonication energy used does not lyse the cells and that all aggregates are dissolved.</li>
	<li>Add 700 &#181;l of PBS to a final volume of 1 ml. Perform a serial dilution (to 10-7) in PBS and spread 100 &#181;l of 3 dilutions on a LB-1.5% agar plate using sterile glass beads. 
	NOTE: The optimal dilutions to be plated should be determined in a preliminary experiment, as this depends on the amount of cells in the biofilm colony of interest and the survival rate of the cells in response to the sterilizing agent.</li>
	<li>Incubate the plates overnight at 30 &#176;C, count the CFU and determine CFU/ml. From the final CFU/ml of each the half biofilm colonies, calculate the percentage of survivors. 
	NOTE: When performed and analyzed as described, the two halves of the control biofilm colony and the untreated versus ethanol-treated half of the untreated biofilm colony should yield differences below 10% in viable cell counts, verifying the symmetry or the resistance of the colony, respectively. Alternatively, the results can be represented in total CFU. The cell counts of the control and untreated biofilm colony should remain in the same order of magnitude. In contrast, the cell counts of the ethanol-treated half of a small molecule-treated biofilm colony are expected to drop by a minimum of two orders of magnitude to claim for an increased sensitivity to the sterilizing agent.</li>
</ol>
3. Biofilm Colony Sample Preparation for Scanning Electron Microscopy
<ol>
	<li>Grow biofilm colonies as described in steps 1.1-1.7 and 1.12-1.14.</li>
	<li>Prepare a fresh batch of 2% (v/v) glutaraldehyde, 3% (v/v) paraformaldehyde solution in 100 mM sodium cacodylate, 5 mM calcium chloride buffer, pH 7.3. Prepare 5 ml of fixative for every Petri dish of 8.5 cm diameter. 
	CAUTION: Glutaraldehyde and paraformaldehyde are hazardous. Handle them with safety equipment inside a chemical hood. Discard the solutions and the contaminated materials to the hazardous waste.</li>
	<li>Carefully add the fixative to the biofilm colonies, without dispensing directly on top of the biofilms. 
	NOTE: Due the hydrophobic character of the biofilm colony, the colonies slowly detach from the agar and start to float.</li>
	<li>Carefully seal the plates with a strip of Parafilm. Incubate on a rotary shaker for 2 hr at room temperature and subsequently transfer the plates to 4 &#176;C for overnight.</li>
	<li>The next day, carefully remove the liquid with a Pasteur glass pipette connected to a vacuum pump.</li>
	<li>Carefully add 10 ml 100 mM sodium cacodylate, 5 mM calcium chloride buffer to wash the biofilm and incubate for 5 min. Gently remove the liquid with the Pasteur glass pipette from the corner of the plate to avoid damaging the biofilm and add fresh washing solution by gentle pipetting. Repeat this step once.</li>
	<li>For the dehydration of the biofilm colonies, proceed with the following steps: 2x 5 min in ddH2O; 2x 20 min in 30% ethanol; 2x 20 min in 50% ethanol; 2x 20 min in 70% ethanol; 2x 20 min in 96% ethanol; 2x 30 min in 100% ethanol.
	<ol>
		<li>Add 15 ml of liquid for every Petri dish of 8.5 cm diameter in each step and remove the liquid carefully after each incubation.</li>
	</ol>
	</li>
	<li>Use one of two different methods for drying the samples from ethanol.
	<ol>
		<li>For air-drying from ethanol:
		<ol>
			<li>Cut a cellulose filter paper (diameter of 9 cm) in quarters. Briefly submerge one quarter in 100% ethanol, and then carefully transfer one floating biofilm colony onto it. Put the wet filter paper in a Petri dish lined with a filter paper. Cover the Petri dish and let the biofilm colonies dry overnight in a chemical hood.</li>
		</ol>
		</li>
		<li>For critical point (CP)-drying using carbon dioxide (CO2) as the transition fluid:
		<ol>
			<li>Fill 75% of the critical point drying machine chamber with 100% ethanol. Transfer the samples into a holder, each sample into its own chamber. If necessary, cut the biofilm with scissors into smaller pieces. Leave the samples submerged in ethanol during all the handling. Then, transfer the holder into the chamber and close the chamber tightly.</li>
			<li>Cool the chamber to 7 &#176;C and start stirring. Fill the chamber completely with liquid CO2. During a 7 min incubation time, let the ethanol mix with the CO2. Then, discharge 25% of the solution. 
			NOTE: Do not empty the chamber below the level of the sample.</li>
			<li>Repeat step 3.8.2.2 four times.</li>
			<li>Repeat step 3.8.2.2 five times with an incubation time of 5 min only. Finally, the ethanol should be completely replaced by CO2.</li>
			<li>During the last round, empty only 5% of the chamber. Turn off the stirring and the cooling. Start heating the chamber to 42 &#176;C. At a temperature of 31.1 &#176;C and a pressure of 73.9 bar, the liquid CO2 reaches its critical point, the state where the gaseous phase has the same density as the liquid phase of the solvent27. Once the temperature reaches 42 &#176;C, incubate for 10 min. At 42 &#176;C, the CO2 in the chamber exists as supercritical gas. 
			NOTE: Constantly check the pressure of the chamber. The pressure should not exceed 120 bar at 42 &#176;C.</li>
			<li>Start to slowly release the gas with continuous heating. This keeps the samples in the CO2-gas phase and prevents the deformation of the sample morphology through the liquid surface tension. Set the flowmeter to 5 L/hr by fine tuning the metering valve controlling the flowmeter. Wait until the all the pressure in the chamber is released. Now open the chamber and remove the samples carefully from the holder.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Coat an electron microscopy stub with carbon tape. With the help of tweezers, carefully transfer the biofilm colonies onto the stub. Connect each colony to the stub by adding a thin bridge from carbon tape, which is crucial for charge elimination under the electron beam. At this stage, handle the biofilm colonies with care as they are very fragile. Store the samples in a desiccator for at least 24 hr or until examination.</li>
	<li>The day of the examination with the scanning electron microscope, sputter-coat the biofilm colonies for 2 min in a 60&#176; angle in a gold-palladium sputter-coater. Repeat this step twice and rotate the samples by 120&#176; in between. At the end, sputter-coat the samples once for 3 min from the top. The 20 nm thin layer of gold-palladium improves the conductivity and enhances the contrast of the sample for the imaging in the SEM.</li>
	<li>Store the samples in a desiccator to avoid the rehydration of the sample28 until imaging with a scanning electron microscope29,30.</li>
</ol>

