We appreciate the help from the Argonne National Laboratory and our collaborating bioinformaticians. This work is supported by various NIH and internal grants.

The Cx3cr1gfp/gfp locus of B6.129P2(Cg)-Cx3cr1tm1Litt/J mice was backcrossed to MRL/MpJ-Faslpr/J (MRL/lpr) for 10 generations to generate MRL/lpr-CX3CR1gfp/gfp mice. Genome screening using single nucleotide polymorphism (SNP) panels confirmed that the genetic background of newly generated mice was more than 97% identical to that of MRL/lpr. After that, mice were bred and maintained in a specific pathogen-free environment following the specific requirements of the Institutional Animal Care and Use Committee (IACUC) at Virginia Tech. Samples were collected when the mice were 13, 14, and 15 weeks old.
1. Collection of microbiota samples from mice
<ol>
	<li>Take each mouse individually out of its cage. Collect a fecal pellet directly from the anus and store it at -80 &#176;C until being processed. Process the samples with sterile and clean forceps, tubes, and gloves. 
	NOTE: A container (e.g., a beaker) can be used to place the mouse while waiting for the fecal sample. Clean the container with ethanol before and after each mouse.</li>
	<li>Add a frozen pellet to a pre-weighed 2 mL screw-cap tube. Record the fecal weight in grams, which should be between 0.02-0.05 g per fecal pellet.</li>
	<li>Add to the pellet a thin layer of 0.1 mm glass beads, 500 &#181;L of lysis buffer (50 mM NaCl, 5 mM Tris, and 50 mM EDTA), and 200 &#181;L of 20% SDS.</li>
	<li>Bead-beat the tube for 4 min in a homogenizer (at maximum power), followed by 3-5 min of vortexing.</li>
	<li>Spin for a short time to eliminate the bubbles and foam (press the button on the centrifuge until it reaches 1,000-1,200 x g, and then release).</li>
</ol>
2. DNA extraction
<ol>
	<li>Transfer 350 &#181;L of supernatant obtained in step 1.5 (ensuring not to carry any debris) to a new 1.5 mL snap cap tube. Add 500 &#181;L of phenol-chloroform-isoamyl alcohol (PCI; 25:24:1, v/v) mixture and vortex for 1 min. 
	NOTE: From now on, samples need to be handled inside a chemical hood. PCI is toxic.</li>
	<li>Spin at 6,000 x g for 3 min at 4 &#176;C. Transfer 180 &#181;L of the aqueous phase (top layer) into a new 1.5 mL snap cap tube. Add 180 &#181;L (1:1) of chloroform, invert, and mix. 
	NOTE: Minimize contamination from the bottom layer when transferring the top layer.</li>
	<li>Spin at 18,400 x g for 3 min at 4 &#176;C. Transfer 180 &#181;L of the aqueous phase into a new snap cap tube. 
	NOTE: After discarding PCI and chloroform, the following steps can be performed in a biological safety cabinet.</li>
	<li>Add 180 &#181;L of cold isopropanol and 36 &#181;L of 5M NH4Ac. Invert a few times to mix, and place the tube on ice for 20 min.</li>
	<li>Spin at 18,400 x g for 20 min at 4 &#176;C. Pour to discard the supernatant. Wash the pellet several times with 500 &#181;L of cold 70% ethanol while inverting. 
	NOTE: Ethanol should be diluted with double deionized sterile water.</li>
	<li>Spin at 18,400 x g for 3 min at 4 &#176;C. Discard the supernatant to remove residual ethanol.</li>
	<li>Air-dry the tube upside down on tissue paper for 20 min, until the pellet becomes clear. Suspend the pellet in 50 &#181;L of molecular-grade water. Heat the liquid at 37 &#176;C for 10 min to fully dissolve large DNA pellets.</li>
	<li>Spin tubes after heating to recover condensation droplets on the lid (3,400 x g for 1 min).</li>
	<li>Measure the concentration and obtain the 260/280 ratio using a spectrophotometer. Use molecular-grade water as a blank. Good quality DNA should have 260/280 ratios ranging between 1.8 and 2. 
	&#8203;NOTE: Expected DNA yield is at least 0.03 g per fecal pellet.</li>
</ol>
3. Sample preparation for 16S rRNA gene sequencing
<ol>
	<li>Send the DNA samples to Argonne National Laboratory, where they undergo library preparation and are sequenced on the Illumina Miseq.
	<ol>
		<li>Send samples in fully-skirted 96-well plates, with samples arranged in rows (A1-A12, B1-B12, etc.), and sealed with foil plate seals.</li>
		<li>Send a final volume of 20 &#181;L per sample per well, ranging in concentration from 1-50 ng/&#181;L. 
		NOTE: Dilutions should be done with molecular-grade water.</li>
		<li>After preparing the samples, spin at 600 x g for 1 min at room temperature before freezing the samples at -80 &#176;C for 24 h.</li>
