We received technical assistance from the Biopolymers Facility at Harvard Medical School for bioanalyzer. This work was supported by National Multiple Sclerosis Society research grant RG-1707-28516 (H.L.W. and S.L.).

All methods involving research animals described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of Brigham and Women&#8217;s Hospital, Harvard Medical School.
All methods involving human research subjects described here are in accordance with the guidelines set by the Partners Human Research Committee.
1. Fecal sample collection
<ol>
	<li>Autoclave or prepare a sterile and nuclease-free 2 mL microcentrifuge tube with a screw cap for each animal subject in an experiment.
	<ol>
		<li>For human subjects, provide an appropriate, nuclease-free, and sterile stool specimen collection device for each subject.</li>
	</ol>
	</li>
	<li>Collect 25-100 mg (approximately 1-4 fecal pellets for mouse fecal samples) of fecal samples from each animal subject in a sterile environment. 
	NOTE: Two or more fecal pellets (~50 mg or heavier) are preferred for obtaining RNA of the highest purity.
	<ol>
		<li>Utilize all necessary Personal Protective Equipment (PPE) and materials, for example: a pair of laboratory gloves, a disinfectant spray and a sterile paper towel, to sterilize the working area, where the animal research subject is placed on, to avoid fecal sample contamination.
		<ol>
			<li>For human subjects, instruct each research subject/collector to collect 100-200 mg of stool samples in an environment as sterile as possible. Use standard sterile operation and avoid stool specimen contamination.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Collect fecal samples from each animal subject directly into a 2 mL microcentrifuge tube with a screw cap without touching any other surfaces to avoid contamination.
	<ol>
		<li>For human subjects, instruct each subject to defecate directly into an applicable collection device provided (e.g., a sterile stool specimen collection kit) to avoid contamination. 
		NOTE: Instruct subject to avoid contamination by toilet surfaces, water, urine, or any other non-sterile surfaces/objects.</li>
	</ol>
	</li>
	<li>Freeze fecal samples collected in 2 mL microcentrifuge tubes immediately at -80 &#176;C or place in a bucket of dry ice for the better quantity and quality of RNA before feces resuspension as described in the steps below.
	<ol>
		<li>For human stool specimens, aliquot each fresh specimen of 200 mg into 2 mL microcentrifuge tubes with screw caps and freeze them at -80 &#176;C before feces resuspension as described below.
		<ol>
			<li>For the storage of stool specimens not in 2 mL microcentrifuge tubes with screw caps, weigh and transfer 100-200 mg each of frozen specimens into separate 2 mL microcentrifuge tubes with screw caps before feces resuspension as described below. 
			NOTE: For human stool specimens, avoid taking more than 200 mg of stool specimens for RNA isolation as it may cause difficulties in the following steps. With an overloaded sample in a 2 mL microcentrifuge tube, the aqueous phase, organic phase and interphase may not be clearly formed and separated. The procedure can be paused here.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
2. Preparations of wash solutions
<ol>
	<li>Add 21 mL of American Chemical Society (ACS) grade 100% ethanol to the Wash Solution 1 provided in the miRNA Isolation Kit&#160;(see Table of Materials)&#160;to reach the final volume of 30 mL, as shown on the bottle. Vortex until everything dissolves in the bottle.</li>
	<li>Add 40 mL of ACS grade 100% ethanol to the Wash Solution 2/3 provided to reach the final volume of 50 mL, as shown on the bottle. Vortex for 5 s or until the final mixture is well blended.</li>
</ol>
3. Preparations of equipment and materials
<ol>
	<li>Spray the working area and equipment, for example: the laboratory bench, the working area in the chemical fume hood and the micro-centrifuge tube racks, with a Ribonuclease (RNase) decontamination solution (e.g., commercially available RNase decontamination solution). To avoid contamination, apply with the RNase decontamination solution on the surfaces wherever and whenever deemed necessary.</li>
	<li>Don a clean laboratory coat, put on a facial mask, and wear appropriate laboratory gloves to protect the RNA in the fecal samples from nucleases present on human skin. Spray gloves with a RNase decontamination solution and change gloves frequently to avoid contamination.</li>
	<li>Prepare a bucket of dry ice for fecal samples stored at -80 &#176;C to prevent thawing before feces resuspension and a bucket of ice for materials, for example: Acid-Phenol: Chloroform, to prolong the shelf life. 
	NOTE: Ensure materials including the media used in the protocol are sterile without contamination of nucleases.</li>
</ol>
4. Feces resuspension
<ol>
	<li>Resuspend 25-100 mg of fecal samples in 600 &#181;L of sterile 1x Dulbecco&#39;s Phosphate-Buffered Saline (DPBS). 
	CAUTION: Fecal samples should be processed immediately when thawed from -80 &#176;C without even partial thawing to minimize the release of RNases and cellular RNA as ice crystals rupture both interior and exterior cellular compartments when cells in sample thaw.
	<ol>
		<li>Add 600 &#181;L of 1x DPBS to the 2 mL microcentrifuge tube with a screw cap containing fecal samples at room temperature (RT).</li>
