The authors would like to acknowledge Vertex Pharmaceuticals and the Cystic Fibrosis Research Innovation Award for funding R. Quinn and the NIH/NIAID for funding grant 1 U01 AI124316-01, a systems biology approach to treatment of multi-drug resistant pathogens. We would also like to thank the Department of Mechanical and Aerospace Engineering at UCSD's undergraduate mechanical engineering senior design course for facilitating the collaboration with the engineering aspects of this work.

1. Preparation of Stocks for the Artificial Sputum Media
<ol>
	<li>Create a 5% mucin solution. Add 1.0 g of dehydrated pig stomach mucin to 20 mL of deionized water. Autoclave the resulting solution. 
	NOTE: The mucin sterilization will destroy its inherent structure; other methods to sterilize the mucin in its dry form include UV sterilization and irradiation. These methods have not been extensively used for the WinCF system however.</li>
	<li>Add 2.2 g of KCl to 50 mL of deionized water and allow for dissolution...

<ol>
	<li>Quinn, R. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Winogradsky-based+culture+system+shows+an+association+between+microbial+fermentation+and+cystic+fibrosis+exacerbation.">A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation.</a> ISME J . 9, 1024-1038 (2015).</li><li>Quinton, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cystic+fibrosis:+impaired+bicarbonate+secretion+and+mucoviscidosis.">Cystic fibrosis: impaired bicarbonate secretion and mucoviscidosis.</a> Lancet. 372 (9636), 415-417 (2008).</li><li>Harrison, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+ecology+of+the+cystic+fibrosis+lung.">Microbial ecology of the cystic fibrosis lung.</a> Microbiology. 153 (Pt 4), 917-923 (2007).</li><li>Caverly, L. J., Zhao, J., LiPuma, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cystic+fibrosis+lung+microbiome:+Opportunities+to+reconsider+management+of+airway+infection.">Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection.</a> Pediatr pulmonol. 50, S31-S38 (2015).</li><li>Blainey, P. C., Milla, C. E., Cornfield, D. N., Quake, S. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+analysis+of+the+human+airway+microbial+ecology+reveals+a+pervasive+signature+for+cystic+fibrosis.">Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis.</a> Sci Transl Med. 4 (153), 153ra130 (2012).</li><li>Willner, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+distribution+of+microbial+communities+in+the+cystic+fibrosis+lung.">Spatial distribution of microbial communities in the cystic fibrosis lung.</a> ISME J. 6 (2), 471-474 (2012).</li><li>Delhaes, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+airway+microbiota+in+cystic+fibrosis:+a+complex+fungal+and+bacterial+community--implications+for+therapeutic+management.">The airway microbiota in cystic fibrosis: a complex fungal and bacterial community--implications for therapeutic management.</a> PloS one. 7 (4), e36313 (2012).</li><li>Rogers, G. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=D.+Bacterial+diversity+in+cases+of+lung+infection+in+cystic+fibrosis+patients:+16S+ribosomal+DNA+(rDNA)+length+heterogeneity+PCR+and+16S+rDNA+terminal+restriction+fragment+length+polymorphism+profiling.">D. Bacterial diversity in cases of lung infection in cystic fibrosis patients: 16S ribosomal DNA (rDNA) length heterogeneity PCR and 16S rDNA terminal restriction fragment length polymorphism profiling.</a> J clin microbiol. 41 (8), 3548-3558 (2003).</li><li>Stenbit, A. E., Flume, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pulmonary+exacerbations+in+cystic+fibrosis.">Pulmonary exacerbations in cystic fibrosis.</a> Curr Opin Pulm Med. 17 (6), 442-447 (2011).</li><li>Twomey, K. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbiota+and+metabolite+profiling+reveal+specific+alterations+in+bacterial+community+structure+and+environment+in+the+cystic+fibrosis+airway+during+exacerbation.">Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation.</a> PloS one. 8 (12), e82432 (2013).</li><li>Carmody, L. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+cystic+fibrosis+airway+microbiota+at+pulmonary+exacerbation.">Changes in cystic fibrosis airway microbiota at pulmonary exacerbation.</a> Ann. Am. Thorac. 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The microbiological makeup of a lung with CF contains a great variety of organisms, but the conditions within the lung likely have a significant influence on what kinds of microbes can survive and thrive13,15. Specific mechanisms through which these conditions change and the exact effects they have on the lung microbiome are generally unclear at present. In this experimental method, we present an analysis of microbiological changes based upon manipulated chemical...

