Name: transformation of probiotic yeast and their recovery from gastrointestinal immune tissues following oral gavage in mice
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Description: Watch this Scientific Journal Video about Transformation of Probiotic Yeast and Their Recovery from Gastrointestinal Immune Tissues Following Oral Gavage in Mice at JoVE.com

The authors acknowledge funding through the Children&#39;s Center for Immunology and Vaccines and an NIH New Innovator Award (1DP2AI112242-01) awarded to Tracey J. Lamb. The authors also thank Natalya P. Degtyareva for the generous contribution of rad1 S. cerevisiae.

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The authors have nothing to disclose.

Together, the protocols herein describe the essential steps necessary for the development and testing of auxotrophic probiotic yeast strains for delivery of heterologous therapeutic protein to the intestine. This manipulation and testing of recombinant probiotic yeast requires techniques and resources with which any individual laboratory may not currently be familiar. Thus, although numerous previous studies have described the above protocols for multiple yeast and mouse strains, these methods have not to the authors&#39; knowledge been presented in a detailed, unified form. Furthermore, the present manuscript places particular emphasis on adapting current standardized protocols for the genetic manipulation of probiotic yeast, which are less well characterized than commonly used laboratory yeast strains. Many steps for both mutagenesis (discussed in part 1) and transformation (part 2) must be optimized for the manipulation of such diploid, probiotic yeast isolates. This manuscript also discusses potential pitfalls associated with animal handling (part 3) and dissection of the Peyer&#39;s patch immune tissues of the small intestine (part 4).
As many industrial and clinically relevant yeast strains are not immediately adaptable to large-scale genetic manipulation, it is first necessary to generate strains such as auxotrophic mutants that can be grown and selected without expensive antibiotics. UV mutagenesis is one such approach that allows for quick nonspecific mutation of auxotrophic genes7,41. Survival curves can easily be generated (Figures 1 and 2) to determine the appropriate dose for screening mutants. However, this approach carries the risk of inducing off target mutations that may affect growth rate or other properties of the yeast strain. Targeted knockouts can instead be generated using PCR constructs or the CRISPR/Cas9 system. Subsequent screening or selection (Figure 3) of mutants allows for identification of auxotrophic yeast. Use of selection by plating onto 5-FOA media, for example, allows for rapid elimination of any yeast still containing a functional URA3 auxotrophic gene. When possible, this selection approach may be preferable to a screen, which requires analysis of all colonies generated. With either selection or screening, however, it is critical to perform repeated streaking of individual yeast colonies onto selective media to confirm auxotrophic status.
Transformation of the generated mutants can be accomplished through different protocols. Although LiOAc transformation is effective in the transformation of many yeast strains, particularly for the most commonly used laboratory S. cerevisiae strains, alternative protocols such as electroporation may transform other yeast isolates with greater efficiency (Figure 4). Each new strain should be tested using multiple protocols to determine the optimal conditions for transformation. Varying incubation times and concentration of DNA, for example, can influence overall transformation efficiency and should be tested and optimized for each strain33.
Oral gavage allows for the delivery of controlled doses of these recombinant yeast directly to the murine gastrointestinal tract, whose immune tissues can then be assayed for yeast and heterologous protein. Proper oral gavage technique (Figure 6) is critical to minimize animal discomfort and increase experimental precision. Furthermore, the Peyer&#39;s patches are key sites to assess uptake of recombinant yeast from the intestine. These clusters of immune tissue are important sites of antigen sampling and induction of mucosal immune responses. Large antigens, including yeast 3-6 &#181;m in diameter, are most likely to be taken up by the M cells of Peyer&#39;s patches in order to cross the gastrointestinal epithelium and interact with immune cells. Care must be taken when dissecting the Peyer&#39;s patches to ensure that only cells from within the patch rather than the intestinal lumen or lamina propria are collected (Figure 7). Further steps must also be taken following dissection to assess proper expression and function of heterologous protein in the recovered yeast (Figure 8). Preparation of total protein from yeast lysates and immunoblotting is one standard method to assess protein expression; however, this approach does not provide information regarding protein folding and function. To assess protein function, yeast can be transformed with a plasmid encoding GFP and analyzed under a fluorescent microscope after recovery from Peyer&#39;s patches to assess functional GFP expression (Figure 5).
In sum, this manuscript presents a unified set of detailed experimental protocols spanning steps from the generation of auxotrophic mutants to the recovery of probiotic yeast from the murine intestine. By compiling protocols that do not traditionally fall within a single area of expertise, these descriptions will facilitate further studies testing immunological responses to probiotic yeast designed as oral drug delivery vectors. The authors hope this study will encourage discussion and promote optimization of experimental methods for each yeast strain tested, paving the way for the most efficient approaches to the development of novel, probiotic-based recombinant therapies.

