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Bacteria were usually microscopic organisms which lived in a variety of environments. Some lived in symbiotic or parasitic relationships with larger lifeforms, and others could be disease-causing agents.
The Ablative was a bacteria which was created by the First Doctor in an experiment which he conducted while at the Time Lord Academy, with the ensuing scandal nearly getting him expelled until it was covered up by the Academy, who believed that all of the samples had been destroyed. The Rani would later recall this incident to the Sixth Doctor. (AUDIO: Planet of the Rani)
The Spiridons had a civilisation, which fell into ruin by the 26th century, when the Daleks saturated the forests with deadly rays (PROSE: Doctor Who and the Planet of the Daleks) and released bacteria which killed off most of the population. (TV: Planet of the Daleks)
In 1665, the first cases of what would become known as the Great Plague of London appeared on London's outskirts. The disease became more widespread and fatal the following year, after a deadlier strain of the bacterium Yersinia pestis was engineered by a group of escaped Terileptil criminals. (TV: The Visitation)
The PoriPhylum was an alien yeast bacteria that took the form of its enemies as a disguise before eating them. They fed on fluids drawn from the bodies of those captured, like blood and water. (COMIC: Dawn of the Living Bread)
Bacteria "the size of a badger" lived on the 1.3 billion-ton creature incubating inside the Moon which was in fact an egg the creature was growing inside. They had eight legs and what looked like teeth and had a similar appearance to a spider. (TV: Kill the Moon)