Name: use of a high-throughput in vitro microfluidic system to develop oral multi-species biofilms
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Description: Watch this Scientific Journal Video about Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms at JoVE.com

The authors thank William Nance (University of Michigan) for help in formulating the biofilm growth protocols and John Battista (Fluxion, San Francisco, CA) for advice concerning technological issues relating to the Bioflux system. This work was supported by the National Institutes of Health (NIH: R21DE018820 to A. H. R.) and University of Michigan start-up funds to A. H. R.

The saliva collection protocol described herein was reviewed by the University of Michigan Institutional Review Board for Human Subject Research. 
NOTE: With regard to institutional reviews for human subject work of this type, prior arrangements and permissions should be garnered from the host institution. In particular, depending on the institution, IRB or ethics approval might need to be sought and approved before saliva collection from human volunteers can proceed. As an aid to preparing an application, a useful ...

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This methods paper highlights the basic steps required to setup and run a microfluidic system in a manner to allow for the development of oral multi-species biofilms derived from pooled human saliva and grown in filter-sterilized 25% pooled human saliva. Approaches to characterize the biofilm are given but it should be remembered that these described approaches are modifiable and additional technologies such as, for example, stains or labels can be introduced. As a matter of example, one could conceivably use labeled ant...

Biofilms are architecturally complex communities of bacteria that are aggregated on surfaces 1. These communities typically contain numerous species that interact with one another within the biofilm 2. Oral biofilms, the most visually conspicuous being dental plaque, are a persistent problem in humans and their uncontrolled development results in the generation of taxonomically diverse multi-species communities 3. The component bacteria of these diverse communities can be up to 1,000 times more resistant to antimicrobials than their free-floating (planktonic) counterparts 4-6. Failure to treat these oral biofilm communities, which can cause dental caries and periodontal disease, has resulted in a significant public health burden: over 500 million visits to the dentist office per annum in the US, and an approximately $108 billion to treat or prevent periodontal disease and dental caries 7.
&#8220;While many microbiologists advocate studying microbial behavior under natural conditions, few of them do so. This is because their morale for overcoming the difficulties is constantly sapped by the attractive ease of working with laboratory cultures.&#8221; &#8212;Smith 8.
At present, oral biofilm research is conducted using a variety of in vivo and in vitro approaches, each with their own advantages and disadvantages 9,10. In vitro approaches often use model biofilm systems that are relatively easy to set up but may lack clinical/real-world relevance 10,11. In vivo approaches typically rely upon animal model systems that may reproduce certain aspects of the human oral environment, but again suffer from limitations due to differences in anatomy, physiology, microbiology and immunology between animals and humans 12,13. It should be noted that oral biofilms can also be developed on enamel surfaces held in a stent within the mouths of human volunteers, but this approach is currently relatively costly and labor-intensive 14,15. Ultimately, novel agents or technologies to improve oral healthcare are tested in humans under controlled clinical trial conditions 11. At present, an often-used modus operandi for identifying and evaluating new oral healthcare agents is to first perform laboratory studies to discern potential efficacy, and then perform animal studies and &#8220;field trials&#8221; that employ clinicians to evaluate the success of the technology 9,16,17. Unfortunately, laboratory studies tend to rely on model systems that occupy a large footprint, are technologically challenging to use, and often contain simplified communities of one or at most a few species to derive potential real-world meaning 10,18. Given that dental plaque biofilms contain multiple species and form in a complex flowing salivary milieu, developing biofilms that contain one or a few species in artificial media is unlikely to generate communities that behave in a similar manner to those in a real-world scenario 10,19. To address the time, cost, training requirements, and the poor representative nature of laboratory model biofilm systems compared to the real-world environment, we recently developed a high throughput and environmentally germane biofilm system 20 (Figure 1). The system benefits from the use of cell-free pooled human saliva (CFS) as medium and untreated pooled human bacterial cell-containing saliva (CCS) as an inoculum. Uniquely, the system also combines microfluidic technology, a confocal laser scanning microscope, and culture-independent bacterial diversity analysis technology. Thus, the model system is environmentally germane (using saliva as an inoculum to grow multi-species biofilms at 37 &#176;C in filter-sterilized flowing saliva) and the oral biofilms contain species (including Streptococcus, Neisseria, Veillonella, and Porphyromonas species) in abundances representative of those found in early supragingival plaque 20.
When considering that this work describes the use of the newly developed model system, particular attention must be given to the amalgamation of a confocal laser scanning microscope (CLSM) microfluidics, and culture-independent diversity analysis technologies. The union of these technologies by our research group was intentional and not only adds a high-throughput capability to the newly developed model system, but also allows questions to be asked that could not be easily addressed before with other systems. Firstly, CLSM has distinct advantages over traditional microscopy as it allows for the three-dimensional analysis of biofilms. Often unappreciated, this is extremely important as biofilms are heterogeneous with respect to species composition and spatial position as well as the physiological conditions being imposed at different spatial locations within the biofilm 6,21. In concert with three-dimensional rendering software and image analysis software, the biofilm architecture, spatial relationships between component species, and extent of antimicrobial killing can be analyzed 22-24. Such abilities are not possible using standard transmitted light or epifluorescence microscopy. Next, microfluidics has garnered particular attention in the field of microbiology as it enables the study of biofilms under carefully controlled conditions (flow, temperature, pH, etc.) and only requires small volumes of liquid 25-27. As a point of comparison, growing an oral biofilm in human saliva within a flow cell model system (a system that is arguably considered the mainstay model for many oral biofilm studies) for 20 hr at a similar flow-rate and shear as that achieved in a microfluidic system requires at least 200 ml, as opposed to 800 &#181;l in the microfluidic device 28-31. Thus, a microfluidic model biofilm system enables the study of quantity-limited material under defined conditions. Finally, pyrosequencing technology has been optimized in the last decade to require only small amounts of material to perform a community analysis and is sufficiently versatile to control depth of sequencing to obtain the identity of even rare biofilm species. The use of this technology, such as bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), has allowed for pertinent questions concerning the ecology of biofilms to be addressed 32,33. Such questions imbued difficulties in the past when pyrosequencing was not available because of the time and costs required to create plasmid libraries and the complex technological and analytical steps required to derive data 33,34. Of course, a great advantage with culture-independent approaches, such as pyrosequencing, is that the bacterial species that cannot be grown in isolation within conventional laboratory media (i.e. viable but non-cultivable species) can be grown and identified within the model system and their relative abundance in the community quantified 35,36. To add perspective, as early as 1963, the late Sigmund Socransky estimated that approximately 50% of the bacteria in material isolated from the human oral gingival crevice could not be cultured using laboratory growth conditions 37.
The objective of this methods paper is to describe the approach to develop oral multi-species biofilms in a commercially available microfluidic (Bioflux) system under: (i) conditions representative of the human oral cavity and (ii) with a species composition and abundance that is comparable to supragingival plaque. Furthermore, using both freeware and commercial software, we highlight how basic biofilm architecture measures can be derived from CLSM data, with a focus on approaches to quantify biofilm biomass, roughness, and viability (based upon Live/Dead staining). Finally, the steps required to harvest biofilm material for diversity analysis by bTEFAP are described.