		<li>Send overnight on dry ice.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Lee, Y. K., Mazmanian, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Has+the+microbiota+played+a+critical+role+in+the+evolution+of+the+adaptive+immune+system.">Has the microbiota played a critical role in the evolution of the adaptive immune system.</a> Science. 330 (6012), 1768-1773 (2010).</li><li>Lee, Y. K., Menezes, J. S., Umesaki, Y., Mazmanian, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proinflammatory+T-cell+responses+to+gut+microbiota+promote+experimental+autoimmune+encephalomyelitis.">Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis.</a> Proceedings of the National Academy of Sciences of the United States of America. 108, 4615-4622 (2011).</li><li>Yeoh, N., Burton, J. P., Suppiah, P., Reid, G., Stebbings, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+the+microbiome+in+rheumatic+diseases.">The role of the microbiome in rheumatic diseases.</a> Current Rheumatology Reports. 15 (3), 314 (2013).</li><li>Larsen, N., 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=Gut+microbiota+in+human+adults+with+type+2+diabetes+differs+from+non-diabetic+adults.">Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults.</a> PLoS One. 5 (2), 9085 (2010).</li><li>Alam, M. T., 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=Microbial+imbalance+in+inflammatory+bowel+disease+patients+at+different+taxonomic+levels.">Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels.</a> Gut Pathogens. 12 (1), (2020).</li><li>Vieira, S. M., Pagovich, O. E., Kriegel, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diet,+microbiota+and+autoimmune+diseases.">Diet, microbiota and autoimmune diseases.</a> Lupus. 23 (6), 518-526 (2014).</li><li>Mu, Q., Zhang, H., Luo, X. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SLE:+another+autoimmune+disorder+influenced+by+microbes+and+diet.">SLE: another autoimmune disorder influenced by microbes and diet.</a> Frontiers of Immunology. 6, 608 (2015).</li><li>Tektonidou, M. G., Wang, Z., Dasgupta, A., Ward, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Burden+of+serious+infections+in+adults+with+systemic+lupus+erythematosus:+a+national+population-based+study.">Burden of serious infections in adults with systemic lupus erythematosus: a national population-based study.</a> Arthritis Care &amp; Research. 67 (8), 1078-1085 (2015).</li><li>Mu, Q., 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=Control+of+lupus+nephritis+by+changes+of+gut+microbiota.">Control of lupus nephritis by changes of gut microbiota.</a> Microbiome. 5 (1), 73 (2017).</li><li>Panek, M., 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=Methodology+challenges+in+studying+human+gut+microbiota+-+effects+of+collection,+storage,+DNA+extraction+and+next+generation+sequencing+technologies.">Methodology challenges in studying human gut microbiota - effects of collection, storage, DNA extraction and next generation sequencing technologies.</a> Scientific Reports. 8 (1), 5143 (2018).</li><li>Fiedorov&#225;, K., 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+impact+of+dna+extraction+methods+on+stool+bacterial+and+fungal+microbiota+community+recovery.">The impact of dna extraction methods on stool bacterial and fungal microbiota community recovery.</a> Frontiers in Microbiology. 10, 821 (2019).</li><li>Gerasimidis, K., 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+effect+of+DNA+extraction+methodology+on+gut+microbiota+research+applications.">The effect of DNA extraction methodology on gut microbiota research applications.</a> BMC Research Notes. 9, 365 (2016).</li><li>Bukin, Y. S., 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+effect+of+16S+rRNA+region+choice+on+bacterial+community+metabarcoding+results.">The effect of 16S rRNA region choice on bacterial community metabarcoding results.</a> Scientific Data. 6 (1), 190007 (2019).</li><li>Galloway-Pe&#241;a, J., Hanson, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tools+for+analysis+of+the+microbiome.">Tools for analysis of the microbiome.</a> Digestive Diseases and Sciences. 65 (3), 674-685 (2020).</li><li>Sharpton, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+introduction+to+the+analysis+of+shotgun+metagenomic+data.">An introduction to the analysis of shotgun metagenomic data.</a> Frontiers in Plant Science. 5, 209 (2014).</li></ol>

The authors declare that there is no conflict of interest.

