Many of the materials used in construction have the danger of outgasing being harmful to our health such as lead and asbestos, as well as being potential breeding grounds for harmful biological organisms. Try to use paints with zero VOC (Volatile Organic Compounds) and low-toxicity finishes such as water-based adhesives and finishes that don't have synthetic formaldehyde resins.
Use of proper natural and mechanical ventilation to alleviate the problems of unhealthy particulates in the air and excessive moisture will help to reduce environmental allergies and bacteria or mold build up.
Some examples of green floors are cork, oak, concrete, and tile. Vinyl contains PVCs and carpet, besides potential outgasing, gathers dust mites, mold spores, bacteria, and viruses.
Remember to always have working carbon monoxide, smoke, humidity, and radon detectors.