Probiotic microorganisms are an intriguing potential means of efficiently and economically delivering heterologous proteins to the gastrointestinal tract. These organisms are capable of surviving passage through the gastrointestinal tract yet do not colonize it1, enabling controlled dosing and limiting exposure to the drug expressed. Furthermore, the ability to easily engineer these organisms to produce heterologous protein on a large scale renders them an economical alternative to synthetic delivery particles. However, development of such an approach, as recently demonstrated using an auxotrophic strain of the probiotic yeast Saccharomyces boulardii2, requires knowledge of laboratory techniques not traditionally combined within a given study, ranging from yeast and molecular biology to animal handling techniques and immunological methods. Thus although the individual procedures described herein are not in themselves novel laboratory protocols, the goal of this manuscript is to present a unified introduction to techniques needed for experimental testing of probiotic yeast as drug delivery vehicles to the murine gastrointestinal tract. Provided is a compilation of essential protocols for: 1) generation of auxotrophic mutant strains of yeast that can easily be genetically manipulated; 2) transformation of yeast cultures to express heterologous protein; 3) administration of recombinant yeast to the intestine via oral gavage; and 4) recovery of viable recombinant probiotic yeast from the murine intestine and assessment of their heterologous protein expression.
First, although numerous positive and negative selection methods exist for the manipulation of yeast species, negative selection such as through the use of auxotrophic markers increases both the efficiency and ease with which yeast can be transformed and selected. Positive selection of transformants using antibiotics, in contrast, significantly increases the cost of yeast manipulation. Furthermore, selection of yeast on antibiotic-containing solid media can allow for increased growth of untransformed background colonies relative to selection of auxotrophic yeast on synthetic drop out solid media (unpublished observations). Auxotrophic yeast is strains which lack enzymes critical for the synthesis of essential amino acids or uracil. Such yeast can grow only if supplemented with the missing metabolite or metabolic gene, thus enabling negative selection when yeast is plated onto synthetic drop out media that lacks the essential metabolite. Many commonly used Saccharomyces cerevisiae laboratory strains are in fact already auxotrophic mutants3. Industrial, clinical, and probiotic yeast strains, however, are typically prototrophic with the ability to synthesize all required nutrients. To enable more efficient genetic manipulation of such yeast, auxotrophic genes can be selectively targeted to generate strains that can be selected without antibiotics. Specific targeting of auxotrophic marker genes can be achieved through PCR-mediated gene disruption relying on homologous recombination or more recently through CRISPR/Cas9 targeting4-6. Alternatively, UV mutagenesis can quickly generate auxotrophic mutants even in yeast strains for which transformation with multiple plasmids is technically difficult7. While PCR targeting and CRISPR/Cas9 have been described extensively elsewhere, presented in part one of this manuscript is a detailed protocol describing a UV mutagenesis approach to create auxotrophic strains that will allow for negative selection rather than positive antibiotic selection of yeast transformants.
The next necessary step in the use of such auxotrophic strains for oral delivery of heterologous protein is yeast transformation with plasmid DNA. Since the first successful transformation of yeast spheroplasts reported for Saccharomyces cerevisiae in 19788, numerous modifications have been characterized to increase the efficiency and ease with which yeast species can be genetically modified. Use of electroporation for the successful transformation of DNA into S. cerevisiae was first described in 19859 and has since been improved via the addition of 1 M sorbitol incubation to osmotically support cells10. Electroporation efficiency has furthermore been shown to depend on the yeast species and strain, cell number and phase of growth, electroporation volume, field strength, and specific buffers11. Lithium acetate (LiOAc) transformation, originally described by Ito et al.12, is among the most commonly used transformation protocols as it requires no special equipment. Additional analyses showed that the efficiency of LiOAc yeast transformation greatly increases when cells are collected in mid-log phase of growth and are heat shocked in the presence of polyethylene glycol (PEG) and DNA at 42 &#176;C12. Incubation of whole intact yeast with PEG is essential for efficient transformation, possibly through improving attachment of DNA to the cell membrane as well as via other effects on the membrane13. Lithium itself also increases the permeability of intact cells14. Although most laboratory S. cerevisiae strains can easily be transformed using LiOAc transformation3, other yeast species may be more efficiently transformed using alternative protocols. Pichia pastoris, for example, is most efficiently transformed via electroporation rather than LiOAc transformation13. It is crucial, therefore, to test multiple methods of transformation and to optimize incubation periods and reagent concentrations when attempting to genetically modify an uncharacterized yeast strain. This manuscript thus describes both LiOAc transformation and electroporation as techniques for the transformation of auxotrophic mutant and wild type S. boulardii. Interested readers are directed to recent reviews for thorough descriptions of the evolution of yeast transformation, alternative protocols, and further discussions of possible mechanisms of action13,15. Transformation of yeast with plasmid encoding an easily detectable protein is furthermore essential for downstream testing in order to ensure proper expression and function of heterologous protein. Myriad different proteins may be selected depending on the ultimate purpose of the therapeutic study and the antibodies available for protein detection by immunoblotting, ELISA, and other techniques. Protocols for these techniques have been thoroughly described elsewhere16,17, and can be used to determine levels of heterologous protein production from transformed yeast by comparison to standard curves. For purposes of demonstration and to show successful production of a very commonly used protein in yeast biology, this manuscript presents transformation with plasmid encoding green fluorescent protein (GFP), which allows for subsequent detection using fluorescence microscopy.
Equally important to the production of probiotic organisms that express heterologous protein is the proper administration and detection of these microorganisms within gastrointestinal tissues, as described in parts three and four. Administration of recombinant yeast via oral gavage allows for delivery of controlled quantities of yeast directly into the stomach, from which C57BL/6 mice are naturally incapable of vomiting18. However, improper animal handling and gavage can lead to esophageal damage and perforation, gastric perforation, tracheal administration, and aspiration pneumonia19,20. Poor technique and inexperience can furthermore increase variability in murine immune responses and experimental results, which have been attributed to animal stress upon oral gavage21,22. Practice in the proper technique can thus not only attenuate animal discomfort, but can also increase precision of experimental results. This manuscript describes and demonstrates animal handling and oral gavage for the administration of controlled doses of recombinant yeast.
Finally, it is vital to confirm successful delivery of recombinant yeast by analyzing lymphoid tissues for the presence of yeast and heterologous protein. The gastrointestinal immune tissues which can most easily and predictably be examined for the presence of yeast are the Peyer&#39;s patches. Peyer&#39;s patches are secondary lymphoid organs along the small intestine that are key sites of mucosal immune response induction23. Antigens from the lumen are transferred transcellularly through microfold (M) cells in the epithelium and are released into the Peyer&#39;s patches, thus exposing enclosed antigen presenting cells to intestinal luminal contents. Although particle uptake across the intestinal epithelium can also be achieved by goblet cells, these cells have been shown to only take up particles less than 0.02 &#181;m in diameter24. Transepithelial dendrites extended from CD103+ dendritic cells (DC) also take up small particles from the intestinal lumen25; however, there are currently no reports demonstrating that CD103+ DCs take up particles larger than bacteria. Thus, intact probiotic yeast, of average size between 3-6 &#181;m in diameter, are most likely to be taken up by M cells and transferred to the Peyer&#39;s patches. Described here is a protocol for collection and screening of Peyer&#39;s patches for viable recombinant yeast, although this procedure can also be easily adapted for evaluating uptake of probiotic bacteria.
In summary, assessing recombinant probiotic yeast for the delivery of therapeutic proteins to the intestine requires proficiency in laboratory techniques spanning molecular biology to animal handling and immunology. Presented here are protocols for 1) the generation and screening of auxotrophic yeast strains which can be easily negatively selected without antibiotics, 2) alternative protocols to transform yeast and enable expression of heterologous protein, 3) demonstrations of proper animal handling techniques and oral gavage for intragastric delivery of recombinant yeast, and 4) protocols for Peyer&#39;s patch dissection and screening for viable recombinant yeast and functional heterologous protein. Combined, these protocols will allow for the generation and testing of a probiotic yeast strain capable of delivering heterologous therapeutic protein to the gastrointestinal tract.