Balanced gut microbiota can protect the human body from diseases. Once this balance is disrupted by external or internal triggers, consequences can be devastating. This method presents a way to analyze the dynamics of gut microbiota in murine models. The method is suitable not only for comparisons among groups but also for tracking the gut microbiota over time to better identify time-dependent factors disrupting the gut microbiota.
All the mice in the experiment must be handled in the same env...

Humans and bacteria have coexisted for a long time. They have established a codependent relationship with mutual beneficial effects that influences host immune responses in quantitative and qualitative ways1. Recent studies suggest an association between the gut microbiota composition and the pathogenesis of autoimmune diseases that include multiple sclerosis2, rheumatoid arthritis3, type 2 diabetes4, Inflammatory bowel disease5, and systemic lupus erythematosus (SLE)6. However, whether the gut microbiota is the main cause or a secondary effect of these autoimmune diseases is still unclear7. Potentially, gut microbiota could exacerbate the disease during the effector phase of autoimmune disorders or play a role in regulating the induction of these diseases8.
Intestinal dysbiosis has been reported in female lupus-prone MRL/Mp-Faslpr (MRL/lpr) mice, and gut microbiota changes with a significant depletion of Lactobacilli were observed9. When a mixture of five Lactobacillus strains was orally administered, lupus-like symptoms were largely attenuated in these mice, suggesting an essential role of microbiota in regulating SLE pathogenesis.
The following technique of DNA extraction allows to follow microbiota fluctuations and analyze them qualitatively and quantitively during the course of murine SLE-like disease in lupus-prone mice. Whether to examine the healthy gut microbiota or define dysbiosis, it is important to critically examine how data is collected and whether it is accurate and reproducible10. Every step is critical in this process. An appropriate methodology must be used to extract microbial DNA as any possible problem introducing biases during the DNA extraction process could result in inaccurate microbial representation. While the phenol-chloroform method is described here, there are commercially available kits to extract DNA from bacteria that work well in particular cases11. However, their usability is limited by the cost and required sample quantity.
The protocol presented here is cost-effective and requires only a small amount of sample. It works fine with any kind of stool sample and is useful in studying the dynamics of the gut microbiota over time as well as comparisons among groups. DNA is isolated with a method of alcohol purification, which uses phenol, chloroform, and isoamyl alcohol. Alcohol-based extraction helps to clean and remove the sample of proteins and lipids, where DNA is precipitated in the final step. The proposed method has significantly high efficiency and quality and has been proven to be accurate in identifying bacterial populations. One critical note during the procedure is that DNA contamination can occur, and thus appropriate sample handling is required12.
The DNA is then analyzed by the Next Generation Sequencing platforms for the 16S rRNA gene, such as the Illumina MiSeq. In particular, the V4 hyper-variable region is analyzed to provide a better quantification for high-rank taxa13. The subsequent bioinformatics analysis is outsourced, followed by in-house analysis using standard statistical methods. There are numerous open-source bioinformatics software programs available for downstream sequencing, and the type of analyses performed depends heavily on the specific biological question of interest14. This protocol focuses specifically on the experimental steps prior to sequencing and provides a more versatile, cost-effective, comparable, and efficient method to obtain DNA from fecal samples.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.1 mm glass beads</td>
			<td>BioSpec Products</td>
			<td>11079101</td>
			<td></td>
		</tr>
		<tr>
			<td>2 mL screw cap tubes</td>
			<td>Thermo Fisher Scientific</td>
			<td>3488</td>
			<td></td>
		</tr>
		<tr>
			<td>20% SDS</td>
			<td>FisherScientific</td>
			<td>BP1311-1</td>
			<td>SDS 20%</td>
		</tr>
		<tr>
			<td>96% Ethanol, Molecular Biology Grade</td>
			<td>Thermo Fisher Scientific</td>
			<td>T032021000CS</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium Acetate (5 M)</td>
			<td>Thermo Fisher Scientific</td>
			<td>AM9071</td>
			<td>NH4AC 5M</td>
		</tr>
		<tr>
			<td>B6.129P2(Cg)-Cx3cr1tm1Litt/J</td>
			<td>Jackson Laboratory</td>
			<td>005582</td>
			<td></td>
		</tr>
		<tr>
			<td>Bullet Blender storm 24</td>
			<td>Next Advance</td>
			<td>4116-BBY24M</td>
			<td>Homogenizer</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>FisherScientific</td>
			<td>C298-500</td>
			<td></td>
		</tr>
		<tr>
			<td>DEPC-Treated Water</td>
			<td>Thermo Fisher Scientific</td>
			<td>AM9916</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethylenediamine Tetraacetic Acid</td>
			<td>FisherScientific</td>
			<td>BP118-500</td>
			<td>EDTA</td>
		</tr>
		<tr>
			<td>Foil plate seal</td>
			<td>FisherScientific</td>
			<td>NC0302491</td>
			<td></td>
		</tr>
		<tr>
			<td>Kimwipes-Kimtech 34256</td>
			<td>FisherScientific</td>
			<td>06-666C</td>
			<td></td>
		</tr>
		<tr>
			<td>MRL/MpJ-Faslpr/J (MRL/lpr) mice</td>
			<td>Jackson Laboratory</td>
			<td>000485</td>
			<td></td>
		</tr>
		<tr>
			<td>Nanodrop 2000 spectrophotomer</td>
			<td>Thermo Fisher Scientific</td>
			<td>ND2000CLAPTOP</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenol: chloroform: isoamylalchohol (25:24:1)</td>
			<td>FisherScientific</td>
			<td>BP1752I-400</td>
			<td>PCI</td>
		</tr>
		<tr>
			<td>Scale with 4 decimals</td>
			<td>Mettler Toledo</td>
			<td>MS205DU</td>
			<td></td>
		</tr>
		<tr>
			<td>Skirted 96-well plates</td>
			<td>Thermo Fisher Scientific</td>
			<td>AB-0800</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>FisherScientific</td>
			<td>15528154</td>
			<td>NaCl</td>
		</tr>
		<tr>
			<td>Tris Hydrochloride</td>
			<td>FisherScientific</td>
			<td>BP1757-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td>Scientific Industries</td>
			<td>SI-0236</td>
			<td></td>
		</tr>
	</tbody>
</table>