		<li>Incubate the mixture of fecal samples submerged in 600 &#181;L of 1x DPBS in the 2 mL microcentrifuge tube capped for 30 min at RT.</li>
		<li>Resuspend the mixture by mashing with 1 mL pipette tip and vortex well with the 2 mL microcentrifuge tube capped. To optimize and increase the quantity and quality of RNA, resuspend the mixture with a homogenizer with the setting for one cycle at S4000 (or 4000 rpm) and 45 s.</li>
	</ol>
	</li>
</ol>
5. Organic extraction
CAUTION: Use the hazardous chemical fume hood for the following steps until Step 6 with the use of acid-phenol: chloroform and ACS grade 100% ethanol due to their toxicity and inflammability. Change PPE as needed and follow proper standard precautions when dealing with hazardous material.
<ol>
	<li>Extract RNA with 600 &#181;L of acid-phenol: chloroform (the volume of acid-phenol: chloroform required equals to the initial volume of added 1x DPBS in Step 4.1).
	<ol>
		<li>Add 600 &#956;L of acid-phenol: chloroform to the suspension from Step 4.1. 
		NOTE: Withdraw acid-phenol: chloroform from the lower phase in the bottle as the upper phase is mixed with an aqueous buffer. If the interphase between these two phases is disturbed, then wait and withdraw acid-phenol: chloroform only when the interphase re-establishes itself to avoid contamination.</li>
	</ol>
	</li>
	<li>Vortex the mixture for 60 s to thoroughly mix. Alternatively, to optimize and increase quantity of RNA in the yield, mix by using a homogenizer with the setting for one cycle at S4000 and 45 s.</li>
	<li>Centrifuge for 15 min at 10,000 x g at RT to separate the aqueous and organic phases with a microcentrifuge. After centrifugation, the interphase should be compact. If not, repeat the centrifugation. 
	NOTE: If the interphase could not be as compact as desired possibly due to uneven ratio of the initial volume to the volume of added acid-phenol: chloroform after several repeats of centrifugation, proceed to recover the aqueous phase with a greater care to avoid contamination.</li>
	<li>Recover the aqueous phase and transfer it to a new 2 mL microcentrifuge tube with a hinge cap (not provided by the miRNA isolation kit).
	<ol>
		<li>Remove the aqueous (or upper) phase carefully without disturbing the lower phase and transfer it to a new 2 mL microcentrifuge tube with a hinge cap. Note the volume transferred (e.g., ~500 &#181;L). 
		NOTE: When the interphase is compact and the upper phase is clearly separated, there are possibly a few tiny residual particles floating on the top of the aqueous phase. Pipette carefully to avoid these residues and only recover visibly and clearly separated aqueous phase to ensure a quality RNA yield, even if you could only obtain a small volume of the aqueous phase.</li>
	</ol>
	</li>
</ol>
6. Final RNA isolation
<ol>
	<li>Add 1.25 volumes of RT ACS grade 100% ethanol to the aqueous phase in the 2 mL microcentrifuge tube (e.g., add 625 &#956;L of 100% ethanol if 500 &#956;L of aqueous phase is recovered from Step 5.4.). Vortex 3 s.</li>
	<li>Load the aqueous phase/ethanol mixture through the filter cartridge provided in the miRNA isolation kit.
	<ol>
		<li>For each sample, place the filter cartridge into one of the collection tubes supplied by the kit.
		<ol>
			<li>Pipette and load 600 &#181;L of the aqueous phase/ethanol mixture into the filter cartridge. 
			NOTE: Vortex the mixture briefly to thoroughly mix the ethanol with aqueous phase before pipetting. No more than 700 &#181;L of the aqueous phase/ethanol mixture can be loaded at a time.</li>
		</ol>
		</li>
		<li>Centrifuge at 10,000 x g for 90 s to filter through the mixture. Spinning at a higher speed may damage the filter.</li>
		<li>Discard the filtrate and repeat Steps 6.2.1 to 6.2.2 until all the mixture is filtered through the same filter membrane in successive applications. Keep and reuse the same collection tube for washing steps below.</li>
		<li>Wash the filter with 700 &#181;L of miRNA Wash Solution 1. 
		CAUTION: miRNA Wash Solution 1 contains guanidine thiocyanate that can cause skin irritation and serious eye damage. Wear necessary PPE, for examples: gloves, face shield, protective laboratory coat. Change gloves frequently as necessary.
		<ol>
			<li>Apply 700 &#181;L of miRNA Wash Solution 1, the working solution prepared with the ACS grade 100% ethanol, into the filter cartridge.</li>
			<li>Centrifuge for 60 s to filter the miRNA Wash Solution 1 through the filter cartridge.</li>
			<li>Discard the filtrate from the collection tube and place the same filter cartridge into the same collection tube.</li>
		</ol>
		</li>
		<li>Wash the filter with Wash Solution 2/3 one time each with volumes of 700 &#181;L, 500 &#181;L, and 250 &#181;L consecutively.
		<ol>
			<li>Apply 700 &#181;L of Wash Solution 2/3, the working solution prepared with the ACS grade 100% ethanol, into the filter cartridge.
			<ol>
				<li>Centrifuge at 10,000 x g for 1 min.</li>
				<li>Discard the filtrate from the collection tube and place the same filter cartridge into the same collection tube.</li>
			</ol>
			</li>
			<li>Apply 500 &#181;L of Wash Solution 2/3 into the filter cartridge.
			<ol>
				<li>Centrifuge at 10,000 x g for 1 min.</li>
				<li>Discard the filtrate from the collection tube and place the same filter cartridge into the same collection tube.</li>
			</ol>
			</li>
			<li>Apply 250 &#181;L of Wash Solution 2/3 into the filter cartridge.
			<ol>
				<li>Centrifuge at 10,000 x g for 1 min.</li>