<table><tbody><tr><td>SmartSpec 3000 Spectrophotometer</td><td>BioRad</td><td>170-2501</td><td>Example of spectrophotometer for determining cell concentration and OD&lt;sub&gt;600&lt;/sub&gt; of yeast cultures</td></tr><tr><td>New Brunswick Roller Drum</td><td>Eppendorf</td><td>M1053-4004</td><td>Example of roller drum for yeast culture incubation</td></tr><tr><td>UV Stratalinker 2400</td><td>Stratagene</td><td>400075-03</td><td>Example stratalinker</td></tr><tr><td>Stuart Colony Counter SC6PLUS</td><td>11983044</td><td>Fisher Scientific</td><td>Plate stand with magnification records colony count upon sensing pressure from pen</td></tr><tr><td>Scienceware Colony Counter&amp;nbsp;</td><td>F378620002</td><td>Bel-Art Scienceware</td><td>Hand held colony counter pen</td></tr><tr><td>Replica plating device</td><td>Fisherbrand</td><td>09-718-1</td><td>Example of replica plating stand and pads&amp;nbsp;</td></tr><tr><td>Velveteen squares</td><td>Fisherbrand</td><td>09-718-2</td><td></td></tr><tr><td>L shaped sterile cell spreaders&amp;nbsp;</td><td>Fisherbrand</td><td>14665230</td><td></td></tr><tr><td>Deoxyribonucleic acid, single stranded from salmon testes</td><td>Sigma-Aldrich</td><td>D7656-1ML</td><td>Example carrier DNA for yeast LiOAc transformation</td></tr><tr><td>Gavage needles</td><td>Braintree Scientific</td><td>N-PK&amp;nbsp;002</td><td>For mice 15-20 g, the suggested needle is a 22 gauge (1.25 mm ball), 1 in long, straight reusable gavage needle. For mice weighing greater than 20&amp;nbsp;g, 20 gauge or larger straight or curved gavage needles may be used</td></tr><tr><td>1 ml sterile slip-tip disposable tuberculin syringe</td><td>Becton Dickinson</td><td>BD 309659</td><td></td></tr><tr><td>Blunt forceps such as Electron Microscopy Sciences 7&quot; (178 mm) serrated tip, broad grip forceps</td><td>Electron Microscopy Sciences</td><td>77937-28</td><td>Example of blunt forceps needed for dissection&amp;nbsp;</td></tr><tr><td>Straight and curved dissection scissors</td><td>Electron Microscopy Sciences</td><td>72966-02 and 72966-03</td><td>Examples of scissors needed for dissection</td></tr><tr><td>IMDM</td><td>Life technologies</td><td>12440053</td><td></td></tr></tbody></table>

transformation of probiotic yeast and their recovery from gastrointestinal immune tissues following oral gavage in mice

Development of recombinant oral therapy would allow for more direct targeting of the mucosal immune system and improve the ability to combat gastrointestinal disorders. Adapting probiotic yeast in particular for this approach carries several advantages. These strains have not only the potential to synthesize a wide variety of complex heterologous proteins but are also capable of surviving and protecting those proteins during transit through the intestine. Critically, however, this approach requires expertise in many diverse laboratory techniques not typically used in tandem. Furthermore, although individual protocols for yeast transformation are well characterized for commonly used laboratory strains, emphasis is placed here on alternative approaches and the importance of optimizing transformation for less well characterized probiotic strains. Detailing these methods will help facilitate discussion as to the best approaches for testing probiotic yeast as oral drug delivery vehicles and indeed serve to advance the development of this novel strategy for gastrointestinal therapy.

