Fig 1.
The assembly and contamination check workflow for the B. subtilis genome.
Table 1.
Genome assembly and annotation statistics of Bacillus coagulans S-lac and Bacillus subtilis TO-A JPC.
Table 2.
DDH values as calculated by GGDC server with B. coagulans as query against other Bacillus strains as reference.
The values are sorted on Formula II.
Table 3.
DDH values as calculated by GGDC server with B. subtilis TO-A JPC as query against other Bacillus strains as reference.
The values are sorted on Formula II.
Fig 2.
26 Housekeeping ML-based phylogenetic analysis of members of genus Bacillus, Lactobacillus, Clostridium and Listeria and other members of family Bacillaceae.
The species have been colored according to the genus they belong to: Bacillus spp. are colored orange, outgroups of Bacillaceae family are colored dark-pink, outgroup members related to Clostridiaceae and Listeriaceae family are colored dark-blue, Lactobacillus spp. are colored blue. The organisms that have been used as probiotics are colored red.
Fig 3.
Core, dispensable and unique sets of proteins a) Orthologous set of proteins in Bacillus coagulans S-lac, Bacillus coagulans GBI-30, Bacillus coagulans 36D1 and Bacillus coagulans 2–6 b) Orthologous set of proteins in Bacillus subtilis TO-A JPC, Bacillus subtilis subsp. subtilis str. 168, Bacillus subtilis subsp. subtilis 6051-HGW and Bacillus subtilis QB928.
Table 4.
The list of probiotic Bacillus and Lactobacillus compared.
Fig 4.
COG categories conserved across Bacillus probiotics vs. Lactobacillus probiotics.
The orthologous proteins conserved across Bacillus probiotics and distribution of proteins in different COG categories are plotted in comparison to COG categories conserved across the Bacillus and Lactobacillus probiotics. X-axis represents the number of proteins and Y-axis represents the COG categories.
Fig 5.
Horizontal gene transfers mapped onto the circular genome for Bacillus coagulans S-lac.
Circles (from inside to outside) 1 and 2 represent GC content and GC skew, Circle 3 (red colored) is the genome itself; circle 4 (green colored) represent the Bacillus coagulans 2–6 genome mapped on the Bacillus coagulans S-lac. Similarly, circle 5 (cyan colored) and 6 (magenta colored) are Bacillus coagulans GBI-30 and Bacillus coagulans 36D1 mapped respectively on Bacillus coagulans S-lac. Circle 7 is the adhesion, sporulation and stress-related proteins that have been mapped onto the genome. The genes corresponding to Clostridium kluyueri genome represents the RM Type III system which lies on a phage element that is also present in Bacillus coagulans strain GBI-30.
Table 5.
Distribution of sporulation proteins in probiotic Bacillus genomes.
Table 6.
The bacteriocins identified in Bacillus probiotics with their matches in NR database.