The method described in this manuscript is called the WinCF system1. The overall goal of WinCF is to provide an experimental setup capable of simulating the environment of a mucus-filled lung bronchiole. This will allow for a tractable system to study microbial pathogens of lung diseases with a mucus hypersecretion phenotype including cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD), asthma and others. The procedure was designed specifically for the study of CF, which is characterized by mutations that cause lung secretions to become thick and hard to clear, eventually filling bronchioles and other small passageways with mucus2. Such blockages in the lung inhibit gas exchange because inhaled air is no longer able to reach many alveoli and also provide a habitat for bacterial colonization3,4. The inability to prevent microbial growth in the excessive lung mucus eventually leads to the development of complex chronic infections of the airway. These communities contain a variety of organisms, including viruses, fungi, and bacteria like Pseudomonas aeruginosa, all interacting with one another5,6,7,8. The activity of the CF lung microbiome is believed to be involved in flares of symptoms called pulmonary exacerbations1,9,10,11. WinCF enables study of the microbial community behavior around these exacerbations and is now being expanded to act as a base experimental system to study lung microbial ecology. Traditionally, exacerbations have been studied through direct analysis of samples taken from the lung. Many confounding factors make direct analysis of microbial behavior in lungs challenging, with the WinCF system, many of these factors are removed and the behavior of the lung microbiome can be studied more directly, allowing for finer analysis of bacterial activity in a mucus-plugged bronchiole.
The WinCF system provides a method to grow and analyze bacteria in a manner that effectively mimics the lung environment. Traditional methods for growing lung bacteria often involved culturing samples on traditional agar plates. These methods leave the samples open to atmospheric oxygen, neglecting to account for the hypoxic and often anoxic conditions found in lung bronchioles plugged with mucus12,13. Culturing on agar under aerobic conditions is nothing like the environment of the CF lung and can mislead clinicians and researchers concerning the behavior of the pathogens that they are trying to treat. Additionally, the nutrients available to bacteria on agar plates are dissimilar to those available in actual sputum, which is accounted for in WinCF by utilizing artificial sputum media (ASM). As shown by the Pseudomonas cultures in Sriramulu et al.14, ASM includes a specific set of components that mimics the resources available to sputum microbes and also replicates the physical consistency of sputum. Because a diseased lung has a specific microbiome, the study of such microorganisms should ideally take place in the specific conditions of the lung as well.
The WinCF system enables rapid analysis and easy manipulation of the experimental conditions to observe microbial changes similar to how they would occur in an actual lung bronchiole. This technique allows for the inoculation of a myriad of related sample types including sputum, saliva, other body secretions and pure or mixed bacterial cultures. The nature of the experimental setup allows for immediate visual interpretation of the microbial community behavior and is designed to enable easy downstream application of a multitude of microbiological and omics procedures. Such studies are important because bacterial community composition changes based upon the physiochemical conditions of their environment. With WinCF the chemical conditions of the media can be manipulated to analyze the effects on bacterial activity. For example, the acidity of the media can be altered prior to inoculation with a sample. After incubation, the bacterial activity in each of these conditions can be directly compared, and conclusions can be drawn about how bacteria in those sputum samples behave in response to varying pH. Here, we outline the procedures for applying the WinCF system and examples of how the media chemistry can be manipulated to study the effects on the lung microbiome.