				<li>Discard the filtrate from the collection tube.</li>
			</ol>
			</li>
			<li>Transfer the filter cartridge into a new collection tube and spin the assembly for 5 min to remove residual fluid from the filter.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
7. Elute RNA with 50 &#181;L nuclease-free water
<ol>
	<li>Transfer the filter cartridge into a new collection tube. Pipette 50 &#181;L of nuclease-free water to the center of the filter and cap the collection tube.
	<ol>
		<li>Incubate at RT for 10 min.</li>
		<li>Spin for 5 min at 8,000 x g to recover RNA into the new collection tube.</li>
		<li>Determine the concentration and purity of recovered fecal RNA using a fluorometer. Recovered fecal RNA can be stored at -80 &#730;C.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Das, 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+extracellular+RNA+communication+consortium:+Establishing+foundational+knowledge+and+technologies+for+extracellular+RNA+research.">The extracellular RNA communication consortium: Establishing foundational knowledge and technologies for extracellular RNA research.</a> Cell. 177 (2), 231-242 (2019).</li><li>Ahmed, F. E., 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=Diagnostic+microRNA+markers+for+screening+sporadic+human+colon+cancer+and+active+ulcerative+colitis+in+stool+and+tissue.">Diagnostic microRNA markers for screening sporadic human colon cancer and active ulcerative colitis in stool and tissue.</a> Cancer Genomics &amp; Proteomics. 6 (5), 281-295 (2009).</li><li>Liu, 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+host+shapes+the+gut+microbiota+via+fecal+microRNA.">The host shapes the gut microbiota via fecal microRNA.</a> Cell Host &amp; Microbe. 19 (1), 32-43 (2016).</li><li>Viennois, E., 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=Host-derived+fecal+microRNAs+can+indicate+gut+microbiota+healthiness+and+ability+to+induce+inflammation.">Host-derived fecal microRNAs can indicate gut microbiota healthiness and ability to induce inflammation.</a> Theranostics. 9 (15), 4542-4557 (2019).</li><li>Liu, 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=Oral+administration+of+miR-30d+from+feces+of+MS+patients+suppresses+MS-like+symptoms+in+mice+by+expanding+Akkermansia+muciniphila.">Oral administration of miR-30d from feces of MS patients suppresses MS-like symptoms in mice by expanding Akkermansia muciniphila.</a> Cell Host &amp; Microbe. 26 (6), 779-794 (2019).</li><li>Masotti, 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=Quantification+of+small+non-coding+RNAs+allows+an+accurate+comparison+of+miRNA+expression+profiles.">Quantification of small non-coding RNAs allows an accurate comparison of miRNA expression profiles.</a> Journal of Biomedicine &amp; Biotechnology. 2009, 659028 (2009).</li><li>Green, M. R., Sambrook, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+to+win+the+battle+with+RNase.">How to win the battle with RNase.</a> Cold Spring Harbor Protocols. 2019 (2), 101857 (2019).</li><li>Franzosa, E. 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=Relating+the+metatranscriptome+and+metagenome+of+the+human+gut.">Relating the metatranscriptome and metagenome of the human gut.</a> Proceedings of the National Academy of Sciences. 111 (22), 2329-2338 (2014).</li><li>Wohnhaas, C. 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=Fecal+microRNAs+show+promise+as+noninvasive+Crohn's+disease+biomarkers.">Fecal microRNAs show promise as noninvasive Crohn's disease biomarkers.</a> Crohn's &amp; Colitis. 2 (1), 003 (2020).</li><li>Tomkovich, 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=Human+colon+mucosal+biofilms+and+murine+host+communicate+via+altered+mRNA+and+microRNA+expression+during+cancer.">Human colon mucosal biofilms and murine host communicate via altered mRNA and microRNA expression during cancer.</a> mSystems. 5 (1), (2020).</li><li>Tarallo, 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=Altered+fecal+small+RNA+profiles+in+colorectal+cancer+reflect+gut+microbiome+composition+in+stool+samples.">Altered fecal small RNA profiles in colorectal cancer reflect gut microbiome composition in stool samples.</a> mSystems. 4 (5), 70 (2019).</li><li>Xing, 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=Breed+differences+in+the+expression+levels+of+gga-miR-222a+in+laying+hens+influenced+H2S+production+by+regulating+methionine+synthase+genes+in+gut+bacteria.">Breed differences in the expression levels of gga-miR-222a in laying hens influenced H2S production by regulating methionine synthase genes in gut bacteria.</a> Research Square. , (2020).</li><li>Teng, Y., 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=Plant-derived+exosomal+microRNAs+shape+the+gut+microbiota.">Plant-derived exosomal microRNAs shape the gut microbiota.</a> Cell Host &amp; Microbe. 24 (5), 637-652 (2018).</li><li>Moloney, G. M., Viola, M. F., Hoban, A. E., Dinan, T. G., Cryan, J. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Faecal+microRNAs:+indicators+of+imbalance+at+the+host-microbe+interface.">Faecal microRNAs: indicators of imbalance at the host-microbe interface.</a> Beneficial Microbes. , 1-10 (2017).</li><li>Giannoukos, G., 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=Efficient+and+robust+RNA-seq+process+for+cultured+bacteria+and+complex+community+transcriptomes.">Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.</a> Genome Biology. 13 (3), 23 (2012).</li></ol>

