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The classification of prokaryotic life is subject to a lot of change and in the past has been a very controversial subject.

For years the main kingdoms were considered to be Prokaryotes, Animals, Plants and Fungi but this has subsequently proven to be too broad.

The Prokaryotic kingdom was initially split into two new kingdoms:

Eubacteria
and
archaebacteria

Recent RNA studies of these kingdoms have revealed that this classification is too simplified too and that despite being single celled organisms with no true organelles the Eubacteria differ sufficiently within their own kingdom to be split into further kingdoms.

This means that they can be considered to be as different from one another as plants are from animals.

The Eubacteria classification is therefore one of a Superkingdom. The two kingdoms within it contain, for the sake of simplicity, the gram negative and gram positive bacteria (those who don't take up the gram stain and those who do).

The first of these are called protobacteria and contain E. Coli and other similar bacteria that are human pathogens. However other human pathogens such as Staphylococcus are in the gram positive kingdom.

Many scientists have been trying to discover if any archaebacteria can be human pathogens but at the time of writing we have been unable to find evidence of any.

The superkingdom that contains bacterial pathogens is therefore eubacteria and both kingdoms within it contain pathogens.

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