The authors have nothing to disclose.

Bacillus subtilis forms robust and highly structured biofilms both in liquid (pellicles) and on solid medium (colonies). Hence, it serves as an ideal model organism to characterize the mode of action of specific biofilm inhibitors. On solid media, cells form multicellular structures with distinctive features that are not evident in pellicles, like wrinkles radiating from the center to the edge. Thus, pellicles and colonies are complementary systems to study B. subtilis multicellularity.
<p class="jo...

Multi-cellular bacterial communities play significant roles in natural and anthropogenic environments, and can be beneficial or highly deleterious. These multi-cellular colonies are known as biofilms, wherein the individual cells are embedded in a self-produced extracellular polymeric substances (EPS) matrix. The EPS strongly adhere the cells to the surface they colonize. They serve as a shield against mechanical and chemical forces and create close contact between neighboring cells, facilitating cellular communication1. A biofilm can be viewed as a differentiated community, where cells use highly regulated, orchestrated processes to coordinate their activities within the community, as well as across species2-5. The transition from a planktonic, free-living mode of growth to a biofilm state is often associated with developmental processes. A good example is the Gram-positive soil bacterium Bacillus subtilis, and therefore an undomesticated strain serves as a robust model organism to study the developmental stages leading to biofilm formation. In this bacterium, motile cells organize themselves into conspicuous multicellular structures that carry out specialized tasks4. One group of cells, the matrix-producers secrete exopolysaccharides6, the amyloid protein TasA7,8, and the surface hydrophobicity protein BslA9,10; all of which participate in the assembly of the EPS11-13.
Given the abundance of biofilms in natural and anthropogenic niches and the putative fatal damage they can cause, there is a pressing need to find ways to prevent their formation. Small molecule inhibitors can aid in the discovery of new regulatory pathways, enzymes and structural proteins involved in biofilm formation, and thereby promote insights in the complex processes of multicellular community assembly. As B. subtilis is a well-studied model for biofilm formation14,15, it can be used to assess the effects of various biofilm inhibitors. This study tackles four fundamental methods that are key for evaluating the response of biofilms to small molecule inhibitors. First, to ensure that these inhibitors have a biofilm-specific target, the separation of the effect on planktonic growth from the effect on biofilm formation is critical. Most antibacterial agents target cells in their planktonic growth phase, but molecules that target the biofilm lifestyle are rare. Additionally, as molecules that do not affect planktonic growth are not toxic, they can reduce the selective pressure favoring antibiotic resistant mutants16. For example, when biofilms are treated with D-amino acids or certain other cell wall-interfering molecules, they are either disturbed or disassembled, but these inhibitors only mildly affect planktonic growth12,17. In contrast, many antibiotics dramatically impair planktonic growth, with little or no effect on biofilm formation17.
Second, establishing a consistent and robust experimental framework to study the effect of the small molecules is crucial. We observed that the active concentration range of small molecule inhibitors was sensitive to the pre-culture conditions and to the experimental setup used to study the effect of these small molecule inhibitors. Various reports, particularly those studying B. subtilis, revealed variations in the concentration range at which D-amino acids inhibit the formation of pellicles &#8212; the floating bacterial biofilms12,17-19. The results presented here suggest that the following factors account for differences in the active concentration range: the pre-culture conditions (logarithmic12,17 versus late-stationary20 growth phase), the growth medium used in the pre-culture condition (rich, undefined [Luria Broth, LB] versus defined [monosodium glutamate-glycerol, MSgg]), the inoculation ratio and especially the removal of the pre-culture medium before inoculation. The temperature of static pellicle growth showed a less important role in the activity range of the small molecule inhibitor D-leucine, a representative D-amino acid used in this study.
Finally, once the biofilms are treated with specific biofilm inhibitors, robust and informative methods are required to characterize the effects of these inhibitors on biofilm fitness. Here, two methods to independently characterize the effect of small molecule inhibitors are described in detail: (1) The effect on single cells within a biofilm colony and their resistance to antimicrobial agents. Cells in biofilms are typically more resistant to antibiotics when compared to free-living bacteria21-23. While this phenomenon is multifactorial, the ability of the EPS to reduce antibiotic penetration was often considered as an appealing explanation24. This method assesses the survival of pre-established biofilm cells after exposure to antibacterial substances. (2) The effect on the biofilm colony architecture, from the large to the small scale. Biofilm colonies are characterized by their three-dimensional structure and the presence of the EPS. Utilizing scanning electron microscopy, changes in the cell morphology, biofilm colony structure and the architecture and abundance of the EPS can be visualized from the large (mm) to the small scale (&#181;m).

