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Background   Bacillus endophyticus  is a soil plant-endophytic bacterium, while  B. anthracis  is the causative agent of anthrax. The virulence factors of  B. anthracis  are the plasmid encoded tripartite toxins (pXO1) and poly-γ-glutamic acid (PGA) capsule (pXO2).  B. endophyticus  isolated alongside  B. anthracis  from animals that died of anthrax in Northern Cape Province (NCP), South Africa, harbored polyglutamate genes. The study compared the characteristics of  B. anthracis  and  B. endophyticus  with other  Bacillus  species with a focus on the presence of the PGA capsule or/and unbound PGA. The morphology and whole genome sequence analysis of  B. endophyticus  strains and  B. anthracis  were compared.    Results  In conventional microbiology,  B. endophyticus  showed gram-positive round-shaped rods in single/short chains, which were endospore-forming, non-motile, non-haemolytic with white and dry colonies, and γ-phage resistant.  B. anthracis  was differentiated from  B. endophyticus  based on the latter’s box-shaped rods in pairs/long chains, white-grey and slimy colonies, encapsulated and γ-phage susceptible. The study identified a PGA polyglutamate synthase operon that consisted of  pgs BCA, γ-glutamyltranspeptidase ( ggt ) and  pgs E in  B. endophyticus  genomes.    Conclusions  PGA regions of  B. anthracis  contain  cap BCADE genes located in the pXO2 required for capsulation formation, while  B. endophyticus  contain the  pgs BCAE genes in the chromosome. Whole genome and microbiology analysis identified  B. endophyticus , as a non-capsuled endospore-forming bacterium that consists of PGA required for biosynthesis.  B. endophyticus  strains do not synthesize surface associated PGA, therefore capsule visualization of  B. anthracis  is a key diagnostic characteristic. The study highlights the significance of using whole genome shotgun sequencing to identify virulence and other important genes that might be present amongst unknown samples from natural outbreaks. None of the  B. anthracis  related plasmids or virulence genes were found in the  B. endophyticus  genomes.    Electronic supplementary material  The online version of this article (10.1186/s12866-018-1205-9) contains supplementary material, which is available to authorized users.

Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa