Molecular and Genomic Characterization of PFAB2: A Non-virulent Bacillus anthracis Strain Isolated from an Indian Hot Spring

Abstract

Background: Thermophilic bacilli in both aerobic or facultative anaerobic forms have been isolated for over a hundred years from different mesophilic or thermophilic environments as they are potential source of bioactive secondary metabolites. But the taxonomic resolution in the Bacillus genus at species or at strain level is very challenging for the insufficient divergence of the 16S rRNA genes. One such recurring problem is among Bacillus anthracis, B. cereus and B. thuringiensis. The disease-causing B. anthracis strains have their characteristic virulence factors coded in two wellknown plasmids, namely pXO1 (toxin genes) and pXO2 (capsule genes). Objective: The present study aimed at the molecular and genomic characterization of a recently reported thermophilic and environmental isolate of B. anthracis, strain PFAB2. Methods: We performed comparative genomics between the PFAB2 genome and different strains of B. anthracis, along with closely related B. cereus strains. Results: The pangenomic analysis suggests that the PFAB2 genome harbors no complete prophage genes. Cluster analysis of Bray-Kurtis similarity resemblance matrix revealed that gene content of PFAB2 is more closely related to other environmental strains of B. anthracis. The secretome analysis and the in vitro and in vivo pathogenesis experiments corroborate the avirulent phenotype of this strain. The most probable explanation for this phenotype is the apparent absence of plasmids harboring genes for capsule biosynthesis and toxins secretion in the draft genome. Additional features of PFAB2 are good spore-forming and germinating capabilities and rapid replication ability. Conclusion: The high replication rate in a wide range of temperatures and culture media, the nonpathogenicity, the good spore forming capability and its genomic similarity to the Ames strain together make PFAB2 an interesting model strain for the study of the pathogenic evolution of B. anthracis.

Diagnostic challenges within the Bacillus cereus-group: finding the beast without teeth

“…1 TYGS GBDP tree showing relationships between isolates and references. Figure was generated by TYGS [ 30 ], with genomes sequenced in our hospital (blue + in “User genomes” column), and additional genomes added for context (green +): GCA_000008445.1 and GCF_001758315.1 [ 19 ] to reflect B. anthracis which is otherwise absent from the TYGS database, GCF_001619425.1 and GCF_002566425.1 to represent members of B. basilensis sp. nov..…”

“…Many remain convinced that only tightly related, monomorphic, toxin-carrying strains qualify for the name [ 18 , 33 ]. By dDDH analysis, using the 70% cutoff, the species can be more broadly defined, including non-toxin carrying strains, and those described here [ 3 , 19 ]. B. anthracis is absent from the TYGS database, as no type strain genome sequence exists, which complicates identification, and shows that these tools must be used with caution.…”

“…Using any of these methods, cases of discrepancy in allocating isolates to species have been described. To add to the confusion, the presence of virulence factors does not always correlate with species identification, as some isolates closely related to B. anthracis do not carry pXO1 and pXO2 [ 3 , 19 , 20 ]. Conversely, these plasmids have been found within the genome of other Bacillus species [ 21 ].…”

Stress Dependent Biofilm Formation and Bioactive Melanin Pigment Production by a Thermophilic Bacillus Species from Chilean Hot Spring

“…The formation of pellicles was carried out in culture tubes under static conditions [25,26] for NB media (Difco), Luria Bertani (LB) (Difco), and Marine Broth (MB) (Difco), separately. For this, B. haynesii CamB6 cells in the logarithmic phase (10 8 CFL mL −1 ) were inoculated in 15 mL of cultures in the culture test tubes (1:5, v/v), which were incubated at 55 • C for 4 days (BJP-H50 BIOBASE, Jinan, China).…”

Systems Genomics in the Age of Next Generation Sequencing (Part I)

“…Aparna Banerjee et al [4], in their pangenomic study titled "Molecular and Genomic Characterization of PFAB2: A Nonvirulent Bacillus anthracis Strain Isolated from an Indian Hot Spring", aimed to characterize thermophilic and environmental isolates of B. anthracis strain PFAB2. The phenotype they obtained could serve as an interesting model strain for deciphering the pathogenesis.…”