<table><tbody><tr><td>Luria Broth, Lennox</td><td>Difco</td><td>240230</td><td></td></tr><tr><td>Bacto Agar</td><td>Difco</td><td>214010</td><td></td></tr><tr><td>potassium phosphate monobasic&amp;nbsp;</td><td>Sigma, 136.09 g/mol</td><td>P0662-500G</td><td></td></tr><tr><td>potassium phosphate dibasic&amp;nbsp;</td><td>Fisher Scientific, 174.18 g/mol</td><td>BP363-1</td><td></td></tr><tr><td>3-(&lt;em&gt;N&lt;/em&gt;-morpholino)propanesulfonic acid</td><td>Fisher Scientific, 209.27 g/mol</td><td>BP308-500</td><td></td></tr><tr><td>magnesium chloride hexahydrate&amp;nbsp;</td><td>Merck, 203.30 g/mol&amp;nbsp;</td><td>1.05833.0250</td><td></td></tr><tr><td>calcium chloride anhydrous</td><td>J.T. Baker, 110.98 g/mol</td><td>1311-01</td><td></td></tr><tr><td>manganese(II) chloride tetrahydrate</td><td>Sigma, 197.91 g/mol</td><td>31422-250G-R</td><td></td></tr><tr><td>iron(III) chloride hexahydrate&amp;nbsp;</td><td>Sigma, 270.30 g/mo)</td><td>F2877-500G</td><td></td></tr><tr><td>zinc chloride anhydrous&amp;nbsp;</td><td>Acros Organics, 136.29 g/mol</td><td>424592500</td><td></td></tr><tr><td>thiamine hydrochloride</td><td>Sigma, 337.27 g/mol</td><td>T1270-100G</td><td></td></tr><tr><td>L-tryptophan</td><td>Fisher Scientific, 204.1 g/mol</td><td>BP395-100</td><td></td></tr><tr><td>L-phenylalanine</td><td>Sigma, 165.19 g/mol</td><td>P5482-100G</td><td></td></tr><tr><td>L-threonine</td><td>Sigma, 119.12 g/mol</td><td>T8625-100G</td><td></td></tr><tr><td>glycerol anhydrous</td><td>Bio-Lab Itd</td><td>712022300</td><td></td></tr><tr><td>L-glutamic acid monosodium salts hydrate&amp;nbsp;</td><td>Sigma, 169.11 g/mol</td><td>G1626-1KG</td><td></td></tr><tr><td>D-leucine</td><td>Sigma, 169.11 g/mol</td><td>855448-10G</td><td></td></tr><tr><td>ethanol anhydrous</td><td>Gadot</td><td>830000054</td><td></td></tr><tr><td>razor blade</td><td>Eddison</td><td>NA</td><td></td></tr><tr><td>circular cellulose filter papers</td><td>Whatman, 90 mm</td><td>1001-090</td><td></td></tr><tr><td>glutaraldehyde</td><td>EMS (Electron Micoscopy Science), 25% in water</td><td>16220</td><td></td></tr><tr><td>paraformaldehyde&amp;nbsp;</td><td>EMS, 16% in water</td><td>15710</td><td></td></tr><tr><td>sodium cacodylate</td><td>Merck, 214.05 g/mol&amp;nbsp;</td><td>8.2067</td><td></td></tr><tr><td>calcium chloride 2-hydrate</td><td>Merck, 147.02 g/mol&amp;nbsp;</td><td>1172113</td><td></td></tr><tr><td>stub-aluminium mount</td><td>EMS, sloted head</td><td>75230</td><td></td></tr><tr><td>carbon adhesive tape</td><td>EMS</td><td>77825-12</td><td></td></tr><tr><td>Shaker 37 &amp;deg;C</td><td>New Brunswick Scientific Innowa42</td><td>NA</td><td></td></tr><tr><td>Centrifuge</td><td>Eppendorf table top centrifuge 5424</td><td>NA</td><td></td></tr><tr><td>Digital Sonifier, Model 250, used with Double Step Microtip</td><td>Branson</td><td>NA</td><td></td></tr><tr><td>Incubator 30 &amp;deg;C</td><td>Binder</td><td>NA</td><td></td></tr><tr><td>Incubator 23 &amp;deg;C</td><td>Binder</td><td>NA</td><td></td></tr><tr><td>Filter System, 500 ml, polystyrene</td><td>Cornig Incorporated</td><td>NA</td><td></td></tr><tr><td>Rotary Shaker - Orbitron Rotatory II</td><td>Boekel</td><td>NA</td><td></td></tr><tr><td>S150 Sputter Coater&amp;nbsp;</td><td>Edwards</td><td>NA</td><td></td></tr><tr><td>CPD 030 Critical Point Dryer</td><td>BAL-TEC</td><td>NA</td><td></td></tr><tr><td>Environmental Scanning Electron Microscope</td><td>XL30 ESEM FEG Philips (FEI)</td><td>NA</td><td></td></tr></tbody></table>