analysis of fecal microbiota dynamics in lupus-prone mice using a simple, cost-effective dna isolation method

Gut microbiota has an important role in educating the immune system. This relationship is extremely important for understanding autoimmune diseases that are not only driven by genetic factors, but also environmental factors that can trigger the onset and/or worsen the disease course. A previously published study on the dynamics of the gut microbiota in lupus-prone MRL/lpr female mice showed how changes of the gut microbiota can alter disease progression. Here, a protocol is described for extracting representative samples from the gut microbiota for studies of autoimmunity. Microbiota samples are collected from the anus and processed, from which the DNA is extracted using a phenol-chloroform method and purified by alcohol precipitation. After PCR is performed, purified amplicons are sequenced using a Next Generation Sequencing platform at Argonne National Laboratory. Finally, the 16S ribosomal RNA gene sequencing data is analyzed. As an example, data obtained from gut microbiota comparisons of MRL/lpr mice with or without CX3CR1 are shown. Results showed significant differences in genera containing pathogenic bacteria such as those in the phylum Proteobacteria, as well as the genus Bifidobacterium, which is considered part of the healthy commensal microbiota. In summary, this simple, cost-effective DNA isolation method is reliable and can help the investigation of gut microbiota changes associated with autoimmune diseases.

The results from Argonne National Laboratory are analyzed by a qualified bioinformatician, followed by an in-house analysis of the data using standard statistical methods. Typical microbiome analyses involve clustering of similar sequences into operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) as a proxy for different microorganisms in a sample. Counts of OTUs or ASVs across samples can then be used to test for changes in within-sample (alpha) diversity and between-sample (beta) diversity. They can ...

Watch this Scientific Journal Video about Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method at JoVE.com

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

This protocol provides a simple, cost-effective DNA isolation method for the analysis of murine gut microbiota alterations during the development of autoimmune disease.

