Ag Kit Instructions
User Manual:
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Page Count: 5
1
Please read the entire packet before starting.
Check o each step once it has been completed.
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Sampling tip
Sample shaft (Do Not Handle!)
Red handling cap
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4
This will take you through the required consent process, participant survey, and optional sur-
veys, if you are adding a human sample.
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See Appendix A for specic sample type collection instructions. Deviations from these instruc-
tions are at your expense. Cap the sample tube once done.
6
Record the date, time (in 24-hour format), and sample type in the corresponding areas on the
tube label.
7Wrap the tube in absorbent tissue, such as facial tissue or paper towels, and mail it back within
48 hours of sample collection.
If you have multiple samples, it is okay to send them one at a time. If you cannot mail them all
at the same time, please store the tubes at room temperature in a dry, cool, location (such as a
cabinet or closet).
Please do not freeze or refrigerate samples prior to shipment, unless we have directed you
otherwise.
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These instructions are extremely important. Deviations will cause issues with sample process-
ing, sequencing, and data analysis. We cannot guarantee that we will be able to process your
sample and we cannot oer replacements if the instructions are not followed. Please do not
hesitate to email us with questions at info@americangut.org.
Use “Assign Sample” on the left-hand navigation menu on microbio.me to associate your sam-
ple to your participant prole. We cannot process a sample until it has been assigned.
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Quicklist Instructions & Checklist
What Your Kit Contains
Sample Tube/SWUBE Pre-addressed Return Envelope
This will be used to mail your sample
back. Please note that proper postage
is required when sending the kit back.
Credentials Sheet
This will contain your assigned
kit ID, password, and barcode
number(s). Retain this sheet for
your records as your kit ID is
permanent for logging into the
participant website.
REGISTRATION
Register your kit at http://microbio.me/AmericanGut/ using a desktop computer or laptop.
VERIFY YOUR KIT
Input your emailed verification code (sent after completing Step 1) and confirm that you
have received the correct barcode numbers found on your sample tubes.
CREATE A PARTICIPANT PROFILE
COLLECT SAMPLE
RECORD SAMPLE DETAILS
ASSIGN YOUR SAMPLE
MAIL SAMPLE
ATTN: Gregy Humphrey,
Knight Lab
BRF II Room 1220D
9500 Gilman Drive
La Jolla, CA 92093-0763
ank you for participating in the American
Gut Project!
Barcodes: 00000
Kit ID: abcdef
Password: 00000
TM
Detailed Instructions
A desktop computer or laptop is required for Steps 1-3 and 6.
1. Registration: Register your kit at http://microbio.me/AmericanGut/ using the kit ID and password
found on the Credentials Sheet.
2. Verify Your Kit: Once registered, a 5-digit verification code will be emailed to you. When you login,
confirm that the list of barcode numbers match the label numbers on the sample tubes (more than
one will show up if you have ordered a kit for two or more). Check the boxes next to the barcode
numbers and enter the verification code. If you did not receive a verification code or the barcode
numbers listed, contact info@americangut.org immediately.
3. Create A Participant Profile: Sample options – human, animal, or environmental.
üHuman: Must complete a consent form and the participant survey*. Providing formal consent is
mandatory so we can process your sample.
üAnimal: You will be asked to fill out a short survey. No consent is necessary.
üEnvironmental: No consent and no surveys are required. Skip Step 3 and proceed to step 4.
Hover your mouse over the appropriate sample
category on the left navigation menu and click the
“Add ____ source” option. (See Figure 1.)
NOTE: If there are multiple people using the sample
tubes, you can repeat this step to add an additional
participant.
After adding a source, next is the consent (parental
consent is required for participants under the age of
18) and survey. After submitting your survey, you
will be emailed a copy of the signed consent form
(for your records).
*All human sample survey questions are optional. If
you choose not to take the survey, you may leave
fields blank and proceed by clicking on “Submit”.
However, your survey data is beneficial to this
research and we would greatly appreciate your input.
ADDITIONAL SURVEYS:
After completing the American Gut survey, the confirmation page has links to additional surveys.
These optional surveys ask for additional specific information like your diet.
You may complete these surveys at a later time by clicking on your name after hovering over “Human
Samples” and clicking on the survey name.
Do not collect a sample until you have completed Step 3.
Figure 1.