methodologies for studying b. subtilis biofilms as a model for characterizing small molecule biofilm inhibitors

This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and resilience of Bacillus subtilis biofilms. First, methods are presented that select for small molecule inhibitors with biofilm-specific targets in order to separate the effect of the small molecule inhibitors on planktonic growth from their effect on biofilm formation. Next, we focus on how inoculation conditions affect the sensitivity of multicellular, floating B. subtilis cultures to small molecule inhibitors. The results suggest that discrepancies in the reported effects of such inhibitors such as D-amino acids are due to inconsistent pre-culture conditions. Furthermore, a recently developed protocol is described for evaluating the contribution of small molecule treatments towards biofilm resistance to antibacterial substances. Lastly, scanning electron microscopy (SEM) techniques are presented to analyze the three-dimensional spatial arrangement of cells and their surrounding extracellular matrix in a B. subtilis biofilm. SEM facilitates insight into the three-dimensional biofilm architecture and the matrix texture. A combination of the methods described here can greatly assist the study of biofilm development in the presence and absence of biofilm inhibitors, and shed light on the mechanism of action of these inhibitors.

The pellicle assay is one method to study the highly regulated and dynamic processes of B. subtilis multicellularity. Besides this, the pellicle assay is suited to test a range of either pre-starter conditions or small molecule concentrations in a single cell-culture multidish plate in one experiment. However, B. subtilis pellicle formation is sensitive to the pre-culture conditions (e.g., growth medium of the pre-culture and its growth phase), the inoculation ratio and the removal of the pre-c...

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Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

This study presents the development of reproducible methodologies to study biofilm inhibitors and their effects on Bacillus subtilis multicellularity.

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and ...

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15.0K Views.  Weizmann Institute of Science. This study presents the development of reproducible methodologies to study biofilm inhibitors and their effects on Bacillus subtilis multicellularity.