Gut microbiota has an important role in educating the immune system. This relationship is extremely important for understanding autoimmune diseases that ...

analysis-fecal-microbiota-dynamics-lupus-prone-mice-using-simple-cost

Research

JoVE Journal

Immunology and Infection

2.0K Views.  Virginia Polytechnic Institute and State University. This protocol provides a simple, cost-effective DNA isolation method for the analysis of murine gut microbiota alterations during the development of autoimmune disease.

Video: Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice Using a Simple, Cost-Effective DNA Isolation Method

Comprehensive &amp; Cost Effective Laboratory Monitoring of HIV/AIDS: an African Role Model

We present the video about assisting anti-retroviral therapy (ART) by an apt laboratory service - representing a South-African role model for economical large scale diagnostic testing. In the low-income countries inexpensive ART has transformed the prospects for the survival of HIV seropositive patients but there are doubts whether there is a need for the laboratory monitoring of ART and at what costs - in situations when the overall quality of pathology services can still be very low. The appropriate answer is to establish economically sound services with better coordination and stricter internal quality assessment than seen in western countries. This video, photographed at location in the National Health Laboratory Services (NHLS-SA) at the Witwatersrand University, Johannesburg, South Africa, provides such a coordinated scheme expanding the original 2-color CD4-CD45 PanLeucoGating strategy (PLG). Thus the six modules of the video presentation reveal the simplicity of a 4-color flow cytometric assay to combine haematological, immunological and virology-related tests in a single tube. These video modules are: (i) the set-up of instruments; (ii) sample preparations; (iii) testing absolute counts and monitoring quality for each sample by bead-count-rate; (iv) the heamatological CD45 test for white cell counts and differentials; (v) the CD4 counts, and (vi) the activation of CD8+ T cells measured by CD38 display, a viral load related parameter. The potential cost-savings are remarkable. This arrangement is a prime example for the feasibility of performing &gt; 800-1000 tests per day with a stricter quality control than that applied in western laboratories, and also with a transfer of technology to other laboratories within a NHLS-SA network. Expert advisors, laboratory managers and policy makers who carry the duty of making decisions about introducing modern medical technology are frequently not in a position to see the latest technical details as carried out in the large regional laboratories with huge burdens of workload. Hence this video shows details of these new developments.

Anti-retroviral therapy to treat HIV/AIDS is monitored in South Africa on a large scale. Flow cytometry is combined for haematology (CD45), immunology (CD4) and viral-load linked CD38 assay. Recorded at NHLS-SA laboratories, Johannesburg, these modern methods are cost-efficient with heightened local internal quality control, serving as role-models for resource-limited diagnostics.

We present the video about assisting anti-retroviral therapy (ART) by an apt laboratory service - representing a South-African role model for economical ...

Cost-effective Method for Microbial Source Tracking Using Specific Human and Animal Viruses

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant limitations, viruses are more resistant to many inactivation processes and standard fecal indicators do not inform on the source of contamination. The development of cost-effective methods for the concentration of viruses from water and molecular assays facilitates the applicability of viruses as indicators of fecal contamination and as microbial source tracking (MST) tools. Adenoviruses and polyomaviruses are DNA viruses infecting specific vertebrate species including humans and are persistently excreted in feces and/or urine in all geographical areas studied. In previous studies, we suggested the quantification of human adenoviruses (HAdV) and JC polyomaviruses (JCPyV) by quantitative PCR (qPCR) as an index of human fecal contamination. Recently, we have developed qPCR assays for the specific quantification of porcine adenoviruses (PAdV) and bovine polyomaviruses (BPyV) as animal fecal markers of contamination with sensitivities of 1-10 genome copies per test tube. In this study, we present the procedure to be followed to identify the source of contamination in water samples using these tools. As example of representative results, analysis of viruses in ground water presenting high levels of nitrates is shown.
Detection of viruses in low or moderately polluted waters requires the concentration of the viruses from at least several liters of water into a much smaller volume, a procedure that usually includes two concentration steps in series. This somewhat cumbersome procedure and the variability observed in viral recoveries significantly hamper the simultaneous processing of a large number of water samples.
In order to eliminate the bottleneck caused by the two-step procedures we have applied a one-step protocol developed in previous studies and applicable to a diversity of water matrices. The procedure includes: acidification of ten-liter water samples, flocculation by skimmed milk, gravity sedimentation of the flocculated materials, collection of the precipitate and centrifugation, resuspension of the precipitate in 10 ml phosphate buffer. The viral concentrate is used for the extraction of viral nucleic acids and the specific adenoviruses and polyomaviruses of interest are quantified by qPCR. High number of samples may be simultaneously analyzed using this low-cost concentration method.
The procedure has been applied to the analysis of bathing waters, seawater and river water and in this study, we present results analyzing groundwater samples. This high-throughput quantitative method is reliable, straightforward, and cost-effective.

The study describes a cost-effective method for the identification of the source of fecal/urine contamination or contamination by nitrates in water using qPCR for the specific quantification of human/porcine/bovine DNA viruses, adenoviruses and polyomaviruses, proposed as MST tools.

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant ...

A Method for Labeling Vasculature in Embryonic Mice

The establishment of a functional blood vessel network is an essential part of organogenesis, and is required for optimal organ function. For example, in the thymus proper vasculature formation and patterning is essential for thymocyte entry into the organ and mature T-cell exit to the periphery. The spatial arrangement of blood vessels in the thymus is dependent upon signals from the local microenvironment, namely thymic epithelial cells (TEC). Several recent reports suggest that disruption of these signals results in thymus blood vessel defects 1,2. Previous studies have described techniques used to label the neonatal and adult thymus vasculature 1,2. We demonstrate here a technique for labeling blood vessels in the embryonic thymus. This method combines the use of FITC-dextran or Griffonia (Bandeiraea) Simplicifolia Lectin I (GSL 1 - isolectin B4) facial vein injections and CD31 antibody staining to identify thymus vascular structures and PDGFR-&beta; to label thymic perivascular mesenchyme 3-5. The option of using cryosections or vibratome sections is also provided. This protocol can be used to identify thymus vascular defects, which is critical for defining the roles of TEC-derived molecules in thymus blood vessel formation. As the method labels the entire vasculature, it can also be used to analyze the vascular networks in multiple organs and tissues throughout the embryo including skin and heart 6-10.

This article describes a method for labeling embryonic skin and thymus blood vessels.

The establishment of a functional blood vessel network is an essential part of organogenesis, and is required for optimal organ function. For example, in ...

A Simple Chelex Protocol for DNA Extraction from Anopheles spp.

Endemic countries are increasingly adopting molecular tools for efficient typing, identification and surveillance against malaria parasites and vector mosquitoes, as an integral part of their control programs1,2,3,4,5. For sustainable establishment of these accurate approaches in operations research to strengthen malaria control and elimination efforts, simple and affordable methods, with parsimonious reagent and equipment requirements are essential6,7,8. Here we present a simple Chelex-based technique for extracting malaria parasite and vector DNA from field collected mosquito specimens.
We morphologically identified 72 Anopheles gambiae sl. from 156 mosquitoes captured by pyrethrum spray catches in sleeping rooms of households within a 2,000 km2 vicinity of the Malaria Institute at Macha. After dissection to separate the head and thorax from the abdomen for all 72 Anopheles gambiae sl. mosquitoes, the two sections were individually placed in 1.5 ml microcentrifuge tubes and submerged in 20 &mu;l of deionized water. Using a sterile pipette tip, each mosquito section was separately homogenized to a uniform suspension in the deionized water. Of the ensuing homogenate from each mosquito section, 10 &mu;l was retained while the other 10 &mu;l was transferred to a separate autoclaved 1.5 ml tube. The separate aliquots were subjected to DNA extraction by either the simplified Chelex or the standard salting out extraction protocol9,10. The salting out protocol is so-called and widely used because it employs high salt concentrations in lieu of hazardous organic solvents (such as phenol and chloroform) for the protein precipitation step during DNA extraction9.
Extracts were used as templates for PCR amplification using primers targeting arthropod mitochondrial nicotinamide adenine dinucleotide dehydrogenase (NADH) subunit 4 gene (ND4) to check DNA quality11, a PCR for identification of Anopheles gambiae sibling species10 and a nested PCR for typing of Plasmodium falciparum infection12. Comparison using DNA quality (ND4) PCR showed 93% sensitivity and 82% specificity for the Chelex approach relative to the established salting out protocol. Corresponding values of sensitivity and specificity were 100% and 78%, respectively, using sibling species identification PCR and 92% and 80%, respectively for P. falciparum detection PCR. There were no significant differences in proportion of samples giving amplicon signal with the Chelex or the regular salting out protocol across all three PCR applications. The Chelex approach required three simple reagents and 37 min to complete, while the salting out protocol entailed 10 different reagents and 2 hr and 47 min' processing time, including an overnight step. Our results show that the Chelex method is comparable to the existing salting out extraction and can be substituted as a simple and sustainable approach in resource-limited settings where a constant reagent supply chain is often difficult to maintain.

