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. 2019 Dec 30;19(1):307.
doi: 10.1186/s12866-019-1680-7.

Composite Genome Sequence of Bacillus Clausii, a Probiotic Commercially Available as Enterogermina ®, and Insights Into Its Probiotic Properties

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Composite Genome Sequence of Bacillus Clausii, a Probiotic Commercially Available as Enterogermina ®, and Insights Into Its Probiotic Properties

Indu Khatri et al. BMC Microbiol. .
Free PMC article

Abstract

Background: Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.

Results: We report the composite genome of Bacillus clausii ENTPro from a commercially available probiotic Enterogermina® and compare it with the genomes of other Bacillus probiotics. We find that the members of B. clausii species harbor high heterogeneity at the species as well as genus level. The genes conferring resistance to chloramphenicol, streptomycin, rifampicin, and tetracycline in the B. clausii ENTPro strain could be identified. The genes coding for the bacteriocin gallidermin, which prevents biofilm formation in the pathogens Staphylococcus aureus and S. epidermidis, were also identified. KEGG Pathway analysis suggested that the folate biosynthesis pathway, which depicts one of the important roles of probiotics in the host, is conserved completely in B. subtilis and minimally in B. clausii and other probiotics.

Conclusions: We identified various antibiotic resistance, bacteriocins, stress-related, and adhesion-related domains, and industrially-relevant pathways, in the genomes of these probiotic bacteria that are likely to help them survive in the harsh gastrointestinal tract, facilitating adhesion to host epithelial cells, persistence during antibiotic treatment and combating bacterial infections.

Keywords: Bacteriocins; Gastrointestinal-tract; Pathogenicity; Phylogeny; Resistome.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Circular representation of the B. clausii ENTPro composite genome. Here, B. clausii ENTPro was taken as reference genome and circles from inside to outside represents as: Circle 1 and 2 represent GC content and GC skew of B. clausii ENTPro, circle 3 represent encoded RNAs in B. clausii ENTPro; circle 4 represent genes encoded by B. clausii ENTPro; circle 5 depicts B. clausii ENTPro composite chromosome; Circle 6 depicts the mapping of B. clausii ENTPro genome against genome of B. clausii KSM-K16; further the circles 7 to 13 represents the genomes of B. sp. JCM 19045, B. sp. JCM 19046, B. sp. JCM 19047, B. lehensis G1, B. halodurans C-125, B. cellulosilyticus DSM 2522, B. pseudofirmus OF4 mapped on B. clausii ENTPro respectively. BRIG 0.95 was used to build the circular representation. Mapping studies were done using BLASTn with an E-value cut-off 1e− 5
Fig. 2
Fig. 2
Cluster of Orthologous groups (COG) categories in B. clausii genomes. The X-axis represents the COG groups and the Y-axis represents the average number of proteins in respective COG groups. The genomes of B. clausii are clustered as per the properties. B. clausii Heroin represents all the organisms isolated from the Heroin samples [PRJNA395369]. B. clausii Probiotics represents all the probiotic strains as a single category. The COG categories are identified by capital letters as follows: A, RNA processing and modification; B, Chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation; K, transcription; L, replication; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, post-translational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking and secretion; V, defense mechanisms; and X, Mobilome: prophages, transposons
Fig. 3
Fig. 3
Housekeeping proteins based Maximum Likelihood phylogenetic tree The outgroups are colored with a yellow background, Bacillus species are colored with light green background and B. clausii members are colored with dark green background. The Bacillus probiotics are written with red labels with double the size of the rest of the organisms. Values on branches represent the bootstrap values.
Fig. 4
Fig. 4
The binary matrix of Antibiotic resistance in Bacillus probiotics. Red color fill marks the presence whereas black color represents the absence of antobiotic resistance genes. The rows represent the name of the Antibiotic resistance categories and the columns are the Bacillus probiotics
Fig. 5
Fig. 5
The binary matrix of Bacteriocins in Bacillus probiotics. Red color marks the presence of the bacteriocin whereas black color represents absence of bacteriocins. The rows represent the name of the bacteriocins, and the columns are the Bacillus probiotics
Fig. 6
Fig. 6
The binary matrix of components of folate biosynthesis pathways in Bacillus probiotics. Sea green marks the presence whereas yellow is absent. The rows represent the name of the Bacillus probiotics whereas column represents the pathway components

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