Video: Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

Microtiter Dish Biofilm Formation Assay

Biofilms are communities of microbes attached to surfaces, which can be found in medical, industrial and natural settings. In fact, life in a biofilm probably represents the predominate mode of growth for microbes in most environments. Mature biofilms have a few distinct characteristics. Biofilm microbes are typically surrounded by an extracellular matrix that provides structure and protection to the community. Microbes growing in a biofilm also have a characteristic architecture generally comprised of macrocolonies (containing thousands of cells) surrounded by fluid-filled channels. Biofilm-grown microbes are also notorious for their resistance to a range of antimicrobial agents including clinically relevant antibiotics.
The microtiter dish assay is an important tool for the study of the early stages in biofilm formation, and has been applied primarily for the study of bacterial biofilms, although this assay has also been used to study fungal biofilm formation. Because this assay uses static, batch-growth conditions, it does not allow for the formation of the mature biofilms typically associated with flow cell systems. However, the assay has been effective at identifying many factors required for initiation of biofilm formation (i.e, flagella, pili, adhesins, enzymes involved in cyclic-di-GMP binding and metabolism) and well as genes involved in extracellular polysaccharide production. Furthermore, published work indicates that biofilms grown in microtiter dishes do develop some properties of mature biofilms, such a antibiotic tolerance and resistance to immune system effectors.
This simple microtiter dish assay allows for the formation of a biofilm on the wall and/or bottom of a microtiter dish. The high throughput nature of the assay makes it useful for genetic screens, as well as testing biofilm formation by multiple strains under various growth conditions. Variants of this assay have been used to assess early biofilm formation for a wide variety of microbes, including but not limited to, pseudomonads, Vibrio cholerae, Escherichia coli, staphylocci, enterococci, mycobacteria and fungi.
In the protocol described here, we will focus on the use of this assay to study biofilm formation by the model organism Pseudomonas aeruginosa. In this assay, the extent of biofilm formation is measured using the dye crystal violet (CV). However, a number of other colorimetric and metabolic stains have been reported for the quantification of biofilm formation using the microtiter plate assay. The ease, low cost and flexibility of the microtiter plate assay has made it a critical tool for the study of biofilms.

The assay describes a rapid means to measure early biofilm formation in bacteria and fungi. This method uses a microtiter plate as the substratum for microbial biofilm formation, and the biofilm is visualized using crystal violet strain. The assay provides either a qualitative or quantitative assay for early biofilm formation.

Biofilms are communities of microbes attached to surfaces, which can be found in medical, industrial and natural settings.  In fact, life in a biofilm ...

Single-cell Analysis of Bacillus subtilis Biofilms Using Fluorescence Microscopy and Flow Cytometry

Biofilm formation is a general attribute to almost all bacteria 1-6. When bacteria form biofilms, cells are encased in extracellular matrix that is mostly constituted by proteins and exopolysaccharides, among other factors 7-10. The microbial community encased within the biofilm often shows the differentiation of distinct subpopulation of specialized cells 11-17. These subpopulations coexist and often show spatial and temporal organization within the biofilm 18-21.
Biofilm formation in the model organism Bacillus subtilis requires the differentiation of distinct subpopulations of specialized cells. Among them, the subpopulation of matrix producers, responsible to produce and secrete the extracellular matrix of the biofilm is essential for biofilm formation 11,19. Hence, differentiation of matrix producers is a hallmark of biofilm formation in B. subtilis.
We have used fluorescent reporters to visualize and quantify the subpopulation of matrix producers in biofilms of B. subtilis 15,19,22-24. Concretely, we have observed that the subpopulation of matrix producers differentiates in response to the presence of self-produced extracellular signal surfactin 25. Interestingly, surfactin is produced by a subpopulation of specialized cells different from the subpopulation of matrix producers 15.
We have detailed in this report the technical approach necessary to visualize and quantify the subpopulation of matrix producers and surfactin producers within the biofilms of B. subtilis. To do this, fluorescent reporters of genes required for matrix production and surfactin production are inserted into the chromosome of B. subtilis. Reporters are expressed only in a subpopulation of specialized cells. Then, the subpopulations can be monitored using fluorescence microscopy and flow cytometry (See Fig 1).
The fact that different subpopulations of specialized cells coexist within multicellular communities of bacteria gives us a different perspective about the regulation of gene expression in prokaryotes. This protocol addresses this phenomenon experimentally and it can be easily adapted to any other working model, to elucidate the molecular mechanisms underlying phenotypic heterogeneity within a microbial community.

Single-cell Analysis of Bacillus subtilis Biofilms Using Fluorescence Microscopy and Flow Cytometry

Microbial biofilms are generally constituted by distinct subpopulations of specialized cells. Single-cell analysis of these subpopulations requires the use of fluorescent reporters. Here we describe a protocol to visualize and monitor several subpopulationswithin B. subtilis biofilms using fluorescence microscopy and flow cytometry.