A Simple Chelex Protocol for DNA Extraction from Anopheles spp.

A rapid and affordable way to extract quality malaria parasite and vector DNA from mosquito specimens is described. Capitalizing on chelating properties of Chelex resin, the simple method enables genotyping of malaria parasites in mosquito mid-gut and salivary gland phases, as well as molecular identification of the Anopheles sibling species by PCR.

Endemic countries are increasingly adopting molecular tools for  efficient typing, identification and surveillance against malaria parasites and  vector ...

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Whole genome amplification and sequencing of single microbial cells enables genomic characterization without the need of cultivation 1-3. Viruses, which are ubiquitous and the most numerous entities on our planet 4 and important in all environments 5, have yet to be revealed via similar approaches. Here we describe an approach for isolating and characterizing the genomes of single virions called 'Single Virus Genomics' (SVG). SVG utilizes flow cytometry to isolate individual viruses and whole genome amplification to obtain high molecular weight genomic DNA (gDNA) that can be used in subsequent sequencing reactions.

Isolation and Genome Analysis of Single Virions using &#039;Single Virus Genomics&#039;

Single Virus Genomics (SVG) is a method to isolate and amplify the genomes of single virons. Viral suspensions of a mixed assemblage are sorted using flow cytometry onto a microscope slide with discrete wells containing agarose, thereby capturing the virion and reducing genome shearing during downstream processing. Whole genome amplification is achieved using multiple displacement amplification (MDA) resulting in genomic material that is suitable for sequencing.

Whole genome amplification and sequencing of single microbial cells enables genomic characterization without the need of cultivation 1-3. Viruses, which ...

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota

The emerging role of the gut microbiome in several human diseases demands a breakthrough of new tools, techniques and technologies. Such improvements are needed to decipher the utilization of microbiome modulators for human health benefits. However, the large-scale screening and optimization of modulators to validate microbiome modulation and predict related health benefits may be practically difficult due to the need for large number of animals and/or human subjects. To this end, in vitro or ex vivo models can facilitate preliminary screening of microbiome modulators. Herein, it is optimized and demonstrated an ex vivo fecal microbiota culture system that can be used for examining the effects of various interventions of gut microbiome modulators including probiotics, prebiotics and other food ingredients, aside from nutraceuticals and drugs, on the diversity and composition of the human gut microbiota. Inulin, one of the most widely studied prebiotic compounds and microbiome modulators, is used as an example here to examine its effect on the healthy fecal microbiota composition and its metabolic activities, such as fecal pH and the fecal levels of organic acids including lactate and short-chain fatty acids (SCFAs). The protocol may be useful for studies aimed at estimating the effects of different interventions of modulators on fecal microbiota profiles and at predicting their health impacts.

This protocol describes an in vitro batch-culture fermentation system of human fecal microbiota, using inulin (a well-known prebiotic and one of the most widely studied microbiota modulators) to demonstrate the use of this system in estimating effects of specific interventions on fecal microbiota composition and metabolic activities.

The emerging role of the gut microbiome in several human diseases demands a breakthrough of new tools, techniques and technologies. Such improvements are ...

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

Human intestinal microorganisms have recently become an important target of research in promoting human health and preventing diseases. Consequently, investigations of interactions between endobiotics (e.g., drugs and prebiotics) and gut microbiota have become an important research topic. However, in vivo experiments with human volunteers are not ideal for such studies due to bioethics and economic constraints. As a result, animal models have been used to evaluate these interactions in vivo. Nevertheless, animal model studies are still limited by bioethics considerations, in addition to differing compositions and diversities of microbiota in animals vs. humans. An alternative research strategy is the use of batch fermentation experiments that allow evaluation of the interactions between endobiotics and gut microbiota in vitro. To evaluate this strategy, bifidobacterial (Bif) exopolysaccharides (EPS) were used as a representative xenobiotic. Then, the interactions between Bif EPS and human gut microbiota were investigated using several methods such as thin-layer chromatography (TLC), bacterial community compositional analysis with 16S rRNA gene high-throughput sequencing, and gas chromatography of short-chain fatty acids (SCFAs). Presented here is a protocol to investigate the interactions between endobiotics and human gut microbiota using in vitro batch fermentation systems. Importantly, this protocol can also be modified to investigate general interactions between other endobiotics and gut microbiota.

