The human microbiota is the aggregate of microorganisms, a microbiome that resides on the surface and in deep layers of skin (including in mammary glands), in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts.They include bacteria, fungi, and archaea.he main bacterial inhabitants of the stomach include: Streptococcus, Staphylococcus, Lactobacillus, Peptostreptococcus, and types of yeast. Helicobacter pylori is a Gram-negative spiral organism that establishes on gastric mucosa causing chronic gastritis and peptic ulcer disease.