The authors declare no relevant or material financial interests that are related to the research method described in this protocol paper.

It is important to use RNase-free technique to prevent RNase contamination during the isolation7. After centrifugation and the formation of a compact interphase, it is key to avoid the interphase, lower phase, and the particle contaminant floating on the top of the aqueous phase when recovering the aqueous phase. Additionally, two washing steps with 500 &#181;L and 250 &#181;L Wash Solution 2/3 are added to eliminate contaminants in the filter membrane for optimized quality. Furthermore, a start sample material of more than 200 mg is not recommended as it may create difficulty in the clear formation of an interphase. Similarly, a sample material of less than 25 mg is not recommended as it may not be sufficient to extract enough RNA samples for downstream analysis.
The incredible growth in microbiome study has driven the measurements of microbial species, genes to metatranscriptional studies of the microbial profile8. MicroRNAs in the stool have been studied as markers for diseases9,10,11. Since the first report of fecal microRNA mediating host-microbe interactions3, increasing studies start to investigate the contributions of host and diet in the gut ecosystem12,13,14. Noteworthily, due to the richness of microbes in the gut lumen and feces, studies focusing on host arm of the host-microbe interaction demands minimal RNA contamination from microbes. Thus, an RNA extraction protocol that includes steps of cell lysing15 is not ideal for the study of RNAs released from host and diet. As such, we adapted this protocol to eliminate lysis steps for minimizing contaminations of RNA from living bacteria and living host cells in feces.
This protocol works for studies where extracellular RNA in the fecal or gut lumen content is an aim of interest. RNA isolated using this protocol is total RNA, including microRNA as major component. This protocol does not distinguish whether the RNA is in exosome, microvesicles, or in a vesicle-free form.

Extracellular RNA is getting recognized as a significant factor that mediates many biological processes1. Extracellular RNA in feces was first reported in 2008 as a marker for colon cancer and active ulcerative colitis2, and it was recently revealed as a normal component of the gut lumen and feces and mediates host-microbe communications3,4,5. The purpose of this RNA isolation protocol is to extract high quality extracellular RNA from fecal samples collected from animal and human subjects. The protocol was adapted from a commercial miRNA Isolation Kit. The RNA acquired is utilized for downstream analyses such as RNA sequencing, RT-PCR, and micro-array. The protocol includes several important and useful tips to maximize the quantity and quality of RNA found in the feces of animals and humans. The reason to develop and optimize this method of RNA (including microRNA) isolation is to decrease microbial RNA in the feces, limit the variables in the research studies and analyze the RNA composition in the gut without accounting various confounding factors and sources of contamination. Of note, this RNA isolation minimizes the release of RNA from living cell and living microbes (cellular RNA). It focuses on extracellular RNAs that have been released by gut cells or been acquired via food intake. Principally, this method is not suitable for studies where the microbial transcriptome is investigated.

<table>
	<tbody>
		<tr>
			<td>Acid-Phenol: Chloroform, pH 4.5 (with IAA, 125:24:1)</td>
			<td>Thermo Fischer Scientific</td>
			<td>AM9720</td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS, no calcium, no magnesium</td>
			<td>Thermo Fischer Scientific</td>
			<td>14190-144</td>
			<td></td>
		</tr>
		<tr>
			<td>Gloves</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>mirVana miRNA Isolation Kit</td>
			<td>Thermo Fischer Scientific</td>
			<td>AM1561</td>
			<td></td>
		</tr>
		<tr>
			<td>Nuclease-Free microcentrifuge tubes (1.5 mL, 2 mL)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Nuclease-Free Water (Not DEPC-treated)</td>
			<td>Thermo Fischer Scientific</td>
			<td>AM9937</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipettor and Nuclease-Free Pipette tips (with filter)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PowerLyzer 24 Homogenizer</td>
			<td>QIAGEN</td>
			<td>13155</td>
			<td></td>
		</tr>
		<tr>
			<td>RNaseZap RNase Decontamination Solution</td>
			<td>Thermo Fischer Scientific</td>
			<td>AM9780</td>
			<td></td>
		</tr>
		<tr>
			<td>Vortex Shaker</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