Described here is a protocol to investigate the interactions between endobiotics and human gut microbiota using in vitro batch fermentation systems.

Human intestinal microorganisms have recently become an important target of research in promoting human health and preventing diseases. Consequently, ...

A DNA/Ki67-Based Flow Cytometry Assay for Cell Cycle Analysis of Antigen-Specific CD8 T Cells in Vaccinated Mice

The cell cycle of antigen-specific T cells in vivo has been examined by using a few methods, all of which possess some limitations. Bromodeoxyuridine (BrdU) marks cells that are in or recently completed S-phase, and carboxyfluorescein succinimidyl ester (CFSE) detects daughter cells after division. However, these dyes do not allow identification of the cell cycle phase at the time of analysis. An alternative approach is to exploit Ki67, a marker that is highly expressed by cells in all phases of the cell cycle except the quiescent phase G0. Unfortunately, Ki67 does not allow further differentiation as it does not separate cells in S-phase that are committed to mitosis from those in G1 that can remain in this phase, proceed into cycling, or move into G0.
Here, we describe a flow cytometric method for capturing a &#34;snapshot&#34; of T cells in different cell cycle phases in mouse secondary lymphoid organs. The method combines Ki67 and DNA staining with major histocompatibility complex (MHC)-peptide-multimer staining and an innovative gating strategy, allowing us to successfully differentiate between antigen-specific CD8 T cells in G0, in G1 and in S-G2/M phases of the cell cycle in the spleen&#160;and draining lymph nodes of mice after vaccination with viral vectors carrying the model antigen gag of human immunodeficiency virus (HIV)-1.
Critical steps of the method were the choice of the DNA dye and the gating strategy to increase the assay sensitivity and to include highly activated/proliferating antigen-specific T cells that would have been missed by current criteria of analysis. The DNA dye, Hoechst 33342, enabled us to obtain a high-quality discrimination&#160;of the G0/G1 and G2/M DNA peaks, while preserving membrane and intracellular staining. The method has great potential to increase knowledge about T cell response in vivo and to improve immuno-monitoring analysis.

Clonal expansion is a key feature of antigen-specific T cell response. However, the cell cycle of antigen-responding T cells has been poorly investigated, partly because of technical limitations. We describe a flow cytometric method to analyze clonally expanding antigen-specific CD8 T cells in spleen and lymph nodes of vaccinated mice.

The cell cycle of antigen-specific T cells in vivo has been examined by using a few methods, all of which possess some limitations. Bromodeoxyuridine ...

Fecal (micro) RNA Isolation

It is becoming clear that RNA exists in the gut lumen and feces in animals and humans. The protocol described below isolates total RNA including microRNAs from fecal samples of animal and human subjects. The aim is to isolate total RNA with high purity and quantity for downstream analyses such as RNA sequencing, RT-PCR, and micro-array. The advantages of this optimized protocol in the miRNA isolation are capabilities of isolating highly purified RNA products with additional washing steps described, increased quantity of RNA obtained with an improved method in the resuspension of sample, and important tips of decontamination. One limitation is the inability to process and purify larger sample of more than 200 mg as these sample sizes would cause a difficulty in the clear formation of the interphase. Consequently, the large sample size may contaminate the aqueous phase to be extracted as described in the protocol with organic matters that affect the quality of RNA isolated in the end. However, RNA isolates from a sample of up to 200 mg are sufficient for most of downstream analyses.

Fecal micro RNA Isolation

This protocol isolates high quality total RNA from fecal samples of animal and human subjects. A commercial miRNA isolation kit is used with significant adaption to isolate pure RNA with optimized quantity and quality. The RNA isolates are good for most downstream RNA assays such as sequencing, micro-array, and RT-PCR.

It is becoming clear that RNA exists in the gut lumen and feces in animals and humans. The protocol described below isolates total RNA including microRNAs ...

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 ...