Generation of a survival curve following UV irradiation requires plating of diluted yeast cells such that distinct colony forming units (CFU) are able to form. Each 500 &#181;l sample collected as described above contains approximately 5 x 106 cells; however, greater than 100 colonies per plate are difficult to accurately distinguish. Plating undiluted sample as well as serial 1:10 dilutions of irradiated cells thus ensures that CFU can be enumerated at each UV dose, as demonstrated in Figure 1. The CFU count, multiplied by the dilution factor, is then divided by the total number of original irradiated cells in each 500 &#181;l sample in order to determine percent survival at each dose. Figure 2 shows the calculated percentage of diploid wild type S. boulardii cells able to survive 0 &#181;J, 5,000 &#181;J, 10,000 &#181;J, 15,000 &#181;J, 20,000 &#181;J, 22,500 &#181;J, 25,000 &#181;J, 35,000 &#181;J, and 50,000 &#181;J. These data establish a clear curve that can be used to find the dose corresponding to 50% survival.
After selection of UV dose and irradiation of yeast cells, it is critical to screen mutant colonies to confirm lack of a functional auxotrophic marker gene. Use of a selection method, as described in 1.2.3.1 and shown in Figure 3, significantly increases the efficiency of phenotype confirmation. Shown is an example of URA3 selection that takes advantage of the conversion of 5-FOA to the toxin 5-FU by intact Ura3. Analogous approaches are available for LYS2 and LYS5; TRP1; and MET2 and MET15 and increase efficiency of selection for these mutations. Care must be taken to select individual colonies during screening. The consistent growth of mutant colonies on YPD and 5-FOA, but not uracil-, plates indicates auxotrophic phenotype.
Figure 4 shows transformation efficiency for wild type S. boulardii (S.b.) relative to a commonly used laboratory S. cerevisiae strain (S.c.) using both the LiOAc (LiOAc) and electroporation (Electro) techniques. Although LiOAc transformation is very efficient for S. cerevisiae, transformation efficiency for S. boulardii is greatly improved using electroporation. Figure 5 shows use of fluorescence microscopy as an example method of analyzing proper protein expression from transformed yeast. Brightfield (A) and fluorescence (B) images are shown for S. cerevisiae transformed with a URA3 plasmid encoding GFP, demonstrating functional expression of heterologous protein from the transformed yeast. Cells can be immobilized for better visualization using coverslips coated in concanavalin A (coat 5 &#181;l of a 2 mg/ml stock solution in water onto each 22 x 22 &#181;m coverslip and air dry).
Figure 6A shows a C57BL/6 mouse held just prior to oral gavage. The hand grasps the back and neck of the mouse firmly such that the mouse is not able to move the head in any direction. This hold allows the gavage needle to be placed accurately and with decreased risk of tissue damage. Figure 6B shows the gavage needle held after the mouse swallows the gavage needle. Following the incubation period, the small intestine of the sacrificed mouse should be carefully teased apart from the surrounding tissues, as shown in Figure 7. This manipulation allows for easy identification of Peyer&#39;s patches and for clean dissection of the patches without collecting any of the surrounding lamina propria. Finally, Figure 8 shows typical recovery of viable yeast CFU from Peyer&#39;s patches.
<table fo:keep-together.within-page="1">
	<tbody>
		<tr>
			<td>Solutions</td>
			<td>Yeast Media and Plates</td>
			<td>Transformation Reagents</td>
		</tr>
		<tr>
			<td>Polyethylene glycol (PEG) 50%:</td>
			<td>YPD:</td>
			<td>TE/LiOAc:</td>
		</tr>
		<tr>
			<td>250 g PEG 3350</td>
			<td>20 g peptone</td>
			<td>50 ml 10x TE</td>
		</tr>
		<tr>
			<td>500 ml sterile water</td>
			<td>20 g dextrose</td>
			<td>50 ml 10x (1M) LiOAc</td>
		</tr>
		<tr>
			<td>Filter sterilize</td>
			<td>10 g yeast extract</td>
			<td>400 ml sterile water</td>
		</tr>
		<tr>
			<td></td>
			<td>1 L water</td>
			<td>Filter sterilize</td>
		</tr>
		<tr>
			<td></td>
			<td>Autoclave</td>
			<td></td>
		</tr>
		<tr>
			<td>TE 10x:</td>
			<td>YPD plates:</td>
			<td>PEG/TE/LiOAc:</td>
		</tr>
		<tr>
			<td>100 mM Tris</td>
			<td>20 g peptone</td>
			<td>400 ml 50% PEG</td>
		</tr>
		<tr>
			<td>10 mM EDTA</td>
			<td>20 g dextrose</td>
			<td>50 ml 10x TE</td>
		</tr>
		<tr>
			<td>pH to 7.5 and filter sterilize</td>
			<td>20 g agar</td>
			<td>50 ml 10x (1M) LiOAc</td>
		</tr>
		<tr>
			<td></td>
			<td>10 g yeast extract</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>1 L water</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Autoclave</td>
			<td></td>
		</tr>
		<tr>
			<td>20% glucose:</td>
			<td>Uracil- selective media</td>
			<td>Carrier DNA (SS DNA):</td>
		</tr>
		<tr>
			<td>200 g dextrose</td>
			<td>2 g amino acid mix lacking uracil</td>
			<td>Store at -20 &#176;C and prior to use heat for 1-2 min at 100 &#176;C to melt strands and store on ice</td>
		</tr>
		<tr>
			<td>1 L water</td>
			<td>6.7 g yeast nitrogen base without amino acids</td>
			<td></td>
		</tr>
		<tr>
			<td>Filter sterilize</td>
			<td>1 L water</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Sterilize by autoclaving or sterile filtering</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Add 20% glucose 1:10 before use</td>
			<td></td>
		</tr>
		<tr>
			<td>50% glycerol:</td>
			<td>Uracil- plates:</td>
			<td>Electroporation buffer:</td>
		</tr>
		<tr>
			<td>500 ml glycerol</td>
			<td>In a 250 ml flask:</td>
			<td>1 M Sorbitol</td>
		</tr>
		<tr>
			<td>500 ml water</td>
			<td>2 g amino acid mix lacking uracil</td>
			<td>1 mM CaCl2</td>
		</tr>
		<tr>
			<td>Autoclave</td>
			<td>6.7 g yeast nitrogen base without amino acids</td>
			<td>Fill with distilled water</td>
		</tr>
		<tr>
			<td></td>
			<td>150 ml water</td>
			<td>Autoclave and store at 4 &#176;C</td>