Representative RNAs were isolated from 50 mg mouse fecal samples (2 mouse fecal pellets) and 100 mg human stool specimens respectively and eluted in 50 &#181;L nuclease-free water. Spectrophotometer analysis of the concentration suggests a total amount of 49 &#181;g and 16 &#181;g RNA were isolated respectively (Table 1). The RNA purity was high as indicated by an A260/A280 ratio of ~2.0 and an A260/A230 ratio of ~1.8 (Table 1). As reported3, the majority of RNAs in the feces are microRNA and those microRNAs can exist in the exosome. Consistent with this, a chip-based electrophoresis assay of RNA suggests that representative RNA isolates from mouse and human feces are low in or lack of 18S and 28S rRNA compositions, and the size of RNA isolates falls in the small RNA region (Figure 1A). A further small RNA electrophoresis with the chip-based electrophoresis reveals that a large portion of the RNAs are of microRNA size (Figure 1B).&#160;This is consistent with the observation that the quantification completed by using a small RNA bioanalyzer is comparable to that obtained with previous assays6.
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Sample ID</td>
			<td>Elution volume (&#181;L)</td>
			<td>RNA concentration (ng/&#181;L)</td>
			<td>A260/A280</td>
			<td>A260/A230</td>
			<td>Yield (ng)</td>
		</tr>
		<tr>
			<td>Mouse</td>
			<td>50</td>
			<td>978.333</td>
			<td>2.036</td>
			<td>1.897</td>
			<td>48916.65</td>
		</tr>
		<tr>
			<td>Human</td>
			<td>50</td>
			<td>330.759</td>
			<td>1.981</td>
			<td>1.849</td>
			<td>16537.95</td>
		</tr>
	</tbody>
</table>
Table 1: Representative nanodrop analysis of RNA isolated with this protocol. Representative RNAs were isolated from 2 mouse fecal pellets or 100 mg human stool specimens, eluted in 50 &#181;L nuclease-free water. RNA concentration, ratio of A260/A280, and ratio of A260/A230 were measured with nanodrop.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61908/61908fig01.jpg" /> 
Figure 1: Representative chip-based electrophoresis analyses of size distribution of fecal RNA isolates.&#160;(A) Representative RNAs isolated from 2 mouse fecal pellets (left panel) and 100 mg human stool specimens (right panel) using the protocol described here were characterized using the chip-based electrophoresis assay.&#160;This assay&#160;suggests that the majority of RNA isolates were small RNA. (B) The isolates were then subjected for the small RNA electrophoresis with the chip-based electrophoresis system to analyze the size distribution of the isolates. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/61908/61908fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Fecal micro RNA Isolation at JoVE.com

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.

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 ...

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4.5K Views.  Brigham and Women's Hospital and Harvard Medical School. 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.

Video: Fecal micro RNA Isolation

RNA Interference in Ticks

Ticks are obligate hematophagous ectoparasites of wild and domestic animals and humans, and are considered to be second worldwide to mosquitoes as vectors of human diseases1 and the most important vectors affecting cattle industry worldwide2. Ticks are classified in the subclass Acari, order Parasitiformes, suborder Ixodida and are distributed worldwide from Arctic to tropical regions3. Despite efforts to control tick infestations, these ectoparasites remain a serious problem for human and animal health4,5.
RNA interference (RNAi)6 is a nucleic acid-based reverse genetic approach that involves disruption of gene expression in order to determine gene function or its effect on a metabolic pathway. Small interfering RNAs (siRNAs) are the effector molecules of the RNAi pathway that is initiated by double-stranded RNA (dsRNA) and results in a potent sequence-specific degradation of cytoplasmic mRNAs containing the same sequence as the dsRNA trigger7-9. Post-transcriptional gene silencing mechanisms initiated by dsRNA have been discovered in all eukaryotes studied thus far, and RNAi has been rapidly developed in a variety of organisms as a tool for functional genomics studies and other applications10.
RNAi has become the most widely used gene-silencing technique in ticks and other organisms where alternative approaches for genetic manipulation are not available or are unreliable5,11. The genetic characterization of ticks has been limited until the recent application of RNAi12,13. In the short time that RNAi has been available, it has proved to be a valuable tool for studying tick gene function, the characterization of the tick-pathogen interface and the screening and characterization of tick protective antigens14. Herein, a method for RNAi through injection of dsRNA into unfed ticks is described. It is likely that the knowledge gained from this experimental approach will contribute markedly to the understanding of basic biological systems and the development of vaccines to control tick infestations and prevent transmission of tick-borne pathogens15-19.