4. Collect Sample: See Appendix A for specific collection instructions. It is critical to handle the tube
by the red cap only and to touch the cotton tips only to the surface of the sample being collected. If
your sample is accidentally contaminated, please contact us and we will work with you on a solution.
It may not be possible for us to replace samples free of charge.
5. Record Sample Details: Write the date, the time (24-hour format), and the sample type in the
appropriate fields on the tube label. (see Figure 2.) If you have been provided a SWUBE/glass tube
for sampling (see Figure 3.), then no information is required to be written down on the tube. For
both types of tubes, please write down and save your sample details for Step 6.
Figure 2. Tube Recording Example:
The tube contains a specimen sample collected on June 5, at 11:00.
Figure 3. SWUBE Example.
6. Assign YOUR sample to YOUR participant profile: Click “Assign Sample” on the left navigation
menu when logged into microbio.me. Select the name you want to assign a sample to, then fill out
the requested form with your sample details. Assigning your sample MUST be completed before
your sample can be processed.
7. Mail Sample: Wrap the ENTIRE sample tube (swabs inside!) in absorbent tissue (e.g. facial tissue or
paper towels) and mail it back within 48 hours of sample collection. The absorbent tissue will help to
keep the relative humidity within the package low. The sooner we receive your sample, the sooner
we can store and prepare it for processing! If you have been provided a SWUBE, place it in the bubble
wrap bag as well for additional protection. If you cannot send your sample immediately, please do not
freeze or refrigerate the sample prior to shipment unless directed otherwise.
We recommend taking the sample to the post office for proper postage to avoid a transit delay. If samples
are delayed, they will likely not produce the highest quality results. We also recommend using an
additional reinforced envelope to reduce losing the sample due to damaged packaging.
All American Gut samples should be mailed to:
ATTN: Greg Humphrey, Knight Lab
BRF II Room 1220D
9500 Gilman Drive
La Jolla, CA 92093-0763
Appendix A: Sample Type Collection Instructions
1. FECAL: Rub both cotton tips on a fecal specimen (ideally, a used piece of toilet paper). Collect a small
amount of biomass, saturating half the swab at maximum. More is not better! The ideal amount of
biomass collected is shown in Figure 4.
Figure 4. A fecal sample showing an ideal amount of material collected. Excessive amounts
of material will result in the nonrefundable exclusion of your sample. See also Figure 5.
It is important that the amount of material collected is small for two reasons:
1. The amount of material could bias the sample’s results (e.g. mold growth might contaminate the sample).
2. Excess material cannot be handled by our processing pipeline.
Our molecular methods are incredibly sensitive and require nanograms (billionths of a gram) of DNA.
Previous studies have shown that even a tiny amount of material, like in the picture above, is sufficient to
assess the microbial life in your gastrointestinal tract.
The images below represent good and bad fecal samples.
Figure 5:
þ
Represents Good Sample!
V
= Bad Sample
DIFFICULTY OBTAINING FECAL SPECIMENS: We recognize that some participants have chronic
constipation. In these instances, we recommend the “catch and release” method, using no more than 2-4
paper towels, enough material to prevent fecal contact on you and to avoid clogging the toilet. If the
specimen is not soft, please just rub both sides of the cotton swabs on it to get a light smear. Be certain to
wash your hands afterwards!
2. ORAL: Firmly rub both sides of both cotton tips on the surface of the tongue for 20 seconds.
Take great caution not to touch the inside of your cheeks, teeth, or lips. An example of the area of
sampling for the tongue is shown in Figure 6.
Figure 6. Example of where to rub the cotton swabs on the tongue if you are collecting an oral sample.
3. SKIN: Do not wash the skin surface for at least two hours prior to sampling. Firmly rub both sides of
both cotton tips over the skin surface being sampled for 20 seconds. Some examples of the area of
sampling are shown in Figure 7 and 8. Note that for skin samples, it is necessary to press relatively hard
with the sampling tips.
Figure 7. Example of where to rub the cotton swabs if you are collecting a forehead sample.
Figure 8. Example of where to rub the cotton swabs if you are collecting a sample from the palm.
NOTE: Submitting oral and skin samples will take a longer time than the expected 3 months to process
and return results as we prioritize processing fecal samples.
Once you have completed sampling, cap the swabs back into the tube.
If you have further questions or issues:
First consult the FAQ section: http://www.microbio.me/AmericanGut/faq/.
If you cannot find the answer to your question, email info@americangut.org.