		</tr>
		<tr>
			<td></td>
			<td>In a 2 L flask:</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>20 g agar</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>750 ml water</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Autoclave flasks separately, then mix together with 100 ml 20% glucose</td>
			<td></td>
		</tr>
		<tr>
			<td>Complete IMDM</td>
			<td>5-FOA+ plates:</td>
			<td>LiOAc/DTT</td>
		</tr>
		<tr>
			<td>500 ml Iscove&#39;s Modified Dulbecco&#39;s Media</td>
			<td>Autoclave in a 2 L flask:</td>
			<td>0.1 M LiOAc</td>
		</tr>
		<tr>
			<td>5 ml penicillin streptomycin glutamine 100x</td>
			<td>20 g agar</td>
			<td>10 mM DTT</td>
		</tr>
		<tr>
			<td>500 &#956;l 2-mercaptoethanol</td>
			<td>750 ml water</td>
			<td></td>
		</tr>
		<tr>
			<td>10% heat inactivated fetal bovine serum&#160;</td>
			<td>Mix:</td>
			<td></td>
		</tr>
		<tr>
			<td>2.5 ml sodium pyruvate 100 mM</td>
			<td>6.7 g yeast nitrogen base without amino acids</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>2 g amino acid mix without uracil</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>150 ml warm water</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>When cool, add:</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>0.05 g uracil powder</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>1 g 5-FOA</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Stir and filter sterilize</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Add to autoclaved agar solution</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Mix with 100 ml 20% glucose</td>
			<td></td>
		</tr>
	</tbody>
</table>
Table 1. Reagents List. Described are the reagents needed for making each of the solutions, yeast media and plates, and transformation buffers used for the protocols in this manuscript.
<img alt="Figure 1" src="/files/ftp_upload/53453/53453fig1.jpg" /> 
Figure 1. Yeast colonies grown on YPD media. Example YPD plate showing viable colony forming units (CFU) of probiotic yeast after UV irradiation. Cells were serially diluted such that individual CFU can be distinguished and counted. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/53453/53453fig2.jpg" /> 
Figure 2. Survival curve for diploid probiotic yeast. Number of viable S. boulardii CFU as a percent of total plated cells was plotted for each &#181;J dose of UV irradiation (solid line). The vertical red line indicates the &#181;J UV dose corresponding to 50% survival of this yeast strain. A rad1 S. cerevisiae mutant, which cannot repair damage from UV mutagenesis, is shown as a control (dashed line). <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" src="/files/ftp_upload/53453/53453fig3.jpg" /> 
Figure 3. Confirmation of ura3- phenotype of UV irradiated cells on YPD, uracil-, and 5-FOA plates. Cells from individual UV mutant colonies were collected using the tip of a sterile toothpick and gently streaked across YPD, uracil-, and 5-FOA plates. Cells were first streaked in two perpendicular crossing lines, then a new toothpick was used to pass through the second line and continue spreading cells until individual cells separate. A true ura3- mutant (mut) grows on YPD media and in the presence of 5-FOA, but not in the absence of uracil. Control ura3- S. cerevisiae (ura3-) and URA3+ S. boulardii (URA3+) are shown for comparison and to confirm proper preparation of yeast media. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" src="/files/ftp_upload/53453/53453fig4.jpg" /> 
Figure 4. Transformation Efficiency of Saccharomyces strains.&#160; Wild type S. boulardii (S.b.) and a laboratory S. cerevisiae strain (S.c.) were transformed using the described LiOAc (LiOAc) and electroporation (Electro) protocols. Results are plotted as mean CFU obtained per &#181;g of plasmid encoding a kanamycin resistance marker. Bars show the mean of duplicate experiments with error bars depicting the standard error of the mean. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" src="/files/ftp_upload/53453/53453fig5.jpg" /> 
Figure 5. Functional Protein Expression by Transformed Yeast. S. cerevisiae transformed with empty plasmid (A) and plasmid encoding GFP (B) were analyzed using a fluorescent microscope. Fluorescence in the yeast cells transformed with GFP plasmid indicates successful production of functional GFP. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" src="/files/ftp_upload/53453/53453fig6.jpg" /> 
Figure 6. Proper handling of a C57BL/6 mouse for oral gavage. The mouse is held tightly in the non-dominant hand with the tail tucked under the small finger so that no movement is possible (A). The gavage needle is inserted into the pharynx along the roof of the mouth. The mouse is allowed to swallow the bulb of the gavage needle, allowing the solution to then enter the stomach as the plunger is depressed (B). <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" src="/files/ftp_upload/53453/53453fig7.jpg" /> 
Figure 7. Preparation and dissection of Peyer&#39;s patches. The small intestine is shown dissected away from the other internal organs and tissue, with arrows pointing to a few of the Peyer&#39;s patches. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig7large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 8" src="/files/ftp_upload/53453/53453fig8.jpg" /> 
Figure 8. Yeast Recovery from Peyer&#39;s Patches. An example of viable CFU detected after dissection, homogenization, and plating of total Peyer&#39;s patch cells from a mouse gavaged with S. boulardii. Cells were plated onto YPD yeast media and incubated at 30 &#176;C for 2 days. Typical yield of CFU recovered per mouse is less than 10. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/53453/53453fig8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Transformation of Probiotic Yeast and Their Recovery from Gastrointestinal Immune Tissues Following Oral Gavage in Mice at JoVE.com