A method for RNA interference (RNAi) by injection of dsRNA into unfed ticks is described. RNAi is the most widely used gene-silencing technique in ticks where the use of other methods of genetic manipulation has been limited.

Ticks are obligate hematophagous ectoparasites of wild and domestic animals and humans, and are considered to be second worldwide to mosquitoes as vectors ...

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

RNA viruses use RNA dependent RNA polymerases to replicate their genomes. The intrinsically high error rate of these enzymes is a large contributor to the generation of extreme population diversity that facilitates virus adaptation and evolution. Increasing evidence shows that the intrinsic error rates, and the resulting mutation frequencies, of RNA viruses can be modulated by subtle amino acid changes to the viral polymerase. Although biochemical assays exist for some viral RNA polymerases that permit quantitative measure of incorporation fidelity, here we describe a simple method of measuring mutation frequencies of RNA viruses that has proven to be as accurate as biochemical approaches in identifying fidelity altering mutations. The approach uses conventional virological and sequencing techniques that can be performed in most biology laboratories. Based on our experience with a number of different viruses, we have identified the key steps that must be optimized to increase the likelihood of isolating fidelity variants and generating data of statistical significance. The isolation and characterization of fidelity altering mutations can provide new insights into polymerase structure and function1-3. Furthermore, these fidelity variants can be useful tools in characterizing mechanisms of virus adaptation and evolution4-7.

The present article describes the steps required to isolate and characterize RNA polymerase fidelity variants of RNA viruses and how to use mutation frequency data to confirm fidelity changes in tissue culture.

RNA viruses use RNA dependent RNA polymerases to replicate their genomes. The intrinsically high error rate of these enzymes is a large contributor to the ...

Development of Cell-type specific anti-HIV gp120 aptamers for siRNA delivery

The global epidemic of infection by HIV has created an urgent need for new classes of antiretroviral agents. The potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases including HIV. Many previous reports have shown that novel RNAi-based anti-HIV/AIDS therapeutic strategies have considerable promise; however, a key obstacle to the successful therapeutic application and clinical translation of siRNAs is efficient delivery. Particularly, considering the safety and efficacy of RNAi-based therapeutics, it is highly desirable to develop a targeted intracellular siRNA delivery approach to specific cell populations or tissues. The HIV-1 gp120 protein, a glycoprotein envelope on the surface of HIV-1, plays an important role in viral entry into CD4 cells. The interaction of gp120 and CD4 that triggers HIV-1 entry and initiates cell fusion has been validated as a clinically relevant anti-viral strategy for drug discovery. 
Herein, we firstly discuss the selection and identification of 2'-F modified anti-HIV gp120 RNA aptamers. Using a conventional nitrocellulose filter SELEX method, several new aptamers with nanomolar affinity were isolated from a 50 random nt RNA library. In order to successfully obtain bound species with higher affinity, the selection stringency is carefully controlled by adjusting the conditions. The selected aptamers can specifically bind and be rapidly internalized into cells expressing the HIV-1 envelope protein. Additionally, the aptamers alone can neutralize HIV-1 infectivity. Based upon the best aptamer A-1, we also create a novel dual inhibitory function anti-gp120 aptamer-siRNA chimera in which both the aptamer and the siRNA portions have potent anti-HIV activities. Further, we utilize the gp120 aptamer-siRNA chimeras for cell-type specific delivery of the siRNA into HIV-1 infected cells. This dual function chimera shows considerable potential for combining various nucleic acid therapeutic agents (aptamer and siRNA) in suppressing HIV-1 infection, making the aptamer-siRNA chimeras attractive therapeutic candidates for patients failing highly active antiretroviral therapy (HAART).

Several 2&#x2019;-Fluoro RNA aptamers against HIV-1Ba-L gp120 with nanomole affinity are isolated from a RNA library by in vitro SELEX procedure. A new dual inhibitory function anti-gp120 aptamer-siRNA chimera is created and shows considerable promise for systemic anti-HIV therapy.

The global epidemic of infection by HIV has created an urgent need for new classes of antiretroviral agents. The potent ability of small interfering ...

RNA Isolation of Pseudomonas aeruginosa Colonizing the Murine Gastrointestinal Tract

Pseudomonas aeruginosa (PA) infections result in significant morbidity and mortality in hosts with compromised immune systems, such as patients with leukemia, severe burn wounds, or organ transplants1. In patients at high-risk for developing PA bloodstream infections, the gastrointestinal (GI) tract is the main reservoir for colonization2, but the mechanisms by which PA transitions from an asymptomatic colonizing microbe to an invasive, and often deadly, pathogen are unclear. Previously, we performed in vivo transcription profiling experiments by recovering PA mRNA from bacterial cells residing in the cecums of colonized mice 3 in order to identify changes in bacterial gene expression during alterations to the host&#x2019;s immune status.
As with any transcription profiling experiment, the rate-limiting step is in the isolation of sufficient amounts of high quality mRNA. Given the abundance of enzymes, debris, food residues, and particulate matter in the GI tract, the challenge of RNA isolation is daunting. Here, we present a method for reliable and reproducible isolation of bacterial RNA recovered from the murine GI tract. This method utilizes a well-established murine model of PA GI colonization and neutropenia-induced dissemination4. Once GI colonization with PA is confirmed, mice are euthanized and cecal contents are recovered and flash frozen. RNA is then extracted using a combination of mechanical disruption, boiling, phenol/chloroform extractions, DNase treatment, and affinity chromatography. Quantity and purity are confirmed by spectrophotometry (Nanodrop Technologies) and bioanalyzer (Agilent Technologies) (Fig 1). This method of GI microbial RNA isolation can easily be adapted to other bacteria and fungi as well.

