Why not use "Microbe" but "Microbes"?

The term 'Man,' quite often is used to refer to all humanity, including women. 'Microbe' has never been used to describe all micro-organisms, so that's why 'microbes' is used. It's one of the peculiarities of English.

The topic being considered is microbes in the plural. All varieties and types, viewed generically. See also animals, birds, fishes, mountains, cars, cats, dogs.

"Man" is a special case.

Exactly, 'man' can refer to the individual, or the whole of humanity. There's also the alliterative effect of Man and Microbes that you don't get if you substituted something like 'humanity.'

Will feminists protest against the use of Man for sexism ?

Thank you both.

Feminists have protested about it before, hence their adoption of 'wimmin' to avoid the derivation of man.