Streptococcus pneumoniae is a major cause of otitis media, meningitis, septicaemia and community and hospital acquired pneumonia. As well as being a potentially deadly pathogen, the pneumococcus often resides in the human nasopharynx without causing harm, a situation known as carriage. Identified as a constituent of the oral microbiome by Human Oral Microbiome Database.
This species has been identified as a resident in the human gastrointestinal tract based on the phylogenetic framework of its small subunit ribosomal RNA gene sequences.[PMC 4262072]