Raoultella planticola

Raoultella planticola was a bacterium.

History
In 2017, Agrofuel Research Operations genetically modified a sample of the bacteria using the enzyme EC 31. It was meant to break down the root system of a plant. However, due to a misplaced decimal point, the bacteria became world-ending by killing life forms completely and turning it mostly into "gunk."

Attempting to gain "consent" to take over the Earth by saving it, the Monks detected a future where the bacteria would end the world within a year. The Monks attempted to leverage this to get the needed consent, but the Twelfth Doctor refused and instead attempted to save the world without involving the Monks. With the help of his companion Nardole, the Doctor tracked down Agrofuel Research Operations where Erica was desperately trying to stop the spread of the bacteria. Erica informed the Doctor that when the lab's vents cycled, the bacteria would be released into the Earth's atmosphere and begin the future foreseen by the Monks.

Working together, the Doctor and Erica realised that the bacteria produced ethanol, which filled the greenhouse as well as the lab. Using this information, the Doctor decided to use the ethanol and a makeshift ignitor to sterilise the bacteria by blowing up half of the lab. Though Bill Potts had to consent to the Monks to save the Doctor due to his blindness, the bacteria was destroyed before it could be released into the atmosphere. (TV: The Pyramid at the End of the World)

While aiding the Doctor, Nardole was contaminated by the bacteria. Due to his alien physiology, he survived, but it left him too sick to do anything for six weeks. (TV: The Pyramid at the End of the World, The Lie of the Land)

Alternate timeline
In an alternate timeline predicted by the Monks, the bacteria was released onto the Earth and wiped out all life on the planet within a year. After seeing a vision of this timeline, the Twelfth Doctor stated that the Earth was "as dead as the Moon." The only living things that hadn't been turned to gunk appeared to be a few dead trees amongst the devastation. (TV: The Pyramid at the End of the World)

Behind the scenes
Although the complete name of the bacteria is not given on-screen, the name "R. planticola" can be seen on the screen of Agrofuel's computer.