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			<td>Thermo Fisher Scientific Inc</td>
			<td>NC0542269</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">BioFlux microfluidic system</td>
			<td>Fluxion</td>
			<td>Bioflux 200 system</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Bioflux 24-channel plate</td>
			<td>Fluxion</td>
			<td>910-0004</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">PBS (Gibco)</td>
			<td>Thermo Fisher Scientific Inc</td>
			<td>10010023</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">LIVE/DEAD stain (Invitrogen)&#160;</td>
			<td>Invitrogen</td>
			<td>L7012</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Confocal Laser Scanning Microscope</td>
			<td>Lecia</td>
			<td>SPE or eqivalent system</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Epifluorescence Microscope</td>
			<td>Multiple choices</td>
			<td>Multiple choices</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Pyrosequencing facilities</td>
			<td>Multiple choices</td>
			<td>Multiple choices</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Decon SaniHol 70 Ethanol Solution</td>
			<td>Fisher Scientific</td>
			<td>04-355-122</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#160;Ultra Low Temperature Freezer -80&#176;C</td>
			<td>Multiple choices</td>
			<td>Multiple choices</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Tips (20, 200, and 1000uL)</td>
			<td>Multiple choices</td>
			<td>Multiple choices</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Single Channel Variable Volume Pipettors (20, 200, 1000uL)</td>
			<td>Multiple choices</td>
			<td>Multiple choices</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;"></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SOFTWARE</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;"></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Bioflux dedicated software</td>
			<td>Bioflux</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Imaris</td>
			<td>Bitplane</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Leica SPE</td>
			<td>Leica</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">ImageJ</td>
			<td>Freeware (http://imagej.nih.gov/ij/)</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">COMSTAT/COMSTAT 2</td>
			<td colspan="2">Freeware (http://www.comstat.dk/)</td>
		</tr>
	</tbody>
</table>

use of a high-throughput in vitro microfluidic system to develop oral multi-species biofilms

There are few high-throughput in vitro systems which facilitate the development of multi-species biofilms that contain numerous species commonly detected within in vivo oral biofilms. Furthermore, a system that uses natural human saliva as the nutrient source, instead of artificial media, is particularly desirable in order to support the expression of cellular and biofilm-specific properties that mimic the in vivo communities. We describe a method for the development of multi-species oral biofilms that are comparable, with respect to species composition, to supragingival dental plaque, under conditions similar to the human oral cavity. Specifically, this methods article will describe how a commercially available microfluidic system can be adapted to facilitate the development of multi-species oral biofilms derived from and grown within pooled saliva. Furthermore, a description of how the system can be used in conjunction with a confocal laser scanning microscope to generate 3-D biofilm reconstructions for architectural and viability analyses will be presented. Given the broad diversity of microorganisms that grow within biofilms in the microfluidic system (including Streptococcus, Neisseria, Veillonella, Gemella, and Porphyromonas), a protocol will also be presented describing how to harvest the biofilm cells for further subculture&#160;or DNA extraction and analysis. The limits of both the microfluidic biofilm system and the current state-of-the-art data analyses will be addressed. Ultimately, it is envisioned that this article will provide a baseline technique that will improve the study of oral biofilms and aid in the development of additional technologies that can be integrated with the microfluidic platform.

3D Rendering of Biofilms
Representative results are shown in Figure 3. A useful tool in IMARIS software is the option to examine each slice of the collected biofilm stack and to combine them to create three-dimensional reconstructions. In addition, artificial shadowing effects can be added to help visually interpret three-dimensional structures. The rendered biofilms can be orientated in any direction with different magnifications to explore biofilm o...

Watch this Scientific Journal Video about Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms at JoVE.com

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

The goal of this methods paper is to describe the use of a microfluidic system for the development of multi-species biofilms that contain species typically identified in human supragingival dental plaque.&#160;Methods to describe biofilm architecture, biofilm viability, and an approach to harvest biofilm for culture-dependent or culture-independent analyses are highlighted.

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

There are few high-throughput in vitro systems which facilitate the development of multi-species biofilms that contain numerous species commonly detected ...

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