Always capitalize the genus name and the abbreviated form of the genus name when it is accompanied by a species name.
Haemophilus influenzae, H. influenzae
Staphylococcus aureus, S. aureus
Escherichia coli, E. coli
NOTE: This differs from the AMA Manual of Style, which specifies that the formal name of a genus is capitalized when used in the singular, with or without a species name.
Do not capitalize the genus name when it is used in plural and adjectival forms, or when used in the vernacular or when it stands alone without a species name. (See exception note above.)
The suffixes -osis and -iasis indicate disease caused by a particular class of infectious agents or types of infection. These are common nouns and are not capitalized.
Do not capitalize the name of a species, variety or subspecies of organism.
Do capitalize phylum, class order or family.