Comments (2)
Yesterday (2017-06-24), @bemert and I plated the samples on Lysogeny broth plates. I'll let @bemert fill in the details. Thanks to the following indivuduals for their plating advice:
Email from Elisabeth Bik on 2017-06-22
Elisabeth "Elies" Bik is a Science Editor at uBiome, who runs the popular Twitter account @MicrobiomDigest. She gave us the following advice:
For growing bacteria, of course with the restriction that many bacteria won't be able to grow, it would be best to pick a general rich nutrient medium, such as Luria Broth (LB) agar - without any antibiotics. For example, see this paper where environmental isolates from the ISS were grown.
LB agar is a very commonly used agar type. Prepoured plates can e.g be bought here or here
I would recommend making 10-fold serial dilutions of the fratjuice and plating out 100 ul per plate using a spreader or sterile glass beads (I can give more directions if needed). Some dilutions will produce confluent plates (too full), and others might not yield anything, but there will hopefully be a dilution/plate that will have the perfect amount of bacteria/fungi for a photo.
Email from Angelyca Jackson on 2017-06-23
Below is an email conversation with Angelyca Jackson where I asked her "Any advice on what media to use?" Angelyca is a scientist with the Deb Hogan Lab at Dartmouth. We met Angelyca when we gave the Hogan Lab a surprise visit the day we began the study. They set us on the right track and enlightened us a bit regarding microbes. Here's Angelyca's plating advice:
For plating the refrigerated samples I would plate on a couple of different non-selective media types for bacteria and for fungi. I recommend this because no matter what media you use, generally you will select for a certain type of 'bug' depending on the carbon, nitrogen, or other nutrient source within your plate.
Here are links to non-selective media for bacteria and for yeast and molds.
I would shoot for one that specifies that it's for broad-range culture without any inhibitors or indicators (so that you get the best chance of everything growing that's still alive in your samples). Keep in mind that your 16S fratseq (great name) data will be richer than what you may culture!
from fratjuice.
As Daniel mentioned, we plated each sample at two dilutions on LB agar. We diluted 10uL of each sample with 90uL LB broth then removed 10uL for a second dilution into 990uL LB broth. 90uL of the initial 1:10 dilution and 100uL of the 1 :1000 dilution were plated on LB agar and incubated overnight at 37ΒΊC.
After incubating for 22 hours, all samples had colonies with the lesser dilution and only samples FJ2 and FJ3 had colonies at the higher dilution(1:100). As a non-microbiologist, I believe there are at least 4 distinct colony types in samples FJ1, FJ3, and FJ5, and at least 2 distinct colony types in samples FJ2 and FJ4. The smell reminds me of overgrown E. coli. Here are some images of the plates:
from fratjuice.
Related Issues (7)
- Experiments to run on the initial samples HOT 1
- Preparing the fratjuice for uBiome fratseq HOT 4
- fratjuice deepart: using deep learning to combine frat and bacteria pics
- Registering samples on the uBiome Explorer HOT 3
- Extracting species abundance from uBiome FASTQ outputs HOT 2
- Accessing fastq files from raw uBiome zips HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from fratjuice.