The beginning of summer (Yes we have seen a bit of it up North) sees the beginning of a busy period. Two different catchments are being sampled, which means it is all go in the in the field and in the lab.
Winter saw the collecting of E.coli from different animals and sewage to look for 4 genes which were first found in Japan. These genes are found in some E.coli and give a MASSIVE hint that these E.coli have come from human bottoms! Collecting E.coli isn’t all that fun, they live in the guts of warm blooded animals, so the easiest way to collect them is by collecting poo… great. The trickiest thing is actually collecting fresh poo without getting any grass/soil/sand/hay/hair/tarmac/sweat, or anything else a wee poo might land on, mixed into your sample (If you don’t believe me imagine collecting a fresh gull poo from a sandy beach!).
A huge shout out goes to the farmers and animal owners of Northumberland, Tyne and Wear and Cumbria for all their help and kindness, oh and for not judging the weird poo collector!
Once back at the lab at Newcastle University, the collected E.coli were grown and given a home (at -80oC! – Cue evil laugh). Many different strains of E.coli live in the gut, but I needed just a single one
from each poo sample. So to grow the E.coli, a tiny bit was spread on an agar plate which contain all the nutrients E.coli need to grow quickly.
The plate, with the tiny bit of poo, is kept at 37oC (Body temperature) over night. E.coli can double in numbers roughly every 20 minutes in the right conditions which is why food is kept chilled and unfortunately why food poisoning caused by E.coli occurs so quickly (6-12 hours after eating)! Luckily for microbiologists the quickly growing E.coli mean that in just one sleep the agar plate is full of E.coli. Each small green dot in the picture is millions of just one single strain of E.coli, how incredible is that!
After all their hard work in growing so quickly the E.coli are rewarded by being boiled alive and split open to get all of their DNA out! Sadly, growing E.coli in the lab smells only marginally better than the collected poo, but on the plus side getting the DNA from E.coli is really easy. Now we can test this DNA to see if it contains one of the four genes that might tell us that is came from a human. These lab tests were really positive all 4 human markers perform equally as well in the UK as in Japan. This is really phenomenal, E.coli growing in the guts of humans in Japan contain 4 genes which E.coli growing in the guts of humans in the UK have, but E.coli growing in animals don’t have! (Disclaimer: Sadly, some E.coli in humans don’t have these genes and a very few sneaky E.coli living in animals have these genes!).
The Next Step…
So great, we grab some sewage, we grow E.coli and we know it came from humans… not exactly rocket science is it. The next steps then is really see how useful these genes are. A fantastic MSc student @olli_crudge is searching for these genes in the Morland catchment, part of the Eden Environmental Test Catchment.
Olli is trying to determine just how much Nitrogen and Phosphorus pollution is coming from humans and how much is coming from agriculture. We are incredibly excited about this work, it is the first time that this technique has been used in the UK and early results look promising. Results to follow shortly!