My name is Hilary Brown I work at the Wellcome Trust Sanger Institute. I’m currently studying for a PhD based on the Intestinal Microbiota of the Human Gut. The human intestinal microbiota is largely made up of bacteria in addition to some viruses and fungi and these bacteria act together as a community, so that they work with each other for their own benefit but for our advantage as well. If there is an imbalance in this community and some species increase in abundance or others lessen this can have a negative effect on our health. We want to understand how this community feigns our health and also identify ways to restore this balance again.
The majority of the intestinal microbiota are beneficial but some of them can be harmful and this is why we study them in a CL2 lab.
CL2 stands for Containment Level 2 and that means we have certain safety procedures in place to protect ourselves. If you are taking antibiotics then you’re not allowed to enter the laboratories. This is because antibiotics – while they will kill the bacteria the hell is reaching you sick – they can also kill a lot of the good guys, which causes an imbalance in your gut and leaves you more prone to further infection. Exclusively authorised parties are allowed to work in the lab.
When I register the laboratories I put on a lab coat and gloves. These protect me from any spillages or bacterial taint. Most of the bacteria that live in your gut are anaerobic; this means they cannot survive in the presence of oxygen. Because of this “were working with” the bacteria in anaerobic punks. These boards are sealed.
They are constantly being spouted with anaerobic gas that contains hydrogen, carbon dioxide emissions and nitrogen. This stops all of the oxygen out and intends the bacteria can survive inside them. The first thing I need to do is to enter the anaerobic closet. I target the sleeves over my forearms and then by pressing these pedals, I can suck all of the air out of the sleeves. The other pedal then blows more anaerobic gas into the sleeves.
I repeat this process three times to ensure I’ve removed as much oxygen as possible before opening the doors and penetrating the anaerobic cabinet. To study these bacteria we need to grow them on Agar plates. The Agar that the bacteria develop on contains a lot of nutrients that would also be present in the human gut. When you fleck the bacteria onto a new plate you can often see new provinces flourishing 24 hours later.
Here I have an individual bacterial species grown in a plate.
One of the jobs I regularly have to do is to re-streak these onto brand-new layers. This is because the bacteria will use up all the accessible nutrients. When I’m working in the anaerobic bonnet I have to work aseptically. This represents working as clean as is practicable and trying to prevent contamination of my experimentation.
For instance, if I’m streaking bacteria on to a brand-new layer, I will use an Inoculating loop but I will merely use this loop-the-loop once- after use it I will discard it and I will use a new loop before moving on to the next plate.
The report contains two ways in which I study these bacteria; one is by understanding their phenotype. This involves studying their biology; how they live and grow, how they respond to different environmental conditions. The other is by studying the genotype. We obtain the DNA from the bacteria and then we do whole genome sequencing of this DNA. When the sequencing is finished I then analyse the data on my computer exercising numerous bioinformatic analysis tools.
Using these tools I can look at how closely related these bacteria are to each other and I can also identify brand-new categories that no one has cultured before. Studying the intestinal microbiota is very exciting because it’s moving very quickly from basic research towards therapeutics. This is unusual really for a discipline of biology, often it takes a much longer time before we start seeing new treats and new drugs on the market place ..