Transformation of Probiotic Yeast and Their Recovery from Gastrointestinal Immune Tissues Following Oral Gavage in Mice

Presented here is a unified description of techniques that can be used to develop, transform, administer, and test heterologous protein expression of the probiotic yeast Saccharomyces boulardii.

Development of recombinant oral therapy would allow for more direct targeting of the mucosal immune system and improve the ability to combat ...

transformation-probiotic-yeast-their-recovery-from-gastrointestinal

Universidad San Sebastian

Research

JoVE Journal

Immunology and Infection

12.3K Views.  Emory University School of Medicine. Presented here is a unified description of techniques that can be used to develop, transform, administer, and test heterologous protein expression of the probiotic yeast Saccharomyces boulardii.

Video: Transformation of Probiotic Yeast and Their Recovery from Gastrointestinal Immune Tissues Following Oral Gavage in Mice

Genetic Engineering of an Unconventional Yeast for Renewable Biofuel and Biochemical Production

Yarrowia lipolytica is a non-pathogenic, dimorphic and strictly aerobic yeast species. Owing to its distinctive physiological features and metabolic characteristics, this unconventional yeast is not only a good model for the study of the fundamental nature of fungal differentiation but is also a promising microbial platform for biochemical production and various biotechnological applications, which require extensive genetic manipulations. However, genetic manipulations of Y. lipolytica have been limited due to the lack of an efficient and stable genetic transformation system as well as very high rates of non-homologous recombination that can be mainly attributed to the KU70 gene. Here, we report an easy and rapid protocol for the efficient genetic transformation and for gene deletion in Y. lipolytica Po1g. First, a protocol for the efficient transformation of exogenous DNA into Y. lipolytica Po1g was established. Second, to achieve the enhanced double-crossover homologous recombination rate for further deletion of target genes, the KU70 gene was deleted by transforming a disruption cassette carrying 1 kb homology arms. Third, to demonstrate the enhanced gene deletion efficiency after deletion of the KU70 gene, we individually deleted 11 target genes encoding alcohol dehydrogenase and alcohol oxidase using the same procedures on the KU70 knockout platform strain. It was observed that the rate of precise homologous recombination increased substantially from less than 0.5% for deletion of the KU70 gene in Po1g to 33%-71% for the single gene deletion of the 11 target genes in Po1g KU70&#916;. A replicative plasmid carrying the hygromycin B resistance marker and the Cre/LoxP system was constructed, and the selection marker gene in the yeast knockout strains was eventually removed by expression of Cre recombinase to facilitate multiple rounds of targeted genetic manipulations. The resulting single-gene deletion mutants have potential applications in biofuel and biochemical production.

We herein report methods on the molecular genetic manipulation of the Yarrowia lipolytica Po1g strain for improved gene deletion efficiency. The resulting engineered Y. lipolytica strains have potential applications in biofuel and biochemical production.

Yarrowia lipolytica is a non-pathogenic, dimorphic and strictly aerobic yeast species. Owing to its distinctive physiological features and metabolic ...

Genetics

A Double Humanized BLT-mice Model Featuring a Stable Human-Like Gut Microbiome and Human Immune System

Humanized mice (hu-mice) that feature a functional human immune system have fundamentally changed the study of human pathogens and disease. They can be used to model diseases that are otherwise difficult or impossible to study in humans or other animal models. The gut microbiome can have a profound impact on human health and disease. However, the murine gut microbiome is very different than the one found in humans. &#160;There is a need for improved pre-clinical hu-mice models that have an engrafted human gut microbiome. Therefore, we created double hu-mice that feature both a human immune system and stable human-like gut microbiome. NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice are one of the best animals for humanization due to their high level of immunodeficiency. However, germ-free NSG mice, and various other important germ-free mice models are not currently commercially available. Further, many research settings do not have access to gnotobiotic facilities, and working under gnotobiotic conditions can often be expensive and time consuming. Importantly, germ-free mice have several immune deficiencies that exist even after the engraftment of microbes. Therefore, we developed a protocol that does not require germ-free animals or gnotobiotic facilities. To generate double hu-mice, NSG mice were treated with radiation prior to surgery to create bone-marrow, liver, thymus-humanized (hu-BLT) mice. The mice were then treated with broad spectrum antibiotics to deplete the pre-existing murine gut microbiome. After antibiotic treatment, the mice were given fecal transplants with healthy human donor samples via oral gavage. Double hu-BLT mice had unique 16S rRNA gene profiles based on the individual human donor sample that was transplanted. Importantly, the transplanted human-like microbiome was stable in the double hu-BLT mice for the duration of the study up to 14.5 weeks post-transplant.

We describe a novel method for generating double humanized BLT-mice that feature a functional human immune system and a stable engrafted human-like gut microbiome. This protocol can be followed without the need for germ-free mice or gnotobiotic facilities.

Humanized mice (hu-mice) that feature a functional human immune system have fundamentally changed the study of human pathogens and disease. They can be ...

Biochemistry

Probiotic Studies in Neonatal Mice Using Gavage

Adult mouse models have been widely used to understand the mechanism behind disease progression in humans. The applicability of studies done in adult mouse models to neonatal diseases is limited. To better understand disease progression, host responses and long-term impact of interventions in neonates, a neonatal mouse model likely is a better fit. The sparse use of neonatal mouse models can in part be attributed to the technical difficulties of working with these small animals. A neonatal mouse model was developed to determine the effects of probiotic administration in early life and to specifically assess the ability to establish colonization in the newborn mouse intestinal tract. Specifically, to assess probiotic colonization in the neonatal mouse, Lactobacillus plantarum (LP) was delivered directly into the neonatal mouse gastrointestinal tract. To this end, LP was administered to mice by feeding through intra-esophageal (IE) gavage. A highly reproducible method was developed to standardize the process of IE gavage that allows an accurate administration of probiotic dosages while minimizing trauma, an aspect particularly important given the fragility of newborn mice. Limitations of this process include possibilities of esophageal irritation or damage and aspiration if gavaged incorrectly. This approach represents an improvement on current practices because IE gavage into the distal esophagus reduces the chances of aspiration. Following gavage, the colonization profile of the probiotic was traced using quantitative polymerase chain reaction (qPCR) of the extracted intestinal DNA with LP specific primers. Different litter settings and cage management techniques were used to assess the potential for colonization-spread. The protocol details the intricacies of IE neonatal mouse gavage and subsequent colonization quantification with LP.

This study details the process of gavaging precise amounts of probiotics to neonatal mice. The experimental set-up was optimized to include but is not limited to probiotic dosing, methods of administration, and quantification of bacteria in the intestines.

Adult mouse models have been widely used to understand the mechanism behind disease progression in humans. The applicability of studies done in adult ...