Biofilm formation is a general attribute to almost all bacteria 1-6. When bacteria form biofilms, cells are encased in extracellular matrix that is mostly ...

Establishing the Minimal Bactericidal Concentration of an Antimicrobial Agent for Planktonic Cells (MBC-P) and Biofilm Cells (MBC-B)

This protocol allows for a direct comparison between planktonic and biofilm resistance for a bacterial strain that can form a biofilm in vitro. Bacteria are inoculated into the wells of a 96-well microtiter plate. In the case of the planktonic assay, serial dilutions of the antimicrobial agent of choice are added to the bacterial suspensions. In the biofilm assay, once inoculated, the bacteria are left to form a biofilm over a set period of time. Unattached cells are removed from the wells, the media is replenished and serial dilutions of the antimicrobial agent of choice are added. After exposure to the antimicrobial agent, the planktonic cells are assayed for growth. For the biofilm assay, the media is refreshed with fresh media lacking the antimicrobial agent and the biofilm cells are left to recover. Biofilm cell viability is assayed after the recovery period. The MBC-P for the antimicrobial agent is defined as the lowest concentration of drug that kills the cells in the planktonic culture.&#160; In contrast, the MBC-B for a strain is determined by exposing preformed biofilms to increasing concentrations of antimicrobial agent for 24 hr. The MBC-B is defined as the lowest concentration of antimicrobial agent that kills the cells in the biofilm.

Establishing the Minimal Bactericidal Concentration of an Antimicrobial Agent for Planktonic Cells MBC-P and Biofilm Cells MBC-B

This protocol allows for a direct comparison between planktonic and biofilm resistance for a bacterial strain that can form a biofilm in vitro using a 96-well microtiter plate. Planktonic or biofilm bacteria are exposed to serial dilutions of the antimicrobial agent of choice. Viability is assayed by growth on agar plates.

This protocol allows for a direct comparison between planktonic and biofilm resistance for a bacterial strain that can form a biofilm in vitro. Bacteria ...

Anti-virulent Disruption of Pathogenic Biofilms using Engineered Quorum-quenching Lactonases

The rapid emergence of multi-drug resistant bacteria has accelerated the need for novel therapeutic approaches to counter life-threatening infections. The persistence of bacterial infection is often associated with quorum-sensing-mediated biofilm formation. Thus, the disruption of this signaling circuit presents an attractive anti-virulence strategy. Quorum-quenching lactonases have been reported to be effective disrupters of quorum-sensing circuits. However, there have been very few reports of the effective use of these enzymes in disrupting bacterial biofilm formation. This protocol describes a method to disrupt biofilm formation in a clinically relevant A. baumannii S1 strain through the use of an engineered quorum-quenching lactonase. Acinetobacter baumannii is a major human pathogen implicated in serious hospital-acquired infections globally and its virulence is attributed predominantly to its biofilm's tenacity. The engineered lactonase treatment achieved significant A. baumannii S1 biofilm reduction. This study also showed the possibility of using engineered quorum-quenching enzymes in future treatment of biofilm-mediated bacterial diseases. Lastly, the method may be used to evaluate the competency of promising quorum-quenching enzymes.

Quorum-quenching enzymes are anti-virulent and anti-bacterial options that can mitigate pathogenesis without risk of incurring resistance, by preventing the expression of virulence factors and genes associated with antibiotic resistance and biofilm formation. In this study, we report a method that demonstrates the efficacy of quorum-quenching enzymes in bacterial biofilm disruption.

The rapid emergence of multi-drug resistant bacteria has accelerated the need for novel therapeutic approaches to counter life-threatening infections. The ...

Targeting Biofilm Associated Staphylococcus aureus Using Resazurin Based Drug-susceptibility Assay

Most pathogenic bacteria are able to form biofilms during infection, but due to the difficulty of manipulating and assessing biofilms, the vast majority of laboratory work is conducted with planktonic cells. Here, we describe a peg plate biofilm assay as performed with Staphylococcus aureus. Bacterial biofilms are grown on pegs attached to a 96-well microtiter plate lid, washed through gentle submersion in buffer, and placed in a drug challenge plate. After subsequent incubation they are again washed and moved to a final recovery plate, in which the fluorescent dye resazurin serves as a viability indicator. This assay offers greatly increased ease-of-use, reliability, and reproducibility, as well as a wealth of data when conducted as a kinetic read. Moreover, this assay can be adapted to a medium-throughput drug screening approach by which an endpoint fluorescent readout is taken instead, offering a path for drug discovery efforts.

