Characterization and in-depth genome analysis of a halotolerant probiotic bacterium Paenibacillus sp. S-12, a multifarious bacterium isolated from Rauvolfia serpentina

Abstract

Background: Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes.

Results: Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability.

Conclusion: The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.

Keywords: CAZymes; Genome; Paenibacillus; Pangenome; Probiotics.

Fig. 1

Phylogenetic tree showing relationship of Paenibacillus sp. S-12 to closely related bacterial strains. The 16 S rRNA gene sequence of closely related species was obtained from NCBI GenBank database. The rooted tree was obtained using Neighbor-joining method of software packages Mega version 7.0, at bootstrap value of (n = 500)

Fig. 2

Circular genome map of Paenibacillus sp. S-12 constructed by DNA plotter. Rings from inside represent the following: (1) GC content, (2) GC skew (3) CDS features (4) rRNA (5) tRNA, (6) repeat region, (7) positions labels for genome length (Mbp)

Fig. 3

a.Comparison of cluster of orthologs groups in five Paenibacillus species. The analysis was done by using Orthovenn2 using default parameters with protein sequences of Paenibacillus sp. S-12, P. alvei DSM29, P. curdlanolyticus YK9, P. polymyxa ATCC 842, P. polymyxa E681 and P. polymyxa SC2, b. The occurrence table contains groups of gene clusters like cluster count and protein count. Row indicates the orthologous gene cluster for multiple species that summarized as a cell graph and column indicates different closely related bacterial species, C. The pairwise protein sequence comparison for heatmap showing orthologs clusters between S-12 and other closely related strains

Fig. 4

The RAST subsystems distribution in the Paenibacillus sp. S-12 genome. The most abundant systems on the category level are shown in the left pie chart, whereas the right column showing the counts of features

Fig. 5

a The clusters of orthologus (COGs) analysis in Paenibacillus sp. S-12 genome, b. The metabolic pathway analysis using KEGG Automatic Annotation Server (KAAS) database. KAAS database is used for functional annotation of genes by BLAST comparisons against KEGG-GENES database

Fig. 6

The genome of Paenibacillus sp. S-12 was annotated for virulence factor identification using the VFDB database (http://www.mgc.ac.cn/VFs) using the Basic Local Alignment Search Tool (BLASTX) through diamond tool

Fig. 7

Identification of putative biosynthetic gene clusters (BGCs) using antiSMASH. antiSMASH analysis identified the 28 BGCs in the Paenibacillus sp. S-12 genome

Fig. 8

The distribution of CAZyme domain sequences such as Glycoside hydrolases (GHs); Glycosyl transferases (GTs); Polysaccharide lyases (PLs); Carbohydrate esterases (CEs); Auxiliary activities (AAs); and Carbohydrate-binding modules (CBMs) among the Paenibacillus sp. S-12 and its closely related species

Fig. 9

a.The matrix illustrating the presence/absence of genes in selected genome, the clustering of tree is shown on the left side, b. The pie chart shows the proportion of core, shell, and cloud genes c. The gene frequency plot demonstrating the distribution of genes per genome