Many researchers use 16S rRNA genes for their studies because they are amenable to rapid sequencing with the advent of the polymerase chain reaction (PCR) method and phylogenetic analyses are thus facilitated.

However, the 16S rRNA gene sequence is not sufficient to identify a Bacillus species.

This is because the horizontal transfer of DNA may occur between species of the same genus. Such a phenomenon is called horizontal gene transfer (HGT), the «process whereby genes from one cell are transferred to and expressed in another cell (See reference no. 1). » HGT may blur the genetic and physiological differences that once were considered constant in each «pure species».

In Bacillus species, the endospore position in the vegetative cell is a key factor in the identification.

Thus, the endospore position may be in the middle, in the end, or between the middle and the end of the vegetative cell.

The endospore may or may not swell the vegetative cell (See reference no. 2).

References

1. 2007. Van Elsas, J.D.; Jansson, J.K.; Trevors, J.T. (Eds). Modern Soil Microbiology. 2nd Edition. CRC Press. Chapter 3, section 3.3.

2. 1952. Smith, N.R.; Gordon, R.E.; Clark, F.E. Aerobic Spore-forming Bacteria. Agriculture Monograph No. 16. United States Department of Agriculture. Pages 45 to 133.

1). Phasing of 16S gene SNPs has been determined highly similar substitution profiles for closely related taxa, indicating that the profiles provide a robust method for species level taxonomic identification.

2). It may be assume that 99%

sequence similarity is an adequate threshold for clustering sequences originating from the similar genome, differences in SNP profiles, reflecting polymorphisms in one or more 16S gene copies reproducibly reflected differences between strains of the similar species.

3). By several results determined that appropriate handling of high-throughput, full length 16S sequence data has the potential to enable accurate classification of individual organisms at very high taxonomic resolution.