Targeting Biofilm Associated Staphylococcus aureus Using Resazurin Based Drug-susceptibility Assay

Most bacterial infections produce a biofilm. By virtue of their environment, biofilm associated bacteria are often phenotypically drug resistant. Novel antibacterial molecules that kill bacteria in biofilms are thus a high priority. We establish an assay to quickly screen for antimicrobial compounds that are effective at eradicating biofilms.

Most pathogenic bacteria are able to form biofilms during infection, but due to the difficulty of manipulating and assessing biofilms, the vast majority ...

A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy

Bacterial biofilms frequently form on fungal surfaces and can be involved in numerous bacterial-fungal interaction processes, such as metabolic cooperation, competition, or predation. The study of biofilms is important in many biological fields, including environmental science, food production, and medicine. However, few studies have focused on such bacterial biofilms, partially due to the difficulty of investigating them. Most of the methods for qualitative and quantitative biofilm analyses described in the literature are only suitable for biofilms forming on abiotic surfaces or on homogeneous and thin biotic surfaces, such as a monolayer of epithelial cells.
While laser scanning confocal microscopy (LSCM) is often used to analyze in situ and in vivo biofilms, this technology becomes very challenging when applied to bacterial biofilms on fungal hyphae, due to the thickness and the three dimensions of the hyphal networks. To overcome this shortcoming, we developed a protocol combining microscopy with a method to limit the accumulation of hyphal layers in fungal colonies. Using this method, we were able to investigate the development of bacterial biofilms on fungal hyphae at multiple scales using both LSCM and scanning electron microscopy (SEM). This report describes the protocol, including microorganism cultures, bacterial biofilm formation conditions, biofilm staining, and LSCM and SEM visualizations.

This protocol describes a new method to grow and qualitatively analyze bacterial biofilms on fungal hyphae by confocal and electron microscopy.

Bacterial biofilms frequently form on fungal surfaces and can be involved in numerous bacterial-fungal interaction processes, such as metabolic ...

A Platform of Anti-biofilm Assays Suited to the Exploration of Natural Compound Libraries

Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are potentially responsible for over 80% of antibiotic-tolerant infections. Biofilms have displayed an exceptionally high tolerance for chemotherapy, which is thought to be multifactorial. For instance, the matrix provides a physical barrier that decreases the penetration of antibiotics into the biofilm. Also, cells within the biofilms are phenotypically diverse. Likely, biofilm resilience arises from a combination of these and other, yet unknown, mechanisms. All of the currently existing antibiotics have been developed against single-cells (planktonic) bacteria. Therefore, so far, a very limited repertoire of molecules exists that can selectively act on mature biofilms. This situation has driven a progressive paradigm shift in drug discovery, in which searching for anti-biofilms has been urged to occupy a more prominent place. An additional challenge is that there are a very limited number of standardized methods for biofilm research, especially those that can be used for large-throughput screening of chemical libraries. Here, an experimental anti-biofilm platform for chemical screening is presented. It uses three assays to measure biofilm viability (with resazurin staining), total biomass (with crystal violet staining), and biofilm matrix (using a wheat germ agglutinin, WGA-fluorescence-based staining of the poly-N-acetyl-glucosamine, PNAG, fraction). All the assays were developed using Staphylococcus aureus as the model bacteria. Examples of how the platform can be used for primary screening as well as for functional characterization of identified anti-biofilm hits are presented. This experimental sequence further allows for the classification of the hits based upon the measured end-points. It also provides information on their mode of action, especially on long-term versus short-term chemotherapeutic effects. Thus, it is very advantageous for the quick identification of high-quality hit compounds that can serve as starting points for various biomedical applications.

Biofilm infections show high tolerance towards chemotherapy. No single assay captures the complexity of biofilms. Instead, complementary assays are needed. We present a screening platform (developed for S. aureus) that combines assays for viability, biomass, and biofilm matrix. It allows anti-biofilm drug discovery, including the assessment of long-term chemotherapeutic effects.

Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are potentially responsible for over 80% of ...