<table border="0" cellpadding="0" cellspacing="0" width="595">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Color-Coded Capillary Tubes</td>
			<td style="width:93px;">Fisher Scientific</td>
			<td style="width:119px;">22-260943</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Cha-seal Tube Sealing Compound</td>
			<td style="width:93px;">Kimble-Chase</td>
			<td align="right" style="width:119px;">43510</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Mucin from porcine stomach</td>
			<td style="width:93px;">Sigma</td>
			<td style="width:119px;">M1778</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Ferritin, cationized from horse spleen</td>
			<td style="width:93px;">Sigma</td>
			<td style="width:119px;">F7879</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Salmon sperm DNA Sodium salt (sonified)</td>
			<td style="width:93px;">AppliChem Panreac</td>
			<td>A2159</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">MEM Nonessential Amino Acids</td>
			<td style="width:93px;">Corning cellgro</td>
			<td style="width:119px;">25-025-CI</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">MEM Amino Acids</td>
			<td style="width:93px;">Cellgro</td>
			<td style="width:119px;">25-030-CI</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Egg Yolk Emulsion, 50%</td>
			<td style="width:93px;">Dalynn Biologicals</td>
			<td style="width:119px;">VE30-100</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Potassium Chloride</td>
			<td style="width:93px;">Fisher Scientific</td>
			<td style="width:119px;">P2157500</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Sodium Chloride</td>
			<td style="width:93px;">Fisher Scientific</td>
			<td style="width:119px;">S271500</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">15mL centriguge tubes with Printed Graduations and Flat Caps</td>
			<td style="width:93px;">VWR</td>
			<td style="width:119px;">89039-666</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">50mL centrifuge tubes with Printed Graduations and Flat Caps</td>
			<td style="width:93px;">VWR</td>
			<td style="width:119px;">89039-656</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">1.5mL microcentrifuge tubes</td>
			<td style="width:93px;">Corning</td>
			<td style="width:119px;">MCT-150-R</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">2.0mL microcentrifuge tubes</td>
			<td style="width:93px;">Corning</td>
			<td style="width:119px;">MCT-200-C</td>
			<td></td>
		</tr>
	</tbody>
</table>

the wincf model - an inexpensive and tractable microcosm of a mucus plugged bronchiole to study the microbiology of lung infections

Many chronic airway diseases result in mucus plugging of the airways. Lungs of an individual with cystic fibrosis are an exemplary case where their mucus-plugged bronchioles create a favorable habitat for microbial colonization. Various pathogens thrive in this environment interacting with each other and driving many of the symptoms associated with CF disease. Like any microbial community, the chemical conditions of their habitat have a significant impact on the community structure and dynamics. For example, different microorganisms thrive in differing levels of oxygen or other solute concentrations. This is also true in the CF lung, where oxygen concentrations are believed to drive community physiology and structure. The methods described here are designed to mimic the lung environment and grow pathogens in a manner more similar to that from which they cause disease. Manipulation of the chemical surroundings of these microbes is then used to study how the chemistry of lung infections governs its microbial ecology. The method, called the WinCF system, is based on artificial sputum medium and narrow capillary tubes meant to provide an oxygen gradient similar to that which exists in mucus-plugged bronchioles. Manipulating chemical conditions, such as the media pH of the sputum or antibiotics pressure, allows for visualization of the microbiological differences in those samples using colored indicators, watching for gas or biofilm production, or extracting and sequencing the nucleic acid contents of each sample.

Microbiological growth across the various chemical conditions induced within the samples varied dramatically in some cases and more subtly in others. Many changes in activity were visual in nature, being readily apparent as soon as the incubation period ended. In the example of pH manipulation, the samples across the pH spectrum varied greatly as shown by multiple factors that became apparent after incubation. When no sputum samples were added to the media, the only change exhibited acros...

Watch this Scientific Journal Video about The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections at JoVE.com

The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections

The mucus plugged airways of cystic fibrosis (CF) patients are an ideal environment for microbial pathogens to thrive. The manuscript describes a novel method for studying the CF lung microbiome in an environment that mimics where they cause disease and how alterations of chemical conditions can drive microbial dynamics.

Many chronic airway diseases result in mucus plugging of the airways. Lungs of an individual with cystic fibrosis are an exemplary case where their ...

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9.0K 次观看.  University of California, San Diego. 粘液堵塞囊性纤维化的气道（CF）患者是微生物病原体茁壮成长的理想环境。手稿描述了用于研究CF肺微生物的环境中模仿其中它们引起的化学条件和疾病如何改变可驱动微生物动力学的新方法。 