Name: three-dimensional patterning of engineered biofilms with a do-it-yourself bioprinter
Uploaded: 2019-05-16T14:00:00
Description: Watch this Scientific Journal Video about Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter at JoVE.com

This work was supported by an AOARD grant (No. FA2386-18-1-4059), the Netherlands Organization for Scientific Research (NWO/OCW) as part of the Frontiers of Nanoscience program, and the Advanced Materials NWO-NSFC program (No. 729.001.016). The authors acknowledge laboratory assistance of Ramon van der Valk and Roland Kieffer.

1. Conversion of a commercial 3D printer into a 3D bioprinter
<ol>
	<li>Remove the extruder and the heater of a commercial 3D printer (Table of Materials) from the printer frame, and unplug the wiring controlling these elements from the main circuit board (Figure 1A). Since the sensor that controls the operational temperature of the printer needs to be functional to communicate with the printer software, remove from the printing software the algorithm that delays printing ...

<ol>
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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Physiological+heterogeneity+in+biofilms.">Physiological heterogeneity in biofilms.</a> Nature Reviews Microbiology. 6 (3), 199-210 (2008).</li><li>Kikuchi, T., Mizunoe, Y., Takade, A., Naito, S., Yoshida, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Curli+Fibers+Are+Required+for+Development+of+Biofilm+Architecture+in+Escherichia+coli+K-12+and+Enhance+Bacterial+Adherence+to+Human+Uroepithelial+Cells.">Curli Fibers Are Required for Development of Biofilm Architecture in Escherichia coli K-12 and Enhance Bacterial Adherence to Human Uroepithelial Cells.</a> Microbiology and Immunology. 49 (9), 875-884 (2005).</li><li>Cranford, S., Buehler, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Materiomics:+biological+protein+materials,+from+nano+to+macro.">Materiomics: biological protein materials, from nano to macro.</a> Nanotechnology, Science and Applications. 3, 127-148 (2010).</li><li>Lehner, B. A. E., Schmieden, D. T., Meyer, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Straightforward+Approach+for+3D+Bacterial+Printing.">A Straightforward Approach for 3D Bacterial Printing.</a> ACS Synthetic Biology. 6 (7), 1124-1130 (2017).</li><li>Wang, X., Smith, D. R., Jones, J. W., Chapman, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+polymerization+of+a+functional+Escherichia+coli+amyloid+protein.">In vitro polymerization of a functional Escherichia coli amyloid protein.</a> Journal of Biological Chemistry. 282 (6), 3713-3719 (2007).</li><li>Hammar, M., Bian, Z., Normark, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nucleator-dependent+intercellular+assembly+of+adhesive+curli+organelles+in+Escherichia+coli.">Nucleator-dependent intercellular assembly of adhesive curli organelles in Escherichia coli.</a> Proceedings of the National Academy of Sciences of the United States of America. 93 (13), 6562-6566 (1996).</li><li>Huang, Y. J., Xia, A. G., Yang, G., Jin, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bioprinting+Living+Biofilms+through+Optogenetic+Manipulation.">Bioprinting Living Biofilms through Optogenetic Manipulation.</a> ACS Synthetic Biology. 7 (5), 1195-1200 (2018).</li><li>Jin, X. F., Riedel-Kruse, I. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilm+Lithography+enables+high-resolution+cell+patterning+via+optogenetic+adhesin+expression.">Biofilm Lithography enables high-resolution cell patterning via optogenetic adhesin expression.</a> Proceedings of the National Academy of Sciences of the United States of America. 115 (14), 3698-3703 (2018).</li><li>Stewart, P. S., Franklin, M. 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The protocol presented here for 3D printing of engineered biofilms has two critical steps. First is the preparation of the agar printing surface, which is the most critical factor to producing a specific printing resolution. It is important to ensure that the printing surface is flat and that the pipette tip on the printhead is positioned at the correct height from the surface. If the surface is not flat, the working distance will change during the printing process. If the working distance is less than 0.1 mm, the CaCl<s...