Systematic Approach to Identify Novel Antimicrobial and Antibiofilm Molecules from Plants' Extracts and Fractions to Prevent Dental Caries

Natural products provide structurally different substances, with a myriad of biological activities. However, the identification and isolation of active compounds from plants are challenging because of the complex plant matrix and time-consuming isolation and identification procedures. Therefore, a stepwise approach for screening natural compounds from plants, including the isolation and identification of potentially active molecules, is presented. It includes the collection of the plant material; preparation and fractionation of crude extracts; chromatography and spectrometry (UHPLC-DAD-HRMS and NMR) approaches for analysis and compounds identification; bioassays (antimicrobial and antibiofilm activities; bacterial &#34;adhesion strength&#34; to the salivary pellicle and initial glucan matrix treated with selected treatments); and data analysis. The model is simple, reproducible, and allows high-throughput screening of multiple compounds, concentrations, and treatment steps can be consistently controlled. The data obtained provide the foundation for future studies, including formulations with the most active extracts and/or fractions, isolation of molecules, modeling molecules to specific targets in microbial cells and biofilms. For example, one target to control cariogenic biofilm is to inhibit the activity of Streptococcus mutans glucosyltransferases that synthesize the extracellular matrix&#8217; glucans. The inhibition of those enzymes prevents the biofilm build-up, decreasing its virulence.

Natural products represent promising starting points for the development of new drugs and therapeutic agents. However, due to the high chemical diversity, finding new therapeutic compounds from plants is a challenging and time-consuming task. We describe a simplified approach to identify antimicrobial and antibiofilm molecules from plant extracts and fractions.

Natural products provide structurally different substances, with a myriad of biological activities. However, the identification and isolation of active ...

Biology

Evaluation of the Efficacy of Organic Peroxyacids for Eradicating Dairy Biofilms Using an Approach Combining Static and Dynamic Methods

The presence of biofilms in the dairy industry is of major concern, as they may lead to the production of unsafe and altered dairy products due to their high resistance to most clean-in-place (CIP) procedures frequently used in processing plants. Therefore, it is imperative to develop new biofilm control strategies for the dairy industry. This protocol is aimed at evaluating the efficacy of organic peroxyacids (peracetic, perpropionic, and perlactic acids and a commercial peracetic acid-based disinfectant) for eradicating dairy biofilms using a combination of static and dynamic methods. All the disinfectants were tested on the strongest biofilm-producing bacteria in either a single or a mixed biofilm using the minimum biofilm eradication concentration (MBEC) assay, a static high-throughput screening method. A contact time of 5 min with the disinfectants at the recommended concentrations successfully eradicated both the single and mixed biofilms. Studies are currently ongoing to confirm these observations using the Center for Disease Control (CDC) biofilm reactor, a dynamic method to mimic in situ conditions. This type of bioreactor enables the use of a stainless-steel surface, which constitutes most industrial equipment and surfaces. The preliminary results from the reactor appear to confirm the efficacy of organic peroxyacids against biofilms. The combined approach described in this study may be used to develop and test new biological or chemical formulations for controlling biofilms and eradicating microorganisms.

This protocol describes an approach combining static and dynamic methods to evaluate the efficacy of organic peroxyacids for eradicating biofilms in the dairy industry. This approach may also be used to test the effectiveness of new biological or chemical formulations for controlling biofilms.

The presence of biofilms in the dairy industry is of major concern, as they may lead to the production of unsafe and altered dairy products due to their ...

Assessment of Acinetobacter Biofilm Formation and Characterization of Biofilms

Quantification, Viability Assessment, and Visualization Strategies for Acinetobacter Biofilms

Acinetobacter causes nosocomial infections and its biofilm formation can contribute to the survival on dry surfaces such as hospital environments. Thus, biofilm quantification and visualization are important methods to assess the potential of Acinetobacter strains to cause nosocomial infections. The biofilms forming on the surface of the microplate can be quantified in terms of volume and cell numbers. Biofilm volumes can be quantified by staining using crystal violet, washing, destaining using ethanol, then measuring the solubilized dye using a microplate reader. To quantify the number of cells embedded in the biofilms, the biofilms are scrapped off using cell scrapers, harvested in the saline, vigorously agitated in the presence of glass beads, and spread on Acinetobacter agar. Then, the plates are incubated at 30 &#176;C for 24-42 h. After incubation, the red colonies are enumerated to estimate the number of cells in biofilms. This viable count method can also be useful for counting Acinetobacter cells in mixed-species biofilms. Acinetobacter biofilms can be visualized using fluorescent dyes. A commercially available microplate designed for microscopic analysis is employed to form biofilms. Then, the bottom-surface attached biofilms are stained with SYTO9 and propidium iodide dyes, washed, then visualized with confocal laser scanning microscopy.

Author Spotlight: A Comprehensive Protocol for Acinetobacter Biofilm Quantification, Assessment, and Visualization 

This protocol describes the preparation of the inoculum, the biofilm quantification on microtiter plates using crystal violet dye, the viable count in biofilms, and the visualization of biofilms of Acinetobacter.

Acinetobacter causes nosocomial infections and its biofilm formation can contribute to the survival on dry surfaces such as hospital environments. Thus, ...

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

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