An Intestinal Gut Organ Culture System for Analyzing Host-Microbiota Interactions

The structure of the gut tissue facilitates close and mutualistic interactions between the host and the gut microbiota. These cross-talks are crucial for maintaining local and systemic homeostasis; changes to gut microbiota composition (dysbiosis) associate with a wide array of human diseases. Methods for dissecting host-microbiota interactions encompass an inherent tradeoff among preservation of physiological tissue structure (when using in vivo animal models) and the level of control over the experiment factors (as in simple in vitro cell culture systems). To address this tradeoff, Yissachar et al. recently developed an intestinal organ culture system. The system preserves a naive colon tissue construction and cellular mechanisms and it also permits tight experimental control, facilitating experimentations that cannot be readily performed in vivo. It is optimal for dissecting short-term responses of various gut components (such as epithelial, immunological and neuronal elements) to luminal perturbations (including anaerobic or aerobic microbes, whole microbiota samples from mice or humans, drugs and metabolites). Here, we present a detailed description of an optimized protocol for organ culture of multiple gut fragments using a custom-made gut culture device. Host responses to luminal perturbations can be visualized by immunofluorescence staining of tissue sections or whole-mount tissue fragments, fluorescence in-situ hybridization (FISH), or time-lapse imaging. This system supports a wide array of readouts, including next-generation sequencing, flow cytometry, and various cellular and biochemical assays. Overall, this three-dimensional organ culture system supports the culture of large, intact intestinal tissues and has broad applications for high-resolution analysis and visualization of host-microbiota interactions in the local gut environment.

This article presents a unique method for analyzing host-microbiome interactions using a novel gut organ culture system for ex vivo experiments.

The structure of the gut tissue facilitates close and mutualistic interactions between the host and the gut microbiota. These cross-talks are crucial for ...

Therapeutic Evaluation of Fecal Microbiota Transplantation in an Interleukin 10-Deficient Mouse Model

With the development of microecology in recent years, the relationship between intestinal bacteria and inflammatory bowel disease (IBD) has attracted considerable attention. Accumulating evidence suggests that dysbiotic microbiota plays an active role in triggering or worsening the inflammatory process in IBD and that fecal microbiota transplantation (FMT) is an attractive therapeutic strategy since transferring a healthy microbiota to IBD patient could restore the appropriate host-microbiota communication. However, the molecular mechanisms are unclear, and the efficacy of FMT has not been very well established. Thus, further studies in animal models of IBD are necessary. In this method, we applied FMT from wild-type C57BL/6J mice to IL-10 deficient mice, a widely used mouse model of colitis. The study elaborates on collecting fecal pellets from the donor mice, making the fecal solution/suspension, administering the fecal solution, and monitoring the disease. We found that FMT significantly mitigated the cardiac impairment in IL-10 knockout mice, underlining its therapeutic potential for IBD management.

The interaction of genetic susceptibility, mucosal immunity, and intestinal microecological environment is involved in the pathogenesis of inflammatory bowel disease (IBD). In this study, we applied fecal microbiota transplantation to IL-10 deficient mice and investigated its impact on colonic inflammation and heart function.

With the development of microecology in recent years, the relationship between intestinal bacteria and inflammatory bowel disease (IBD) has attracted ...

Murine Fecal Isolation and Microbiota Transplantation

Gut microbiota dysbiosis plays a role in the pathophysiology of cardiovascular and metabolic disorders, but the mechanisms are not well understood. Fecal microbiota transplantation (FMT) is a valuable approach to delineating a direct role of the total microbiota or isolated species in disease pathophysiology. It is a safe treatment option for patients with recurrent Clostridium difficile infection. Preclinical studies demonstrate that manipulating the gut microbiota is a useful tool to study the mechanistic link between dysbiosis and disease. Fecal microbiota transplantation may help elucidate novel gut microbiota-targeted therapeutics for the management and treatment of cardiometabolic disease. Despite a high success rate in rodents, there remains translational changes associated with the transplantation. The goal here is to provide guidance in studying the effects of gut microbiome in experimental cardiovascular disease. In this study, a detailed protocol for the collection, handling, processing, and transplantation of fecal microbiota in murine studies is described. The collection and processing steps are described for both human and rodent donors. Lastly, we describe using a combination of the Swiss-rolling and immunostaining techniques to assess gut-specific morphology and integrity changes in cardiovascular disease and related gut microbiota mechanisms.

The goal here is to outline a protocol to investigate the mechanisms of dysbiosis in cardiovascular disease. This paper discusses how to aseptically collect and transplant murine fecal samples, isolate intestines, and use the "Swiss-roll" method, followed by immunostaining techniques to interrogate changes in the gastrointestinal tract.

Gut microbiota dysbiosis plays a role in the pathophysiology of cardiovascular and metabolic disorders, but the mechanisms are not well understood. Fecal ...

Preparation and Maintenance of Bioexclusion IsoPositive Cage Experiment for Human Fecal Transplantation into Germ-Free Mice

Germ-free mice are an important investigation tool for understanding the contribution of microorganisms in host health and disease, enabling assessment of the specific role of individuals, defined or complex groups of microorganisms in host response. Traditionally bred and reared in flexible-film or semi-rigid isolators, germ-free mouse husbandry and experimental manipulation are costly and require numerous trained staff and a large space footprint in animal housing facilities. The IsoPositive caging system allows for experimental manipulation of germ-free mice in individual, hermetically-sealed, positive-pressure isolator cages (isocages), reducing cost and enabling greater flexibility in experimental manipulations. 
Here, a protocol is described for transferring germ-free mice from breeding isolators to isocages and subsequent fecal transfer from human donor stool into mice to create stable long-term gut "humanized" mice for future studies. The materials and preparation needed for the utilization of the isocage system are described, including the use of chlorine-dioxide sterilant chemical sterilant to clean cages, supplies, equipment, and personal protective equipment. The methods for confirming the germ-free status of transferred mice and how to determine contamination in the caging system are discussed. The procedure for husbandry, including bedding, food, and water supply, is further discussed. The protocol for human fecal slurry preparation and gavage into germ-free mice to create gut "humanized" mice, along with stool collection to monitor the microbial community composition of these mice, are described. An experiment illustrates that two weeks post-human fecal transplant allows for stable colonization of donor microbiota in the murine hosts, enabling subsequent experimental usage. Furthermore, the collection of humanized mouse feces in viability preservation media, enabling use in further functional experiments, is described. Overall, these methods allow for the safe and effective establishment of humanized mouse communities in experimental gnotobiotic cages for further manipulation.

