As part of its life cycle, Streptococcus pneumoniae exists as a commensal bacterium that inhabits and colonizes the nasopharynx of up to 20 and 50% of healthy adults and children, respectively [Tuomanen97]. Upon another respiratory tract infection, such as influenza, the organism transitions from being a commensal bacterium to an opportunistic pathogen.

Strains of Streptococcus pneumoniae are categorized into more than 90 serotypes based on the structures of their exopolysaccharide capsules [Bentley06]. Streptococcus pneumoniae D39 is clinical serotype 2 strain isolated from a patient in 1916 and deposited in the National Collection of Type Cultures (NCTC) as NCTC 7466 in 1948. The strain has an important role in the history of science: strain R36A was used in 1944 by Avery and coworkers for the landmark demonstration that DNA is the genetic material [Avery44]. That strain was derived from strain R36, which was derived from strain D39. Unlike D39, strains R36 and R36A lack a capsule, making them competent for natural transformation, a property that was very useful before the discovery of the competence stimulatory peptide [Havarstein95].

Streptococcus pneumoniae D39 has been adopted as a leading model of pneumococcal pathogenesis. Despite being isolated in 1916, the strain remains extremely virulent in animal models of infection and has proven to be highly tractable in genetic mutant constructions. The strain carries a cryptic plasmid (pDP1) [Oggioni99].

Like other Streptococci, Streptococcus pneumoniae D39 obtains energy strictly via fermentation and is incapable of respiratory metabolism, either aerobically or anaerobically. The only carbon and energy sources for the organism are carbohydrates, which are oxidized to pyruvate via glycolysis. Pyruvate is fermented to lactate and acetate.

This Pathway/Genome Database (PGDB) is built from a deep genome annotation of Streptococcus pneumoniae D39V - a D39 strain kept in the laboratory of Dr. Veening at the University of Groningen in the Netherlands [Slager18]. The strain was named D39V to distinguish it from strain D39W, which is kept in the laboratory of Dr. Winkler at Indiana University. Note that the D39V strain has lost the pDP1 plasmid, which was present in the original D39 strain. The annotation submitted by the Veening lab includes extensive regulatory information (transcription start sites, terminators, sRNAs and more) and these features are included in the PGDB. A gene essentiality dataset [Thanassi02] has also been imported. The database was generated on 24-Apr-2023 by the PathoLogic component of the Pathway Tools software version 27.0 [Karp11, Karp16] and MetaCyc version 27.1 [Caspi20].