There is currently an increasing need to develop environmentally-friendly, sustainable solutions for the production of spatially-patterned materials, due to the expanding number of markets for such materials1. This article presents a simple, economical method for the production of such materials and therefore offers a large spectrum of future applications. The method presented here allows three-dimensional (3D) printing of spatially-patterned structures using a bio-ink containing living bacteria. Bacteria remain viable within the printed structures for over one week, enabling the bacteria to perform natural or engineered metabolic activities. Printed bacteria can thereby produce and deposit desired components within the printed structure, for example creating a functional cross-linked biofilm2.
Traditional methods for the production of advanced materials involve high energy expenditures (e.g., high temperatures and/or pressures) and can produce large quantities of chemical waste, often toxic substances that require cost-extensive utilization3,4. In contrast, multiple bacterial species are able to produce materials that can be readily applicable in various industries. These materials include polymers such as polyhydroxyalkanoates (PHA)5 or poly(glycolide-co-lactide) (PGLA)6, bacterial cellulose7, bacterial concrete materials8, biomimetic composites9, amyloid-based adhesives10, or bio-based electrical switches11, among others. Moreover, bacterial production of valuable materials typically takes place at near-ambient temperatures and pressures and in aqueous environments, without requiring or producing toxic compounds. While producing materials with bacteria has been demonstrated in the literature and some industrial applications have already emerged12,13, a reliable method for spatial patterning of such materials remains a challenge.
This article demonstrates a straight-forward method of converting a low-cost commercial 3D printer into a 3D bacterial printer. The protocol shows how to prepare a bio-ink containing and sustaining the living bacteria, as well as how to prepare substrates onto which the 3D printing can be performed. This method is appropriate to use with a variety of natural and engineered bacterial strains able to produce materials. These bacteria can be spatially distributed within a 3D printed structure and still continue their metabolic activity, which will result in a spatial distribution of the desired materials produced by the bacteria.
This printing method enables additive manufacturing of biofilms, aggregates of bacteria surrounded by a self-produced extracellular matrix. Biofilms are heterogeneous 3D networks in which proteins, polymers, bacterial cells, oxygen, and nutrients are all spatially structured14. While in the form of a biofilm, bacteria exhibit an increased antibiotic resistance and structural robustness, making them difficult to eradicate from surfaces including medical catheters and implants. The key to biofilm properties, and also the largest challenge to biofilm research, seems to be the heterogeneity of biofilms15,16,17. Production of spatially-controlled model biofilms is of special interest as it would allow for either reproducing or tuning the spatial patterns of biofilm components, aiding the understanding of the stable deposition of biofilms on virtually any surface in nature.
This article presents a method for the production of biofilms using 3D-printed hydrogels containing engineered E. coli bacteria that produce biofilm proteins in the presence of an inducer, as well as methods of verification of biofilm formation2. The major extracellular matrix components of these biofilms are curli amyloid fibers18 that contain self-assembled CsgA proteins. When engineered E. coli bacteria are induced to express CsgA proteins, they form a stable model biofilm that protects the cells against being washed off of the printing surface. Such a 3D printed biofilm can be spatially controlled and can serve as a useful research tool for the investigation of multiscale biofilm structure-function mechanics or materiomics19. These bespoke biofilms will aid the understanding of the principles of biofilm formation and their mechanical properties, enabling further research into the mechanisms of antibiotic resistance among other applications.

<table>
	<tbody>
		<tr>
			<td>3D printer</td>
			<td>CoLiDo</td>
			<td>3D-P Kit</td>
			<td></td>
		</tr>
		<tr>
			<td>3D printing software</td>
			<td>CoLiDo</td>
			<td>Print-Rite ColiDo Repetier-Host v2.0.1</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Sigma-Aldrich</td>
			<td>05040</td>
			<td></td>
		</tr>
		<tr>
			<td>CaCl2 dihydrate</td>
			<td>Sigma-Aldrich</td>
			<td>C7902</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Eppendorf</td>
			<td>5810 R</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloramphenicol</td>
			<td>Sigma-Aldrich</td>
			<td>3886.1</td>
			<td></td>
		</tr>
		<tr>
			<td>LB broth powder</td>
			<td>Sigma-Aldrich</td>
			<td>L3022</td>
			<td></td>
		</tr>
		<tr>
			<td>Orbital shaker</td>
			<td>VWR</td>
			<td>89032-092</td>
			<td>Model 3500</td>
		</tr>
		<tr>
			<td>Petri dish</td>
			<td>VWR</td>
			<td>25384-326</td>
			<td>150 x 15 mm</td>
		</tr>
		<tr>
			<td>Rhamnose</td>
			<td>Sigma-Aldrich</td>
			<td>83650</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicon tubing</td>
			<td>VWR&#160;</td>
			<td>DENE 3100103/25</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe pump</td>
			<td>ProSense B.V.&#160;</td>
			<td>NE-300</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium alginate</td>
			<td>Sigma-Aldrich</td>
			<td>W201502</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium citrate monobasic</td>
			<td>Sigma-Aldrich</td>
			<td>71498</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium hydrooxide</td>
			<td>VWR</td>
			<td>28244.295</td>
			<td></td>
		</tr>
	</tbody>
</table>