This protocol describes the best practices for germ-free mouse transfer to and housing in experimental single-cage isolators (isocages) while maintaining sterile conditions. Methods for fecal transplant into germ-free mice and the collection of viable bacteria from these gut "humanized" mice for further applications are discussed.

Germ-free mice are an important investigation tool for understanding the contribution of microorganisms in host health and disease, enabling assessment of ...

Fecal Microbiota Transplantation and Detection of Prevalence of IgA-Coated Bacteria in the Gut

Gut microbiota exert pleiotropic roles in human health and disease. Fecal microbiota transplantation (FMT) is an effective method to investigate the biological function of intestinal bacteria as a whole or at the species level. Several different FMT methods have been published. Here, we present an FMT protocol that successfully depletes gut microbiota in a matter of days, followed by transplantation of fecal microbiota from fresh or frozen donor intestinal contents to conventional mice. Real time-PCR is applied to test the efficacy of bacterial depletion. Sequencing of the 16S ribosomal RNA (rRNA) is then applied to test the relative abundance and identity of gut microbiota in recipient mice. We also present a flow cytometry-based detection method of immunoglobulin A (IgA)-coated bacteria in the gut.

We established an efficient way to deplete intestinal bacteria in three days, and subsequently transplant fecal microbiota via gavage of fecal fluid prepared from fresh or frozen intestinal contents in mice. We also present an optimized method to detect the frequency of IgA-coated bacteria in the gut.

Gut microbiota exert pleiotropic roles in human health and disease. Fecal microbiota transplantation (FMT) is an effective method to investigate the ...

Biology

Investigating the Alleviating Effects of Bacillus cereus Administration on Colitis through Gut Microbiota Modulation

Gut microbiota dysbiosis is thought to exert a role in the progression of colitis. However, the precise standards for probiotic administration in alleviating colitis remain undefined. Most analysis methods rely on limited diversity and abundance of gut microorganisms. Therefore, observational studies cannot establish causation. In this study, we applied antibiotic-induced pseudo-germ-free mice to investigate the role of gut microbiota in regulating the probiotic effects of Bacillus&#160;cereus (B. cereus)&#160;on dextran sulfate sodium (DSS)-induced colitis in mice. This process allows for evaluating the bidirectional regulating effect of B. cereus&#160;supplementation on health and provides stable and reproducible results. Here, the detailed protocols for B. cereus cultivation, gavage operation, stool collection, and antibiotic clearance treatment on colitis mice are provided. The optimization methods are also applicable for other chronic inflammatory-associated disorders. The results showed that B. cereus administration decreased body weight loss, colon length shortening, disease activity index, and histopathological scores. However, treatment with antibiotics suppressed the positive effect of B. cereus on colitis. These results indicate that gut microbiota are needed for the alleviating effects of B. cereus on colitis. Therefore, exploring the beneficial effects of probiotics in this research is a promising approach for developing novel treatment strategies for alleviating the symptoms of chronic inflammatory-associated disorders.

Investigating the Alleviating Effects of Bacillus cereus Administration on Colitis through Gut Microbiota Modulation

Here, we present a protocol to establish the antibiotic-induced pseudo-germ-free dextran sulfate sodium-induced colitis mouse model to investigate the role of gut microbiota in regulating the positive effects of Bacillus cereus on colitis.

Gut microbiota dysbiosis is thought to exert a role in the progression of colitis. However, the precise standards for probiotic administration in ...

Evaluating the Effects of Fecal Microbiota Transplantation in an Interleukin-10 Deficient Mouse

Source: Xiao, Y. et al., <a href="https://app-jove-com.bdigitaluss.remotexs.co/v/63350">Therapeutic Evaluation of Fecal Microbiota Transplantation in an Interleukin 10-Deficient Mouse Model.</a>&#160;J. Vis. Exp. (2022)
This video demonstrates a procedure of fecal microbiota transplantation in an interleukin-10 deficient mouse with colon inflammation. Colonized fecal microbes in the gut release secondary metabolites, eliciting anti-inflammatory cytokine release and reducing colon inflammation.

Ocena skutków przeszczepu mikrobioty kałowej u myszy z niedoborem interleukiny-10

All procedures involving animal models have been reviewed by the local institutional animal care committee and the JoVE veterinary review board.
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Transformation of Probiotic Yeast and Their Recovery from Gastrointestinal Immune Tissues Following Oral Gavage in Mice

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Genetic Engineering of an Unconventional Yeast for Renewable Biofuel and Biochemical Production

A Double Humanized BLT-mice Model Featuring a Stable Human-Like Gut Microbiome and Human Immune System

Probiotic Studies in Neonatal Mice Using Gavage

An Intestinal Gut Organ Culture System for Analyzing Host-Microbiota Interactions

Therapeutic Evaluation of Fecal Microbiota Transplantation in an Interleukin 10-Deficient Mouse Model

Murine Fecal Isolation and Microbiota Transplantation

Preparation and Maintenance of Bioexclusion IsoPositive Cage Experiment for Human Fecal Transplantation into Germ-Free Mice

Fecal Microbiota Transplantation and Detection of Prevalence of IgA-Coated Bacteria in the Gut

Investigating the Alleviating Effects of Bacillus cereus Administration on Colitis through Gut Microbiota Modulation

Ocena skutków przeszczepu mikrobioty kałowej u myszy z niedoborem interleukiny-10