Hi Brain-Gut lovers,
It’s been awhile!
So you want to start studying poop, but you aren’t a microbiologist? Read on!
Recently I have started getting some questions about how to start a microbiome study. The word is getting out there! Poop is the way of the future! To address those questions, I decided to start compiling a list of things to think about when setting up your brand spanking new microbiome study. Enjoy!
This list is written from the perspective on a non-microbiologist (me) getting into the microbiome world. These are things that I have found helpful/learned along the way. It is small now (because it is Tuesday night and I am tired), but it will grow as I think of, and learn more, things – so bookmark and check back!
If you have any suggestions of your own be sure to comment and I will integrate them.
How should I collect the poop?
- Can be used for Fecal Microbiome Transplants (FMT’s) – always think of the future studies you might want to do!
- Tried and true method for 16s and metagenomics sequencing
- Some people don’t like storing their poop in their freezer (weird – I know)
- Some people don’t have freezers
- Once it has been frozen it needs to stay frozen, so consider that in the cost of transporting samples.
- Ease of collection – pea sized amount, stored at room temperature, doesn’t smell, so may lead to better participant adherence.
- Shipped at room temperature
- Stable for 60 days at room temperature
- Cannot be used for FMT due to stabilizing liquid.
Collecting from a diaper:
- Some diapers have antimicrobial properties. To avoid that, try to use some cover on the diaper and collect from the protected area of the diaper. We are currently trialling these transparent dressings from 3M.
Where can I learn more about the microbiome and analytics?
- Dr. Dan Knights – University of Minnesota – Microbiome Discovery
- Dr. Knights has a great series of lectures on microbiome analytical considerations on youtube that I found extremely helpful. Clear presentation style, helpful visuals.
- Rob Knight – Gut Check: Exploring your microbiome
- Dr. Knight and co have put together a Coursera course that is an excellent introduction to the microbiome. It is also useful for those who want to learn more about the microbiome but not necessarily the nitty gritty of the analytical techniques.
- Microbiome Digest – Bik’s Picks – Dr. Elizabeth Bik
- In my opinion, this is the best resource available for starting out in the microbiome world. A daily digest with links to the most recent articles on anything microbiome. Beautifully curated and filed by topic and subtopic (e.g., human gut > pathogens), this is a phenomenal archive of the literature. Did I mention this was DAILY!!!
Tutorials I haven’t tried but are on my list:
- Greg Caporoso – Applied Bioinformatics Tools
- Guide to statistical analysis in microbial ecology (GUSTA ME)
- Find the empirical paper associated with this page here.
I want to have a crack at analyzing the microbiome myself. Are there any cool programs I can use?
There are so many, but here are two suites/pipelines that I use a lot.
- QIIME2 – Greg Caporoso
- Check their website for upcoming hands on workshops.
- I went to the workshop in February 2018 and I will write a review of that soon and link to it here. Spoiler alert – it was very good!
- Galaxy – The Huttenhower Lab
- Some fairly easy to use tools here and GUI that is quite intuitive.
- If you have heard of PICRUSt – Predictive metagenomics using 16s data, you can use it here.
What other data should I collect?
When it comes to the microbiome, the more you know about the samples (i.e., the metadata), the better! Try to collect everything imaginable that could potentially affect the microbiome. I have listed some typical information that you would want (specifically for developmental samples) below, but I surely missed many. Use this as a list to stimulate thinking about your own samples.
- Measures of fetal health
- Fetal drug and alcohol exposure
- Maternal prenatal antibiotic exposure
- Mode of birth
- Postnatal antibiotic exposure
- Postnatal infections
- Gestational age at birth
- Age of child
- Breast or bottle fed
- Solid or liquid food and date of transition to solids
- Health variables (e.g., physical and mental illnesses, infections etc)
- Home variables (e.g., pets, siblings, etc)
- Health of parents and siblings
- Diet (including beverages)
- Drug and alcohol exposure (usually for teens and older)
- Current medications
- Use of pro and prebiotic medications
- Current and past antibiotic use
- All of your variables of interest (which may or may not be included above).
That’s it for now. Will update more soon.
-The Two Brains