microbiom and microfluidics

This week we did two independent projects.
1) We sampled our oral and topocal microbiom. We cultured it, and isolated a colony for sequencing.
2) we built a DIY microfluidic device to mix two substances


Human microbiota: all the microorganisms that live on/in the human body.

Metagenomics: Analyzing collections of genomes and genes from a microbial community

Bioinformatics: the science of collecting and analyzing complex biological data such as genetic codes.

Shotgun metagenomic sequencing: A DNA sequencing method that enables comprehensive sampling of all genes in all organisms in a given complex microbial sample.

Gnotobiotic: 'germ-free'; relating to or denoting an environment for rearing or culturing organisms in which all the microorganisms are either known or excluded.

Super donor: A person whose bacteria/microbiome are dominant in any environment

SeqF and SeqR: A DNA sequence is usually sequenced in both directionswith a forward and a reverse primer, denoted as seqF and seqR.

Metagenomics: "Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms." refernece

16s rrna sequencing:

Lab notes:

In order to make a microfuildic device we laminated materials with cut channels. The snipped below is from our lab hand out and shows the order.

We inserted tubing to feed in the substances. Using a ~0.2" sheet of PDMS as the connector. The PDMS was poured into petri dishes, and here cut to size to fit the glass coverslip. We used a biopsy puncher, which is a hollow needle, to punch the hole to fit the tube.

On the left you can see the final device, which just mixes two substances. On the right you can see FALCON written on the petridish.

Part 2 - Our microbiomes

To sample our microbiomes we each took a q-tip and swabbed our mouth and touched it to a petri dish, and took another swab of our hand and touched another plate. The plates were cultured overnight in a warm environment. The next day we isolated a single collony from the culture, with lots of different bacteria colonies, and grew it on a smaller sample plate. These plates ideally only had one strain of bacteria and were sent to be sequenced.

On the left you can see all the smaples from the class.

On the right you can see my microbiome cultures and isolated sample plates. We sent these plates to get 16s rrna sequencing at Genewiz. I BLASTed the results, which stands for Basic Local Alignment Search Tool, and found the top descriptor for each sample which you can see below. All the bolded results are bacteria which shoulded up as the top descriptor in more than one sample. For instance, Prathima and I both sent in samples for Neisseria perflava, which means we have similar bacteria!

Person Oral Skin
Andrew Paracoccus yeei Staphylococcus epidermidis
Jelle Staphylococcus aureus Micrococcus yunnanensis
Judith Nothing found? Staphylococcus pasteuri
Kongo Pantoea anthophila
Lucy Bacillus albus Bacillus paranthracis
Oscar Staphylococcus aureus Staphylococcus lugdunensis
Pat Haemophilus parainfluenzae Acinetobacter johnsonii
Prathima Bacillus velezensis Neisseria perflava
Ren Staphylococcus aureus Staphylococcus saccharolyticus
Priya Lysinibacillus tabacifolii Acinetobacter johnsonii
Rahma Staphylococcus aureus Kocuria rhizophila
Sara Neisseria perflava Staphylococcus pasteuri
Vivian Granulicatella adiacens [Brevibacterium] frigoritolerans
Yiqi Staphylococcus aureus Staphylococcus aureus