three-dimensional patterning of engineered biofilms with a do-it-yourself bioprinter

Biofilms are aggregates of bacteria embedded in a self-produced spatially-patterned extracellular matrix. Bacteria within a biofilm develop enhanced antibiotic resistance, which poses potential health dangers, but can also be beneficial for environmental applications such as purification of drinking water. The further development of anti-bacterial therapeutics and biofilm-inspired applications will require the development of reproducible, engineerable methods for biofilm creation. Recently, a novel method of biofilm preparation using a modified three-dimensional (3D) printer with a bacterial ink has been developed. This article describes the steps necessary to build this efficient, low-cost 3D bioprinter that offers multiple applications in bacterially-induced materials processing. The protocol begins with an adapted commercial 3D printer in which the extruder has been replaced with a bio-ink dispenser connected to a syringe pump system enabling a controllable, continuous flow of bio-ink. To develop a bio-ink suitable for biofilm printing, engineered Escherichia coli bacteria were suspended in a solution of alginate, so that they solidify in contact with a surface containing calcium. The inclusion of an inducer chemical within the printing substrate drives expression of biofilm proteins within the printed bio-ink. This method enables 3D printing of various spatial patterns composed of discrete layers of printed biofilms. Such spatially-controlled biofilms can serve as model systems and can find applications in multiple fields that have a wide-ranging impact on society, including antibiotic resistance prevention or drinking water purification, among others.

The first step for successful 3D printing of biofilms is converting a commercial 3D printer into a bioprinter. This conversion is achieved by removing the extruder and heater of the printer, designed for printing with a polymeric ink, and replacing these with components appropriate for printing bio-ink containing living bacteria (Figure 1A). The extruder is replaced by a pipette tip (or tips, if multiple bio-inks will be used in the printing process) attached...

Watch this Scientific Journal Video about Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter at JoVE.com

Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter

This article describes a method of transforming a low-cost commercial 3D printer into a bacterial 3D printer that can facilitate printing of patterned biofilms. All necessary aspects of preparing the bioprinter and bio-ink are described, as well as verification methods to assess the formation of biofilms.

Biofilms are aggregates of bacteria embedded in a self-produced spatially-patterned extracellular matrix. Bacteria within a biofilm develop enhanced ...

