Bacillus subtilis is an epiphytic Gram-positive bacterium that is known to interact with plants [Zuniga20] and to protect plants against various pathogens [Blake21]. The organism, which is harmless to humans, possesses a potent extracellular protein secretion system and doesn't secrete any toxic metabolites. These qualities have made B. subtitlis an indespensible tool in veterinary medicine and medicine, and a workhorse for different industries such as production of probiotics, immunoactive factors, enzymes, amino acids, and vitamins [vanDijl13, Liu17].

Bacillus subtilis was originally thought to be a strict aerobe. However, it was later found that it can grow anaerobically by respiration with nitrate as a terminal electron acceptor [Hoffmann95], and in the absence of external electron acceptors, it can grow by fermentation [Nakano97].

The parent strain of Bacillus subtilis subtilis 168, known as the "Marburg strain", is now lost [Zeigler08]. It was isolated by Ferdinand Cohn in 1872 from freshly prepared hay infusions. Cohn described its life cycle, including the formation of spores and their subsequent germination (in [Drews00]). Strain 168 is a tryptophan auxotroph mutant of the Marburg strain, obtained in 1947 by X-ray mutagenesis [Burkholder47]. The mutant strain was passed to Charles Yanofsky of Stanford University, who in turn gave it to John Spizizen of the Western Reserve University in Ohio. Spizizen found that the organism could be transformed to prototrophy when exposed to DNA from a different organism [Spizizen58], and this high transformability led to significant interest and the dissemination of strain 168 around the world. By the mid-1970s so many mutant strains have been developed from strain 168 that a centralized repository, the Bacillus Genetic Stock Center (BGSC), was established. It has become a model organism first for sporulation studies [Khanna20], and then for Gram-positive organisms in general.

A mutation in the trpC2 gene of strain 168 results in an inactive EC 4.1.1.48, indole-3-glycerol-phosphate synthase, which results in L-tryptophan auxotrophy. Due to another mutation in the sfp₀ gene, which encodes a 4'-phosphopantetheinyl transferase (EC 2.7.8.7, holo-[acyl-carrier-protein] synthase) involved in secondary metabolism, strain 168 is not able to produce plipastatin A1, bacillibactin, surfactin, or bacillaene. For information about these pathway, consult the MetaCyc database.

The BsubCyc Pathway/Genome Database (PGDB) was built from the annotated genome of GenBank accession number AL009126.3, GI:225184640 [Barbe09]. The genome annotation was partially updated based on the improved annotation released in GenBank in 2018 [Borriss18]; the update included new genes, corrected gene coordinates, and many improved gene product names. A third update was performed in 2024 based on [Bremer23]. BsubCyc has undergone manual curation, including addition of citations to new B. subtilis literature. A subset of the transcriptional regulatory data captured in DBTBS [Sierro08] was imported from an XML file provided by K. Nakai and Y. Makita. 958 new intrinsic terminators were added in 2024 based on [Mandell22]. Gene Ontology terms are imported from the UniProtKB-GOA Gene Association File.