RNA Isolation of Pseudomonas aeruginosa Colonizing the Murine Gastrointestinal Tract

A reliable method for the RNA isolation of Pseudomonas aeruginosa recovered from murine cecums is described. The RNA recovered is of sufficient quantity and quality for subsequent qPCR, transcription profiling, and RNA Seq experiments. This technique can be adapted for RNA isolation of other intestinal microbes.

Pseudomonas aeruginosa (PA) infections result in significant morbidity and mortality in hosts with compromised immune systems, such as patients with ...

Detection of Fluorescent Nanoparticle Interactions with Primary Immune Cell Subpopulations by Flow Cytometry

Engineered nanoparticles are endowed with very promising properties for therapeutic and diagnostic purposes. This work describes a fast and reliable method of analysis by flow cytometry to study nanoparticle interaction with immune cells. Primary immune cells can be easily purified from human or mouse tissues by antibody-mediated magnetic isolation. In the first instance, the different cell populations running in a flow cytometer can be distinguished by the forward-scattered light (FSC), which is proportional to cell size, and the side-scattered light (SSC), related to cell internal complexity. Furthermore, fluorescently labeled antibodies against specific cell surface receptors permit the identification of several subpopulations within the same sample. Often, all these features vary when cells are boosted by external stimuli that change their physiological and morphological state. Here, 50 nm FITC-SiO2 nanoparticles are used as a model to identify the internalization of nanostructured materials in human blood immune cells. The cell fluorescence and side-scattered light increase after incubation with nanoparticles allowed us to define time and concentration dependence of nanoparticle-cell interaction. Moreover, such protocol can be extended to investigate Rhodamine-SiO2 nanoparticle interaction with primary microglia, the central nervous system resident immune cells, isolated from mutant mice that specifically express the Green Fluorescent Protein (GFP) in the monocyte/macrophage lineage. Finally, flow cytometry data related to nanoparticle internalization into the cells have been confirmed by confocal microscopy.

Analysis of nanoparticle interaction with defined subpopulations of immune cells by flow cytometry.

Engineered nanoparticles are endowed with very promising properties for therapeutic and diagnostic purposes. This work describes a fast and reliable ...

Nucleocapsid Annealing-Mediated Electrophoresis (NAME) Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors

RNA or DNA folded in stable tridimensional folding are interesting targets in the development of antitumor or antiviral drugs. In the case of HIV-1, viral proteins involved in the regulation of the virus activity recognize several nucleic acids. The nucleocapsid protein NCp7 (NC) is a key protein regulating several processes during virus replication. NC is in fact a chaperone destabilizing the secondary structures of RNA and DNA and facilitating their annealing. The inactivation of NC is a new approach and an interesting target for anti-HIV therapy. The Nucleocapsid Annealing-Mediated Electrophoresis (NAME) assay was developed to identify molecules able to inhibit the melting and annealing of RNA and DNA folded in thermodynamically stable tridimensional conformations, such as hairpin structures of TAR and cTAR elements of HIV, by the nucleocapsid protein of HIV-1. The new assay employs either the recombinant or the synthetic protein, and oligonucleotides without the need of their previous labeling. The analysis of the results is achieved by standard polyacrylamide gel electrophoresis (PAGE) followed by conventional nucleic acid staining. The protocol reported in this work describes how to perform the NAME assay with the full-length protein or its truncated version lacking the basic N-terminal domain, both competent as nucleic acids chaperones, and how to assess the inhibition of NC chaperone activity by a threading intercalator. Moreover, NAME can be performed in two different modes, useful to obtain indications on the putative mechanism of action of the identified NC inhibitors.

Nucleocapsid Annealing-Mediated Electrophoresis NAME Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors

This protocol describes NAME, an assay that allows the rapid identification of molecules able to inhibit in vitro the chaperone activities of HIV-1 nucleocapsid protein.

RNA or DNA folded in stable tridimensional folding are interesting targets in the development of antitumor or antiviral drugs. In the case of HIV-1, viral ...