3D bioprinting with bacteria is a newly developed technique. This protocol provides an easy way of constructing engineered biofilms 3D printed with bacteria. The main advantage of this technique is the ability to produce 3D printed biofilms using an inexpensive home-built 3D printer.One possible application of our 3D printer is to create reproducible model biofilms that can be used to develop new antibacterial therapies. Our 3D printing approach can be applied to any type of bacteria that is compatible with our alginate based bioink. Preparation of the bioink and of the printing substrates are fairly standard procedures, while the 3D printing process, especially the calibration of the Z-axis is a crucial step that requires some practice.Calibration of the set access height will influence the resolution of our 3D printer, and is strongly dependent on personal experience. This procedure requires manual adjustments, and it's difficult to be described in a written format. Connect a 200 microliter pipette tip to a length of silicone tubing, and mount the pipette tip onto the 3D printer's extruder head as a replacement for the original extruder.Next, add four milliliters of a five molar calcium chloride solution to 400 milliliters of 1%agar dissolved in Luria-Bertani broth, and supplement it with the appropriate antibiotics and inducers. Then, dispense 20 milliliters of the LB agar solution into each 150 millimeter by 15 millimeter Petri dish. Dry the dish for 30 minutes at room temperature, with the lid half open.Prepare a 3%sodium alginate solution, and heat it to the boiling point three times to sterilize the solution. Then, store the sterile solution at four degrees Celsius until it is used. To prepare the bacterial component of the bioink, grow E.coli bacteria carrying plasmids for constitutive GFP expression in 50 milliliters of LB medium containing antibiotics.Shake the culture at 250 RPM and 37 degrees Celsius overnight. After overnight growth of the culture, pellet the bacteria for five minutes at 3, 220 times gravity and then remove the supernatant. Resuspend the bacteria pellet in 10 milliliters of LB medium, and add 10 milliliters of 3%sodium alginate.Connect the 3D printer to a computer, and open the 3D printing software. Click the Home button for the X, Y, and Z axes, to move the print head to its home position. For each print, place a prepared printing substrate onto a particular location on the printing bed.Raise the print head to a height of over 22 millimeters under manual control, so that it will not collide with the edge of the Petri dish during movement. Position the print head over the top of the plate and move it down until the pipette tip contacts the printing surface. Assign this Z-axis position as Z1, the height of the printing surface.Next, raise the print head and manually move it outside of the plate area. If the working distance between the print head and the plate surface is defined as Z2, enter the height of the printing surface plus the working distance into the printing program as the Z value during printing. Load a pre-programmed G-code file containing commands for printing the desired shape.At each command line, the position of the print head may be changed in the X, Y, and or Z axes. Be sure to input the Z value during all printing steps as the height of printing surface plus the working distance. Load the liquid bioink into syringes and mount them in the syringe pump of the 3D bioprinter.Then, set the extrusion speed to 0.3 milliliters per hour. Print the bioink onto the printing substrate by clicking the Print button. Wait to start the syringe pump until after the printing has started, and before the print head comes into contact with the printing surface.During printing, control the print head movement entirely by the software. Stop the syringe pump as soon as the print head arrives at the last point of printing, otherwise excess bioink will drop onto the printing substrate and reduce the printing resolution. For the construction of 3D structures, all the movements of the print head are controlled in the G-code editor.To increase the printing height for the second layer, type in the printing height of the first layer, and increase the Z value in the code by 0.2 millimeters. Thereafter, increase the Z value by 0.1 millimeter, when moving to a higher layer. Incubate the printed samples at room temperature for three to six days to allow the production of the biofilm components such as Curli fibers.Then, place the plate on a fluorescent scanner and image the plates. To dissolve the alginate matrix, add 20 milliliters of a 0.5 molar sodium citrate solution at pH 7, to the printed substrate. Incubate the plate at room temperature for two hours while shaking at 30 rpm.Then, discard the liquid and image the plates again, to compare with the images of the plates before and after the citrate treatment. The 3D bioprinter can create bacteria encapsulating hydrogels in a variety of two-dimensional and three-dimensional shapes. These printed shapes can then be used to assess whether the formation of biofilm was successful or if the alginate matrix is completely dissolved using a sodium citrate solution.In the case of bioink without the inducible Curli production plasmid, the printed pattern was completely dissolved after the sodium citrate treatment, signifying that no biofilm Curli network had formed. The bacteria containing the inducible Curli production plasmid was not dissolved after sodium citrate treatment, indicating that the printed bacteria were able to form a Curli network extensive enough to stabilize the printed pattern of bacteria. To construct multi-layered structures, additional layers can be printed by controlling the G-code editor.Increasing the number of printed layers in a sample caused the width and the height of the printed structures to increase incrementally. When E.coli engineered to inducibly produce Curli proteins were printed into multi-layered structures, sodium citrate treatment did not dissolve the samples, whereas multilayer structures containing non Curli producing E.coli were dissolved. The most critical parts of the 3D printing procedure are the calibration of the Z-axis, and the coordination of starting the print and starting the syringe pump.The bioink developed for this process is fairly soft, with low toughness. Further modification could be made to the bioink, in order to provide and improve mechanical stability. This 3D printing technique enables production of biofilms with excellent mechanical properties, which may enable fabricating biomimetic materials.When handling these bacteria, wear proper protection, such as gloves.

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