Optimization of a Quantitative Micro-neutralization Assay

The micro-neutralization (MN) assay is a standard technique for measuring the infectivity of the influenza virus and the inhibition of virus replication. In this study, we present the protocol of an imaging-based MN assay to quantify the true antigenic relationships between viruses. Unlike typical plaque reduction assays that rely on visible plaques, this assay quantitates the entire infected cell population of each well. The protocol matches the virus type or subtype with the selection of cell lines to achieve maximum infectivity, which enhances sample contrast during imaging and image processing. The introduction of quantitative titration defines the amount of input viruses of neutralization and enables the results from different experiments to be comparable. The imaging setup with a flatbed scanner and free downloadable software makes the approach high throughput, cost effective, user friendly, and easy to deploy in most laboratories. Our study demonstrates that the improved MN assay works well with the current circulating influenza A(H1N1)pdm09, A(H3N2), and B viruses, without being significantly influenced by amino acid substitutions in the neuraminidase (NA) of A(H3N2) viruses. It is particularly useful for the characterization of viruses that either grow to low HA titer and/or undergo an abortive infection resulting in an inability to form plaques in cultured cells.

This study describes an imaging-based micro-neutralization assay to analyze the antigenic relationships between viruses. The protocol employs a flatbed scanner and has four steps, including titration, titration quantitation, neutralization, and neutralization quantitation. The assay works well with current circulating influenza A(H1N1)pdm09, A(H3N2), and B viruses.

The micro-neutralization (MN) assay is a standard technique for measuring the infectivity of the influenza virus and the inhibition of virus replication. ...

Real-time Quaking-induced Conversion Assay for Detection of CWD Prions in Fecal Material

The RT-QuIC technique is a sensitive in vitro cell-free prion amplification assay based mainly on the seeded misfolding and aggregation of recombinant prion protein (PrP) substrate using prion seeds as a template for the conversion. RT-QuIC is a novel high-throughput technique which is analogous to real-time polymerase chain reaction (PCR). Detection of amyloid fibril growth is based on the dye Thioflavin T, which fluoresces upon specific interaction with &#7526;-sheet rich proteins. Thus, amyloid formation can be detected in real time. We attempted to develop a reliable non-invasive screening test to detect chronic wasting disease (CWD) prions in fecal extract. Here, we have specifically adapted the RT-QuIC technique to reveal PrPSc seeding activity in feces of CWD infected cervids. Initially, the seeding activity of the fecal extracts we prepared was relatively low in RT-QuIC, possibly due to potential assay inhibitors in the fecal material. To improve seeding activity of feces extracts and remove potential assay inhibitors, we homogenized the fecal samples in a buffer containing detergents and protease inhibitors. We also submitted the samples to different methodologies to concentrate PrPSc on the basis of protein precipitation using sodium phosphotungstic acid, and centrifugal force. Finally, the feces extracts were tested by optimized RT-QuIC which included substrate replacement in the protocol to improve the sensitivity of detection. Thus, we established a protocol for sensitive detection of CWD prion seeding activity in feces of pre-clinical and clinical cervids by RT-QuIC, which can be a practical tool for non-invasive CWD diagnosis.

Here, we present a protocol to describe a simple, fast and efficient prion amplification technique, the real-time quaking-induced conversion (RT-QuIC) method.

The RT-QuIC technique is a sensitive in vitro cell-free prion amplification assay based mainly on the seeded misfolding and aggregation of recombinant ...

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection

Double-stranded (ds) RNA is produced as a replicative intermediate during RNA virus infection. Recognition of dsRNA by host pattern recognition receptors (PRRs) such as the retinoic acid (RIG-I) like receptors (RLRs) RIG-I and melanoma differentiation-associated protein 5 (MDA-5) leads to the induction of the innate immune response. The formation and intracellular distribution of dsRNA in positive-sense RNA virus infection has been well characterized by microscopy. Many negative-sense RNA viruses, including some arenaviruses, trigger the innate immune response during infection. However, negative-sense RNA viruses were thought to produce low levels of dsRNA, which hinders the imaging study of PRR recognition of viral dsRNA. Additionally, infection experiments with highly pathogenic arenaviruses must be performed in high containment biosafety level facilities (BSL-4). The interaction between viral RNA and PRRs for highly pathogenic RNA virus is largely unknown due to the additional technical challenges that researchers need to face in the BSL-4 facilities. Recently, a monoclonal antibody (Mab) (clone 9D5) originally used for pan-enterovirus detection has been found to specifically detect dsRNA with a higher sensitivity than the traditional J2 or K1 anti-dsRNA antibodies. Herein, by utilizing the 9D5 antibody, we describe a confocal microscopy protocol that has been used successfully to visualize dsRNA, viral protein and PRR simultaneously in individual cells infected by arenavirus. The protocol is also suitable for imaging studies of dsRNA and PRR distribution in pathogenic arenavirus infected cells in BSL4 facilities.

Double-stranded RNA produced during RNA virus replication can be recognized by pattern recognition receptors to induce an innate immune response. For negative-sense RNA viruses, the interaction between the low-level dsRNA and PRRs remains unclear. We have developed a confocal microscopy method to visualize arenavirus dsRNA and PRR in individual cells.

Double-stranded (ds) RNA is produced as a replicative intermediate during RNA virus infection. Recognition of dsRNA by host pattern recognition receptors ...

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 ...